|
This page contains an alphabetical listing of the annotation tracks available
on various Genome Browser assemblies. This page was last updated on
3 March 2005 and is no longer maintained. For more current information on
a specific annotation track, see the description page associated with the
track in the Genome Browser.
To learn more about configuring and using the tracks displayed in the
Genome Browser track window, see the section
Interpreting and fine-tuning the Genome
Browser display in the Genome Browser User's Guide.
[A]
[B]
[C]
[D]
[E]
[F]
[G]
[H]
[J]
[K]
[M]
[N]
[O]
[P]
[Q]
[R]
[S]
[T]
[U]
[V]
[W]
[X]
[Y]
[Z]
2X Reg Potential
This track displays the 2-way regulatory potential (RP) score computed from
alignments of the human and mouse assemblies. RP scores compare frequencies of
short alignment patterns between regulatory elements and neutral DNA.
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Display conventions:
This track uses the display conventions for wiggle tracks. |
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Table details:
To view a text version of the data set, select the
regPotential2X positional table in the Table Browser. To view the table
definition, click
here. |
3X Reg Potential
This track displays the 3-way regulatory potential (RP) score computed from
alignments of the human, mouse, and rat assemblies. RP scores compare frequencies of
short alignment patterns between regulatory elements and neutral DNA.
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Display conventions:
This track uses the display conventions for wiggle tracks. |
-- |
Table details:
To view a text version of the data set, select the
regPotential3X positional table in the Table Browser. To view the table
definition, click
here. |
Acembly Genes
This track shows gene models reconstructed solely from mRNA and EST evidence
by Danielle and Jean Thierry-Mieg and Vahan Simonyan using the Acembly program.
Acembly attempts to find the best alignment of each mRNA against the genome,
and considers alternative splice models. If more than one gene model is
produced that has statistical significance, all of these models are
displayed.
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Display conventions:
This track uses the display conventions for gene prediction
tracks. |
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Track details:
Clicking on an entry in full display mode will show
position information, links to translated protein, predicted mRNA, and genomic
sequence, and a link to an extensive text and graphical annotation of
supporting data at NCBI's AceView. |
-- |
Table details:
To view a text version of the data set, select the
acembly positional table in the Table Browser. To view the table
definition, click
here. |
Affy GNF1H
This track shows the location of the sequences used for the selection of probes
on Affymetrix GNF1H chips.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyGnf1h positional table in the Table Browser. To view the table
definition, click here. |
Affy GNF1M
This track shows the location of the sequences used for the selection of probes
on Affymetrix GNF1M chips.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyGnf1m positional table in the Table Browser. To view the table
definition, click here. |
Affy GNF1H
This track shows the location of the sequences used for the selection of probes
on Affymetrix GNF1M chips.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyGnf1m positional table in the Table Browser. To view the table
definition, click here. |
Affy MOE430
This track shows the location of the sequences used for
the selection of probes on the Affymetrix Mouse MOE430 set of chips (A and B).
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Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
Clicking on an item in one of the fuller modes displays positional
and % identity information. |
-- |
Table details:
To view a text version of the data set, select the
affyMOE430 positional table in the Table Browser. To view the table
definition, click here. |
Affy RAE230
This track shows the location of the sequences used for the selection of probes
on Affymetrix RAE230 chips.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyRAE230 positional table in the Table Browser. To view the table
definition, click here. |
Affy RG-U34A
This track shows the location of the sequences used for the selection of probes
on Affymetrix RG-U34A chips.
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Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyU34A positional table in the Table Browser. To view the table
definition, click here. |
Affy U74
This track shows the location of sequences used for
the selection of probes on the Affymetrix MG-U74v2 set of chips (A, B, and C).
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Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
Clicking on an item in one of the fuller modes displays positional
and % identity information. |
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Table details:
To view a text version of the data set, select the
affyU74 positional table in the Table Browser. To view the table
definition, click here. |
Affy U95
This track shows the location of the consensus and exemplar sequences used for
the selection of probes on the Affymetrix HG-U95Av2 chip.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
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Track details:
Clicking on an item in one of the fuller modes displays positional
and % identity information. |
-- |
Table details:
To view a text version of the data set, select the
affyU95 positional table in the Table Browser. To view the table
definition, click here. |
Affy U133
This track shows the location of the consensus and exemplar sequences used for
the selection of probes on the Affymetrix HG-U133A and HG-U133B chips.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
Clicking on an item in one of the fuller modes displays positional
and % identity information. |
-- |
Table details:
To view a text version of the data set, select the
affyU133 positional table in the Table Browser. To view the table
definition, click here. |
Affy U133Plus2
This track shows the location of the consensus and exemplar sequences used for
the selection of probes on the Affymetrix HG-U133 Plus 2.0 chip.
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Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
Clicking on an item in one of the fuller modes displays positional
and % identity information. |
-- |
Table details:
To view a text version of the data set, select the
affyU133Plus2 positional table in the Table Browser. To view the table
definition, click here. |
Affy Zebrafish (Zebrafish)
This track shows the location of the sequences used for the selection of probes
on the Affymetrix Zebrafish chip.
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Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyZebrafish positional table in the Table Browser. To view the table
definition, click here. |
All Ciona ESTs
See the description for Human ESTs.
Alt-Splicing
This track summarizes the alternative splicing shown in the mRNA and EST tracks.
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Display conventions:
Exons are represented by blocks; possible splice junctions by lines.
In full mode with the resolution set to approximately gene-level,
alternative exons are laid out with minimal overlap and are therefore
easier to view. The level of shading of exons and splice junctions
reflects the quantity of ESTs and mRNAs that contain that exon or splice
junction. |
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Track details:
Clicking on an item in one of the fuller modes displays positional
information and alt-splicing plots, as well as a link to a zoomed-in
browser view of that feature. |
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Table details:
To view a text version of the data set, select the
altGraphX positional table in the Table Browser. To view the table
definition, click here. |
A. gambiae Chain
This track shows A. gambiae genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
A. gambiae ESTs
See the description for Human ESTs.
A. gambiae mRNAs
See the description for Human mRNAs.
A. gambiae Net
This track shows the best A. gambiae chain for every part of the selected genome.
See the Human Net track description for more information.
A. mellifera Chain
This track shows A. mellifera genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
A. mel. ESTs
A. mellifera ESTs. See the description for Human ESTs.
A. mel. mRNAs
A. mellifera mRNAs. See the description for Human mRNAs.
A. mellifera Net
This track shows the best A. mellifera chain for every part of the selected
genome. See the Human Net track description for more information.
Anopheles Ecores
This track shows Anopheles evolutionary conserved regions (ecores) computed
against the selected assembly genome by the Exofish program at Genoscope. For
information on this track, see the Human Ecores track description.
Assembly
This track shows the draft assembly of the human genome. This assembly merges
contigs from overlapping draft and finished clones into longer sequence
contigs. The sequence contigs are ordered and oriented when possible by mRNA,
EST, paired plasmid reads (from the SNP Consortium) and BAC end sequence pairs.
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Display conventions:
In dense display mode, this track depicts in alternating gold and brown the
path through the draft and finished clones (aka the golden path) used to
create the assembled sequence. Individual boxes show the assembly extractable
from a single clone fragment. Where gaps exist in the path, spaces are shown
between the gold and brown blocks. If the relative order and orientation of
the contigs between the two blocks is known, a line is drawn to bridge the
blocks. The display must be sufficiently zoomed in to view the gap and bridge
features. |
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Track details:
Clicking on an item in full display mode will show information about the
clone fragment and bases, position information, and the DNA sequence
corresponding to the fragment. |
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Table details:
To view a text version of the data set, select the
gold positional table in the Table Browser. To view the table
definition, click here. |
BAC End Pairs
This track shows the genome sequence of bacterial artificial chromosomes
(BACs) in which a small amount of the both ends have been sequenced to place
the full insert on the assembly. A valid pair of BAC end sequences must be
separated by at least 50Kb but no more than 600Kb, and must have opposite
orientations. Strand assignment follows
Clone Registry
storage conventions. The BAC end sequences are placed on the assembled
sequence using BLAT.
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Display conventions:
The sequenced BAC ends are represented by black boxes connected by a
line with hatch marks indicating the direction of transcription. |
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Track details:
Clicking on an entry in full display mode will show hyperlinks to the
NCBI clone registry and GenBank, position information, and genomic
alignments. |
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Table details:
To view a text version of the data set, select the
bacEndPairs positional table in the Table Browser. To view the table
definition, click here. |
Bactigs
The rat genome assembly is pieced together from bactig assemblies rather than clone-by-clone assemblies. Bactigs are reassemblies of the reads
from sets of overlapping skimmed BAC clones, including mapped whole shotgun
reads. The assembly process reworks the contigs (splitting some) and
selects them under more stringent criteria than is used for the BAC submissions.
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Display conventions:
Bactig positions are indicated by rectangular blocks. Bactig names are
of the form gaab_gnmm, the internal names of the two bracketing
projects. |
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Track details:
Clicking on an entry in full display mode will show position information
and the first and last contig in the bactig. |
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Table details:
To view a text version of the data set, select the
bactigPos positional table in the Table Browser. To view the table
definition, click here. |
Base Position
Shows the chromosomal coordinates as numbered starting from the telomere of
the short p arm. The coordinates differ between assemblies.
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Display conventions:
Clicking on a position in this track will zoom in the display by 3x,
centered around the click. This track has only on and off modes, and no
dense mode. |
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Track details:
None. |
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Table details:
None. |
BDGP Genes (D. melanogaster)
This track shows protein-coding genes annotated by the Berkeley Drosophila
Genome Project (BDGP).
For a description of the methods used to generate the
data, see the BDGP Methods web page.
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks.
|
-- |
Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, and related links to
outside databases. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
|
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Table details:
To view a text version of the data set, select the
bdgpGene positional table in the Table Browser. To view the table
definition, click here. |
BDGP Insertions (D. melanogaster)
This track shows the locations of P transposable element insertions from
P-Screen, the online database of the
BDGP
Gene Disruption Project. When a stock order number is available
for the strain, a link is provided to the Bloomington stock center. The
project's strain library contains more than 7140 strains disrupting at least
5362 different genes, corresponding to 39% of the 13,666 currently annotated
Drosophila genes.
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Display conventions:
Triangular arrows on the reference sequence indicate the
approximate locations where P elements have inserted themselves
in the mutant strain. Left-pointing arrows indicate insertions
that are oriented in a backwards direction; right-pointing arrows
indicated forwards-oriented insertions.
The item name indicates the strain having a P element disruption
at that location.
|
-- |
Track details:
Clicking on an entry in full display mode provides position and strand
information, strain name, a link to the Bloomington stock center (when
applicable), and a link to the underlying DNA for the feature.
|
-- |
Track configuration:
The track description page allows the user to set the minimum
unnormalized score of the data displayed in the track.
|
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Table details:
To view a text version of the data set, select the
pscreen positional table in the Table Browser. To view the table
definition, click here. |
BDGP Non-Coding Genes (D. melanogaster)
This track shows non-coding genes annotated by the Berkeley Drosophila
Genome Project (BDGP).
For a description of the methods used to generate the
data, see the BDGP Methods web page.
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks.
|
-- |
Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, and related links to
outside databases. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
|
-- |
Table details:
To view a text version of the data set, select the
bdgpNonCoding positional table in the Table Browser. To view
the table definition, click here. |
Best Human
This track displays Blastz alignments of the Nov. 2002 human draft
assembly to the mouse genome filtered to display only the best alignment for any
given region of the mouse genome. See the track's description page for more
details.
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Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
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Track details:
Clicking on an entry in full display mode will show mouse and
human position information, alignment details, and a link to a detailed
view of parts of the alignment. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
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Table details:
To view a text version of the data set, select the
blastzBestHuman positional table in the Table Browser. To view the table
definition, click here. |
Best Mouse
This track displays Blastz alignments of the specified mouse draft
assembly to the human genome filtered to display only the best alignment for any
given region of the human genome. See the track's description page for more
details.
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Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
-- |
Track details:
Clicking on an entry in full display mode will show human and
mouse position information, alignment details, and a link to a detailed
view of parts of the alignment. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
-- |
Table details:
To view a text version of the data set, select the
blastzBestMouse positional table in the Table Browser. To view the table
definition, click here. |
Best Rat
This track displays Blastz alignments of the Nov. 2002 rat draft
assembly to the mouse genome filtered to display only the best alignment for any
given region of the mouse genome. See the track's description page for more
details.
-- |
Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
-- |
Track details:
Clicking on an entry in full display mode will show rat and
mouse position information, alignment details, and a link to a detailed
view of parts of the alignment. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
-- |
Table details:
To view a text version of the data set, select the
blastzBestRat positional table in the Table Browser. To view the table
definition, click here. |
BGI Coverage
This track shows areas of coverage for genomic regions of 3 alternate strains of
chicken sequenced by the Beijing Genomics Institute (BGI): Broiler, Layer, and Silkie.
Single reads from those three strains were mapped to the reference assembly for the Red
Jungle Fowl (RJF).
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Display conventions:
Coverage regions are represented by solid blocks. |
-- |
Track details:
Clicking on an entry in full display mode shows position information and a link
to the DNA underlying this feature.
|
-- |
Table details:
To view a text version of the data set, select the
bgiCov positional table in the Table Browser. To view the table
definition, click here. |
BGI Genes
This track shows protein-coding genes annotated by the Beijing Genomics Institute (BGI).
If Single Nucleotide Polymorphisms (SNPs) and/or insertions/deletions from BGI have been
associated with a gene, those SNPs are listed with links to their details pages.
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. |
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Track details:
Clicking on an entry in full display mode shows position information, GO and
InterPro terms from BGI, BGI SNPs associated with the gene, and links to the
predicted protein, mRNA, and genomic sequences.
|
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Table details:
To view a text version of the data set, select the
bgiGene positional table in the Table Browser. To view the table
definition, click here. |
BGI SNPs
This track shows the single nucleotide polymorphisms (SNPs) and/or insertions/deletions
(indels) determined by the Beijing Genomics Institute (BGI). Genomic sequence reads from
3 alternate strains of chicken (Broiler, Layer and Silkie) were used to determine the SNPs
relative to the reference assembly for the Red Jungle Fowl (RJF). SNPs and indels are
associated with genes (annotations by BGI until Ensembl annotations are ready).
Information on the association can be displayed along with a link to the details page
for the gene.
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Display conventions:
SNP locations are indicated by thin vertical lines. SNP names are of the format
[supercontig].[contig].[position].[type].[strain]. See the track description
page for more information. | |
-- |
Track details:
Clicking in full display mode shows information position and SNP information,
primer sequences, and a link to the DNA underlying the feature.
|
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Table details:
To view a text version of the data set, select the
bgiSnp positional table in the Table Browser. To view the table
definition, click here. |
Binomial Cons
This track displays the conservation scores resulting from an analysis of Zoo
blastz alignments. Conservation scores were generated by weighing the relative
contribution of each species sequence to the overall conservation score, based
on how diverged each species was from the reference sequence. This weighting
scheme was determined by calculating the neutral substitution
rates at 4-fold degenerate positions.
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Display conventions:
This track uses the display conventions for wiggle tracks.
|
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Track configuration:
The track description page contains options to configure
several of the graph characteristics. To read more information
about each option, click the "Graph configuration help" link.
|
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Track details:
Clicking on one of the peaks in the track when in full display mode will
show genome position information for the window and a link to the
underlying DNA sequence. In full mode in
a zoomed-out display, detailed information may not be accessible for an
individual feature. In this case, zoom in and try again. |
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Table details:
To view a text version of the data set, select the
binomialCons2 positional table in the Table Browser. To view the table
definition, click here. |
Blastz Mouse
This track displays blastz alignments of the specified mouse draft
assembly to the selected genome.
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Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
-- |
Track details:
Clicking on an entry in full display mode will position information
for the mouse and the selected genome, alignment details, and a link
to a detailed
view of parts of the alignment. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
-- |
Table details:
To view a text version of the data set, select the
blastzX positional table in the Table Browser, where X represents
the assembly version in which you are interested, e.g. Mm4). To view the
table definition, click here. |
Briggsae Aligns
This track shows best-in-genome C. elegans/C. briggsae alignments
based on the C. elegans/C. briggsae alignment net, i.e. the best
chain for every part of the C. elegans genome. See the D. pseud Aligns
track description for more information.
Briggsae Blastz
This track displays Blastz alignments of the C. briggsae assembly to
selected assembly. See the Blastz Mouse track description for more information.
Briggsae Chain
This track shows C. briggsae genomic alignment to the selected genome
using blastz and axtChain. See the Human Chain track description for more
information.
Briggsae Net
This track shows the best C. briggsae chain for every part of the
selected genome.
See the Human Net track description for more information.
Briggsae Waba
This track shows alignments of C. briggsae to C. elegans
using the Wobble Aware Bulk Aligner (WABA), an alignment tool developed by
Jim Kent for doing large-scale alignments between genomic DNA of different
species.
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Display conventions:
Aligning regions are represented by blocks. The shading indicates the
hidden Markov model (HMM) states of the bases. |
-- |
Track details:
Clicking on an item in full display mode will show alignment details
and the HMM state for each alignment pair`. Markov model .
|
-- |
Table details:
To view a text version of the data set, select the
wabaCbr positional table in the Table Browser. To view the table
definition, click here. |
C. briggsae ESTs
See the description for Human ESTs.
C. briggsae mRNAs
See the description for Human mRNAs.
C. elegans ESTs
See the description for Human ESTs.
C. elegans mRNAs
See the description for Human mRNAs.
Chicken Chain
This track shows chicken genomic alignment to the selected genome using blastz
and axtChain. See the Human Chain track description for more information.
Chicken ESTs
See the description for Human ESTs.
Chicken mRNAs
See the description for Human mRNAs.
Chicken Net
This track shows the best chicken chain for every part of the selected genome.
See the Human Net track description for more information.
Chimp BAC Ends
This track displays BAC alignments of the chimp genome (Pan troglodytes) to human, based on BLAT alignments from Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the MPI for Evolutionary Anthropology.
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Display conventions:
This track follows the display conventions for BLAT tracks. |
-- |
Track details:
Clicking on an item will show details on the chimp sequence fragment and
alignment details, as well as a link to more information on the track data. |
-- |
Table details:
To view a text version of the data set, select the
chimpBac positional table in the Table Browser. To view the table
definition, click here. |
Chimp Blat
This track displays alignments of the chimp genome (Pan troglodytes) to human, based on Blat alignments from Ingo Ebersberger, Joshua Bacher, and Svante Pääbo at the MPI for Evolutionary Anthropology.
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Display conventions:
This track follows the display conventions for BLAT tracks. |
-- |
Track details:
Clicking on an item will show details on the chimp sequence fragment and
alignment details, as well as a link to more information on the track data. |
-- |
Table details:
To view a text version of the data set, select the
chimpBlat positional table in the Table Browser. To view the table
definition, click here. |
Chimp Chain
This track shows chimp genomic alignment to the selected genome using blastz and
axtChain. See the Human Chain track description for more information.
Chimp Deletions
This track displays regions of the human assembly that are deleted in the
chimp assembly. Only regions of between 80 and 12000 bases are included.
The name of each deletion is a unique pointer to that deletion followed by an
underscore and then its length. A similar track, showing human deletions in the
chimp assembly, appears in the chimp Genome Browser.
-- |
Display conventions:
Deletions are indicated by thin vertical lines. |
-- |
Track details:
Clicking on a deletion in full display mode provides the item name,
position, genomic size, and a link to the DNA underlying the feature.
|
-- |
Table details:
To view a text version of the data set, select the
chimpDels positional table in the Table Browser. To view the table
definition, click here. |
Chimp Diff
This track shows simple differences between chimp alignments and the human
assembly within regions of high quality chimp sequence. For a difference to be
included in this track, it had to meet the following criteria:
- the difference must occur at a base of quality 30 or better
- all bases within an 11-base window around this base must have a quality of
25 or better
- the 11-base window must contain no more than two base differences
- no insertions or deletions may be present within the window
Only reciprocal best chimp alignments were considered for this track (see the
Chimp Net track description page for more information about this alignment
strategy).
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Display conventions:
Differences are indicated by thin vertical lines. |
-- |
Track details:
Clicking on a deletion in full display mode provides the item name,
position, genomic size, and a link to the DNA underlying the feature.
|
-- |
Table details:
To view a text version of the data set, select the
chimpSimpleDiff positional table in the Table Browser. To view
the table definition, click here. |
Chimp ESTs
See the description for Human ESTs.
Chimp mRNAs
See the description for Human mRNAs.
Chimp Recip Chain
This track displays "reciprocal best" human/chimpanzee genomic
alignment chains.
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Display conventions:
This track uses the display conventions for chain tracks. |
Track details:
In full display mode, clicking on a box shows details information about
the chain as a whole, while clicking on a line shows information
about the gap. The detailed information is useful in determining the
cause of the gap or, for lower level chains, the genomic
rearrangement.
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Table details:
To view a text version of the data set, select the
rBestChainPanTro1 positional table in the Table Browser.
To view the table definition, click here. |
Chimp Recip Net
This track shows the reciprocal best alignment net between the chimpanzee and the
selected genome assembly. Due to the draft nature of the
initial chimp assembly, this track uses a "reciprocal best" strategy that
attempts to minimize paralog fill-in for missing orthologous chimp sequence by
filtering out of the human net all sequences not in the chimp side of the net.
See the track description page for more information about the methods used to
generate this track.
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Display conventions:
This track uses the display conventions for net tracks. |
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Track details:
In full display mode, clicking on a box shows details information about
the chain as a whole, while clicking on a line shows information
about the gap. The detailed information is useful in determining the
cause of the gap or, for lower level chains, the genomic
rearrangement. |
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Table details:
To view a text version of the data set, select the
rBestNetPanTro1 positional table in the Table Browser, where X
is the assembly version in which you're interested. To view the table
definition, click here. |
Chromosome Band
The light and dark blocks indicate the approximate location of
traditional cytological bands seen on Giemsa-stained chromosomes at an 850
band resolution. The bands were mapped
by fluorescent in situ hybridization (FISH) of large-insert clones
with sequence tags, STS markers, and BAC end sequence locations.
resolution of 862 bands genome-wide. The uncertainty of
mapping to band staining is still a megabase or more.
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Display conventions:
The light and dark blocks indicate the approximate location of the bands on the
assembly sequence. |
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Track details:
Clicking on a band in full display mode will show more details about
the track, a discussion of mapping methods used, and lab
credits. |
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Table details:
To view a text version of the data set, select the
cytoBand positional table in the Table Browser. To view the table
definition, click here. |
C. intestinalis ESTs
See the description for Human mRNAs.
C. intestinalis mRNAs
See the description for Human mRNAs.
Ciona mRNAs
See the description for Human mRNAs.
Conservation
This track shows a measure of evolutionary conservation among several species,
based on a phylogenetic hidden Markov model (phylo-HMM). The multiz
alignments of the various assemblies were used to construct the annotation.
The raw conservation scores used to generate this track can be downloaded
from the [assembly_name]/phastCons directory on the Genome Browser
FTP
server.
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Display conventions:
In full display mode, the track displays pairwise alignments of several
species aligned to the human genome. The pairwise alignments
are displayed in standard UCSC browser "dense" mode using a grey-scale
density gradient. When zoomed-in to the base-display level, the track
shows the base composition of each alignment. The numbers and symbols on
the "human gap" line indicate the lengths of gaps in the human sequence
at those alignment positions. If the gap size is greater than 9, the
"+" symbol is displayed. The track must be zoomed-in to 30,000
or fewer bases to access detailed information about the
alignments at a specific position.
|
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Track details:
Clicking on an entry in full display mode will show detailed alignment
information for each of the organisms. |
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Table details:
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To view an index of the multiz multiple alignment data used to
generate
this track, select one of the following positional tables from the
Table Browser: multiNway (most recent assemblies),
mz*_pHMM (hg16), mz*_phast (canFam1, dm1),
c_briggsae_pwMaf (C. elegans).
|
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To view the wiggle track data used to generate the conservation
display, select onf of the following positional tables: phastCons
(most assemblies), mz*_wig (hg16), mz*phast_wig
(canFam1, dm1).
|
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To download the raw conservation scores displayed in the
Conservation track, download the data files from the
[assembly_name]/phastCons directory on the Genome Browser
FTP
server.
|
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To view the table definition for the multiz multiple alignment
tables, click here.
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To view the table definition for the phastCons tables, click here.
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Contamination (Chicken)
This track shows locations of likely contamination in the chicken (galGal2) assembly, i.e.
high-scoring alignments of E.coli, vector and maize mitochondrion sequence. The
name of each feature indicates the type of contamination found there.
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Display conventions:
Area of contamination are represented by solid blocks.
|
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Track details:
Clicking on an entry in full display mode will show the type of contamination,
position and size information, and a link to display the DNA for the feature.
|
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Table details:
To view a text version of the data set, select the
contamination positional table in the Table Browser.
To view the table definition, click here. |
Contigs (Zebrafish)
This track shows the whole genome shotgun (WGS) contigs of the zebrafish assembly from
The Wellcome Trust Sanger Institute.
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Display conventions:
Contigs are represented by blocks that indicate their location
on the assembly sequence. |
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Track details:
Clicking on an item in full display mode will show contig and positional
information. |
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Table details:
To view a text version of the data set, select the
ctgPos2 positional table in the Table Browser. To view the table
definition, click here. |
Coverage
Shows the coverage level and positions of all clones in the genome.
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Display conventions:
In dense display mode, this track shows the coverage level of the
genome. Finished regions are shown in black. Draft regions are
shown in various shades of gray that correspond to the level of
coverage:
o White: no coverage (gap)
o Light Gray: predraft (less than 4x shotgun)
o Medium Gray: draft (at least 4x shotgun)
o Dark Gray: covered by multiple draft clones
o Black: covered by a finished clone
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In full display mode, this track shows the position of each clone that
aligns to the genome sequence. Finished clones are shown in black and
unfinished clones are shown in gray. In assemblies prior to the April
2003 human release,
coverage for each unfinished clone is represented as a
two-tiered gray box. The fragments inside the clone are shown as numbered
black boxes. Their positions correspond to their relative assembly placement,
including strand assignment. For some assemblies, clones in the sequencing
center tiling path are shown with blue rather than gray backgrounds.
|
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Track details:
Clicking on an item in full display mode will show the clone hyperlink to
GenBank record and the fasta format sequence (one per fragment). |
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Table details:
To view a text version of the data set, select the
clonePos positional table in the Table Browser. To view the table
definition, click here. |
Cow Chain
This track shows cow genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
Cow ESTs
See the description for Human ESTs.
Cow mRNAs
the description for Human mRNAs.
Cow Net
This track shows the best cow chain for every part of the selected
genome. See the Human Net track description for more information.
CpG Islands
This track shows CpG islands, areas rich in the dinucleotide CG. A CpG island
is a region where C's followed by G's (CpGs) are present at significantly
higher levels than is typical for the genome as a whole. The CpG islands
displayed in this browser are all at least 200 bases long, and have a GC
content of at least 50%.
CpG islands are associated with genes, particularly housekeeping genes, in
vertebrates. They are particularly common near transcription start sites, and
may be associated with promoter regions. Normally a CpG is rare in vertebrate
DNA because the C's in such an arrangement tend to be methylated. This
methylation helps distinguish the newly synthesized DNA strand from the parent
strand, which aids in the final stages of DNA proofreading after duplication.
However, over evolutionary time, methylated C's tend to turn into T's due to
spontaneous deamination. The result is that CpGs are relatively rare unless
there is selective pressure to keep them or a region is not methylated for
some reason, perhaps having to do with the regulation of gene expression.
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Display conventions:
CpG islands are represented by green boxes. Darker green items indicate CpG
islands that contain 300 or more bases. |
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Display conventions:
Clicking on a CpG entry in full display mode will show basic track information,
detailed information about the CpG island, and sequence information. |
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Table details:
To view a text version of the data set, select the
cpgIsland positional table in the Table Browser. To view the table
definition, click here. |
C. savignyi Blat
This track displays translated BLAT alignments of the C. savignyi genome
against the C. intestinalis genome assembly. The alignments
were done with Blat in translated protein mode
requiring 2 nearby 4-mer matches to trigger a detailed alignment. The
C. intestinalis genome was masked with RepeatMasker and Tandem Repeats Finder
before running Blat.
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Display conventions:
This track uses the display conventions for BLAT tracks. |
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Track details:
Clicking on an entry in full display mode displays links to the DNA
sequence and the alignment. |
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Table details:
To view a text version of the data set, select the
blatCioSav1 positional table in the Table Browser. To view the table
definition, click here. |
Cytokine Genes (Tetraodon)
This track shows cytokine genes annotated by human experts using
sequence similarity information between Tetraodon and human, mouse and
zebrafish cytokine protein and nucleotide sequences. These annotations
are available only on the following chromosomes: 1, 2, 3, 4, 7, 8, 10, 12, 13,
15, 16, 1_random, 3_random, and Un_random.
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Display conventions:
This track uses the display conventions for gene prediction tracks.
|
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Track configuration:
The track description page contains a control that can be used to turn
on codon coloring. |
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Track details:
Clicking on a track feature in full display mode shows position
information and provides links to the translated protein, predicted mRNA,
and genome sequences. |
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Table details:
To view a text version of the data set, select the
cytokines positional table in the Table Browser. To view the table
definition, click here. |
DBTSS mRNA
This track shows RefSeq mRNA sequences extended to the 5' end, based on sequence
information in the DataBase of
Transcriptional Start Sites (DBTSS). For more information on the process used
to construct this track, refer to the track's description page.
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Display conventions:
This track uses the display conventions for PSL alignment tracks. |
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Track details:
Clicking on an entry in full display mode will show PSL output information
about the item. |
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Table details:
To view a text version of the data set, select the
dbtssAli positional table in the Table Browser. To view the table
definition, click here. |
D. mel. Chain
This track shows D. melanogaster genomic alignment to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
D. mel. Net
This track shows the best D. melanogaster chain for every part of the selected
genome. See the Human Net track description for more information.
D. mel. Proteins (A. gambiae, A. mellifera
This track contains tBLASTn alignments of the peptides from the predicted and
known genes identified in the specified version of FlyBase.
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Display conventions:
This track uses the display conventions for PSL alignment tracks. |
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Track details:
Clicking on an entry in full display mode will provide positional
information, a link to the related FlyBase record, protein length, and
links to the alignment and peptide sequences. |
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Table details:
To view a text version of the data set, select the
blastDm1FB positional table in the Table Browser. To view the table
definition, click here. |
D. melanogaster ESTs
See the description for Human ESTs.
D. melanogaster mRNAs
See the description for Human mRNAs.
DNAse HyperSens (Zoo)
This track depicts DNAse I hypersensitive sites (DHS) mapped to the human genome
sequence. Each track element represents the surrounding 500 bp from the position
of the estimated DHS, as determined from Smith et al. (2000) "Multiple
Potential Intragenic Regulatory Elements in the CFTR Gene", Genomics
64(1):90-6.
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Display conventions:
Each DHS is depicted by a block representing the 500 bp surrounding the
position of the estimated DHS. |
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Track details:
Clicking on an entry in full display mode will show position information
and a link to the underlying DNA sequence. |
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Table details:
To view a text version of the data set, select the
dhs positional table in the Table Browser. To view the table
definition, click here. |
Dog Chain
This track shows dog genomic alignment to the selected genome using blastz
and axtChain. See the Human Chain track description for more information.
Dog ESTs
See the description for Human ESTs.
Dog mRNAs
See the description for Human mRNAs.
Dog Net
This track shows the best dog chain for every part of the selected genome.
See the Human Net track description for more information.
D. ananassae Chain
This track shows D. ananassae genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
D. anan. mRNAs
D. ananassae mRNAs. See the description for Human mRNAs.
D. ananassae Net
This track shows the best D. ananassae chain for every part of the selected
genome. See the Human Net track description for more information.
D. mojavensis Chain
This track shows D. mojavensis genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
D. moj. mRNAs
D. mojavensis mRNAs. See the description for Human mRNAs.
D. mojavensis Net
This track shows the best D. mojavensis chain for every part of the selected
genome. See the Human Net track description for more information.
D. pseudo. Aligns (D. melanogaster)
This track shows blastz scores from the
D. pseudoobscura/D. melanogaster alignment Net track, i.e. the best
D. pseudoobscura/D. melanogaster chain for every part of the
D. melanogaster genome.
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Display conventions:
In dense display mode, darker shading indicates those best chained and
netted alignments that have the higher scores. In full display mode,
the height of the vertical line corresponds to the score.
|
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Track details:
Clicking on an entry in full display mode will show position information
and -- when zoomed in to the base level -- the base composition of the
alignments. |
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Table details:
To view a text version of the data set, select the
axtNetX positional table in the Table Browser, where X
represents the assembly that is being aligned, e.g. Dp1. To view the
table definition, click here. |
D. pseudo. Chain (D. melanogaster)
This track shows D. pseudoobscura genomic alignment to the selected
genome using blastz and axtChain. See the Human Chain track description for
more information.
D. pseudo. ESTs
D. pseudoobscura ESTs. See the description for Human ESTs.
D. pseudo. mRNAs
D. pseudoobscura mRNAs. See the description for Human mRNAs.
D. pseudo. Net (D. melanogaster)
This track shows the best D. pseudoobscura chain for every part of
the selected genome. See the Human Net track description for more information.
D. virilis Chain
This track shows D. virilis genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
D. vir. mRNAs
D. virilis mRNAs. See the description for Human mRNAs.
D. virilis Net
This track shows the best D. virilis chain for every part of the selected
genome. See the Human Net track description for more information.
D. yakuba Chain
This track shows D. yakuba genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
D. yakuba ESTs
D. yakuba ESTs. See the description for Human ESTs.
D. yakuba mRNAs
D. yakuba mRNAs. See the description for Human mRNAs.
D. yakuba Net
This track shows the best D. yakuba chain for every part of the selected
genome. See the Human Net track description for more information.
Duplications
This track shows genomic
duplications greater than 1,000 bp if not overly repeat-masked. Duplications are
more common in unordered and unassigned contigs (i.e., difficult to assign to their
proper position).
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Display conventions:
Duplications are show as red if 99%+ identity (likely unmerged assembly
overlap artifact), as yellow for 98-99% identity (origin uncertain), and as
gray for 90-98% identity (below draft sequencing error, often genuine
pericentromeric or subtelomeric duplication). |
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Track details:
In the left panel of the browser, duplications are named by the chromosome
and start of the other member of the duplication pair. Clicking on an
individual duplication gives details of both locations and match quality
parameters. |
D. yakuba ESTs
See the description for Human ESTs.
D. yakuba mRNAs
See the description for Human mRNAs.
ECgene Genes
This track shows gene predictions generated by combining genome-based EST
clustering and transcript assembly methods. The EST clustering is based on
genomic alignment of mRNA and ESTs similar to that of NCBI's UniGene for the
human genome. The transcript assembly procedure yields gene models for each
cluster that include alternative splicing variants. This algorithm was developed
by Prof. Sanghyuk Lee's Lab of Bioinformatics at Ewha Womans University in
Seoul, Korea. For more information, see the
ECgene web site.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode brings up basic track
information, links to the predicted mRNA, genomic sequence, and
comparative sequence. |
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Table details:
To view a text version of the data set, select the
ECgene positional table in the Table Browser. To view the table
definition, click here. |
Elegans Blastz
This track displays Blastz alignments of the C. elegans assembly
to the C. briggsae assembly
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Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
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Track details:
Clicking on an entry in full display mode will show human and
mouse position information, alignment details, and a link to a detailed
view of parts of the alignment. |
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Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
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Table details:
To view a text version of the data set, select the
blastzX positional table in the Table Browser, where X
represents the C. elegans assembly, e.g. Ce2. To view the table
definition, click here. |
Elegans Chain
This track shows C. elegans genomic alignment to the selected
genome using blastz and axtChain. See the Human Chain track description for
more information.
ENCODE Regions
This track depicts target regions for the NHGRI ENCODE project, which is
described in The
ENCODE Project: ENCyclopedia of DNA Elements. The long-term goal of this
project is to identify all functional elements in the human genome sequence to
facilitate a better understanding of human biology and disease.
During the pilot phase, 44 regions comprising 30 Mb -- approximately 1% of
the human genome -- have been selected for intensive study to identify, locate
and analyze functional elements within the regions. These targets are being
studied by a diverse public research consortium to test and evaluate the
efficacy of various methods, technologies, and strategies for locating genomic
features. The outcome of this initial phase will form the basis for a
larger-scale effort to analyze the entire human genome.
See the track description page for more information.
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Display conventions:
ENCODE regions are represented by blocks. |
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Track details:
Clicking on an item in full display mode shows position information
and provides a link to the DNA sequence associated with this feature.
|
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Table details:
To view a text version of the data set, select the
encodeRegions positional table in the Table Browser, where X
is the assembly version in which you're interested. To view the table
definition, click here. |
Ensembl ESTs
This track shows gene predictions from Project Ensembl based on ESTs. For a description of
the methods used in Ensembl gene prediction, refer to
The Ensembl genome database project, Nucleic Acids Research, 2002, 30(1) 38-41.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode brings up basic track
information, links to the translated protein, predicted mRNA, and
genomic sequences, plus a link to detailed supporting evidence. |
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Table details:
To view a text version of the data set, select the
ensEst positional table in the Table Browser. To view the table
definition, click here. |
Ensembl Genes
This track shows gene predictions from Project Ensembl. For a description of
the methods used in Ensembl gene prediction, refer to
The Ensembl genome database project, Nucleic Acids Research, 2002, 30(1) 38-41.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode brings up basic track
information, links to the translated protein, predicted mRNA, and
genomic sequences, plus a link to detailed supporting evidence. |
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Table details:
To view a text version of the data set, select the
ensGene positional table in the Table Browser. To view the table
definition, click here. |
Exofish ecores
The track displays conserved regions, generally protein-coding homologs,
from a genomics project of long random reads in the
pufferfish, Tetraodon
nigroviridis. Ecore is an acronym for evolutionary conserved
region. The data was
used to estimate the number of human genes.
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Display conventions:
Regions of greater homology are displayed in a darker blue. |
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Track details:
Clicking on an entry in full mode brings up information on a particular
ecore, access the relevant Genoscope page, and the relevant DNA. |
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Table details:
To view a text version of the data set, select the
exoFish positional table in the Table Browser. To view the table
definition, click here. |
Exoniphy
The exoniphy program identifies evolutionarily conserved protein-coding exons in multiple
sequences aligned with multiz using a phylogenetic hidden Markov model (phylo-HMM), a
statistical model that simultaneously describes exon structure and exon evolution.
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Display conventions:
Evoluntionarily-conserved protein-coding exons are represented by blocks.
Arrows indicated the direction of transcription. |
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Track details:
Clicking on an entry in full mode displays positional information and related
sequence links. |
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Table details:
To view a text version of the data set, select the
exoniphy positional table in the Table Browser. To view the table
definition, click here. |
Fgenesh++ Genes
This tracks shows Fgenesh++ gene predictions based on Softberry Inc.'s gene-finding
software. Fgenesh++ uses both hidden Markov models (HMMs) and protein
similarity to find genes in a completely automated manner, with less
emphasis on cDNA/EST data. See the paper
"Ab
initio gene finding in Drosophila genomic DNA", Genome Research 10(4) 516-522
for more information.
NOTE: The data in the softberryGene.txt and
softberryPep.txt tables is free for academic and nonprofit use. Commercial users
should contact Softberry Inc..
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode brings up basic track
information, links to the translated protein, predicted mRNA, and
genomic sequences, plus a link to the best matching protein at GenBank. |
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Table details:
To view a text version data set, select the
softberryGene positional table in the Table Browser.
To view the table definition, click here. |
First EF
This track displays predictions from First Exon Finder (FirstEF), a 5' terminal
exon and promoter prediction program.
Three types of predictions are shown: exon, promoter and CpG window. If two
consecutive predictions are separated by less than 1000 bp, FirstEF treats them
as one cluster of alternative first exons that may belong to same gene.
Each predicted exon is either CpG-related or non-CpG-related, based on a score
of the frequency of CpG dinucleotides. An exon is classified as CpG-related if
the CpG score is greater than a threshhold value and non-CpG-related if
less than the threshold. If an exon is CpG-related, its associated CpG-window is displayed.
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Display conventions:
This track uses the display conventions for BLAT tracks. Higher CpG
scores are shown in darker shades of gray/black. The cluster
number is displayed in parentheses in the item label. For example,
"exon(405-)" represents the exon prediction in cluster number
405 on the minus strand. The exon, promoter and CpG-window are
interconnected by this cluster number. Alternative predictions within
the same cluster are denoted by "#N" where "N" is the
serial number of an alternative prediction in the cluster. |
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Track details:
Clicking on an entry in full display mode displays probability, size,
and position information, and a link to the DNA sequence. |
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Table details:
To view a text version of the data set, select the
firstEF positional table in the Table Browser. To view the table
definition, click here. |
Fish Blat
This track displays translated alignments of 728 million bases
of Tetraodon nigroviridis whole genome shotgun reads vs. the
draft human genome. Areas painted by this track are quite likely to be coding
regions. The alignments were done with BLAT in translated protein mode
requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human
genome was masked with RepeatMasker and Tandem Repeats Finder before running
BLAT. The Tetraodon sequence was provided by Genoscope.
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Display conventions:
This track uses the display conventions for BLAT tracks. |
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Track details:
Clicking on an entry in full display mode brings up links to the DNA
sequence and the alignment. |
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Table details:
To view a text version of the data set, select the
blatFish positional table in the Table Browser. To view the table
definition, click here. |
FISH Clones
Shows the location of fluorescent in situ hybridization (FISH) mapped clones along
the draft assembly sequence.
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Display conventions:
The green blocks depict the clone placements on the assembly sequence. |
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Track details:
Clicking on a specific marker in full display mode will show information on
clone placement, clone registry, its STS markers, and BAC end sequences. |
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Table details:
To view a text version of the data set, select the
fishClones positional table in the Table Browser. To view the table
definition, click here. |
FlyBase Genes (D. melanogaster)
This track shows protein-coding genes annotated by FlyBase (version 3.2).
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, microarray expression data,
protein structure information, homology information and related links to
several tools and databases, including FlyBase. |
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Table details:
To view a text version of the data set, select the
bdgpGene positional table in the Table Browser. To view the table
definition, click here. |
FlyBase Non-coding (D. melanogaster)
This track shows non-coding genes annotated by FlyBase (version 3.2).
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display provides links to FlyBase and BDGP,
basic track information, and links to the corresponding predicted genomic and
predicted mRNA sequences. |
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Table details:
To view a text version of the data set, select the
bdgpGene positional table in the Table Browser. To view the table
definition, click here. |
FlyReg (D. melanogaster)
This track shows DNase I Footprint data from the
FlyReg version 2.0
database. FlyReg provides access to results of the systematic curation and
genome annotation of 1,350 DNase I footprints for the fruitfly
D. melanogaster reported in Bergman, C.M. et al.,
Drosophila DNase I footprint database: a systematic genome
annotation of transcription factor binding sites in the fruitfly, D.
melanogaster, Bioinformatics 2004 Nov. 30 [Epub ahead of
print].
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Display conventions:
Footprint regions are represented by blocks. |
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Track details:
Clicking on an entry in full display provides footprint information,
links to external databases, and a link to view the related genomic
DNA. When available, a footprint motif is also displayed, based on a
MEME matrix computed by Dan Pollard on the set of footprints for
the factor. |
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Table details:
To view a text version of the data set, select the
flyreg2 positional table in the Table Browser. To view the table
definition, click here. |
Fosmid End Pairs
A valid pair of fosmid end sequences must be at least 32Kb but no more than 47Kb
away from each other. The orientation of the first fosmid end sequence must be
"+" and the orientation of the second fosmid end sequence must be "-". End
sequences were trimmed at the NCBI using ssahaCLIP written by Jim Mullikan.
The trimmed end sequences were placed on the assembled sequence using Jim
Kent's BLAT program.
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Display conventions:
This track uses the display conventions for PSL alignment tracks. |
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Track details:
Clicking on an entry in full display mode will show position information
and provide links to genomic alignments of the Fosmid ends. |
-- |
Table details:
To view a text version of the data set, select the
fosEndPairs positional table in the Table Browser. To view the table
definition, click here. |
Fugu Blat
This track displays translated BLAT alignments of Takifugu rubripes whole genome
shotgun reads against the currently selected genome assembly. The alignments
were done with BLAT in translated protein mode
requiring 2 nearby 4-mer matches to trigger a detailed alignment. The human
genome was masked with RepeatMasker and Tandem Repeats Finder before running
BLAT. The fugu sequence used in this track is version 3.0, provided by the
DOE Joint Genome Institute (JGI).
-- |
Display conventions:
This track uses the display conventions for BLAT tracks. |
-- |
Track details:
Clicking on an entry in full display mode brings up links to the DNA
sequence and the alignment. |
-- |
Table details:
To view a text version of the data set, select the
blatFugu positional table in the Table Browser. To view the table
definition, click here. |
Fugu Chain
This track shows Fugu genomic alignment to the selected genome using blastz and
axtChain.
-- |
Display conventions:
This track uses the display conventions for chain tracks. |
-- |
Track details:
Clicking on an item in full display mode shows position information
in the Fugu and the selected genome, the chain ID and score, and provides
links to view details of parts of the chain or to open the Fugu browser
to the corresponding position. |
-- |
Table details:
To view a text version of the data set, select the
chainFrX positional table in the Table Browser, where X
is the assembly version in which you're interested. To view the table
definition, click here. |
Fugu Ecores
This track shows Fugu evolutionary conserved regions (ecores) computed against
the selected assembly genome by the Exofish program at Genoscope. For
information on this track, see the Human Ecores track description.
Fugu ESTs
See the description for Human ESTs.
Fugu mRNAs
See the description for Human mRNAs.
Fugu Net
This track shows the best Fugu chain for every part of the selected genome.
See the Human Net track description for more information.
Gap
This track depicts gaps in the assembly. These gaps - with the
exception of intractable heterochromatic gaps - are closed
during the finishing process.
-- |
Display conventions:
Gaps are represented as black boxes. If the relative order and
orientation of the contigs on either side of the gap is known from mRNA,
ESTs, or paired BAC end reads, it is a "bridged" gap and a white line is
drawn through the black box representing the gap. The display must be
sufficiently zoomed in to view these features: at a coarser scale, the
gaps can appear to coalesce in the the graphic. In full display mode,
the gap label indicates the type
of gap (see below) and whether the gap is bridged. |
|
Strand misorientation errors can occur adjacent to unbridged gaps.
Unbridged gaps are assigned somewhat arbitrary sequence sizes (runs of
N's in genomic DNA); uncertainty is less with bridged gaps. A gap within
contig fragments of a clone is typically smaller than a gap between
draft clones. |
-- |
Track details:
Clicking on an item in full display mode will show the gap type,
bridging information and position information about the gap. Unfinished
clones may have gaps of uncertain size between fragments. |
-- |
Table details:
To view a text version of the data set, select the
gap positional table in the Table Browser. To view the table
definition, click here. |
GC Percent
This shows the percentage of bases that are G or C in a 5-base window. High GC
content is associated with gene rich areas.
-- |
Display conventions:
This track uses the display conventions for wiggle tracks. |
-- |
Track configuration:
The track description page contains options to configure
several of the graph characteristics. To read more information
about each option, click the "Graph configuration help" link.
|
-- |
Track details:
Clicking on one of the peaks in the track when in full display mode will
show position information and provide a link to the underlying DNA
sequence. In full mode in a zoomed-out display, detailed information
may not be accessible for an individual feature. In this case, zoom in
and try again. |
-- |
Table details:
To view a text version of the data set, select the
gc5Base positional table in the Table Browser. To view the table
definition, click here. |
GC Samples (Zoo)
This track shows the percentage of bases that are G or C in small regions across
the genome. Windows with high GC content are plotted at higher vertical
positions than windows with low GC content. High GC content is associated with
gene-rich areas.
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Display conventions:
This track uses the display conventions for wiggle tracks. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
-- |
Track details:
Clicking on one of the peaks in the track when in full display mode will
show position information and provide a link to the underlying DNA
sequence. In full mode in
a zoomed-out display, detailed information may not be accessible for an
individual feature. In this case, zoom in and try again. |
-- |
Table details:
To view a text version of the data set, select the
pGC positional table in the Table Browser. To view the table
definition, click here. |
Gene Annotations (Zoo)
This track displays NISC-generated, curated gene annotations for each of the
zoo species and human. Exon locations of known genes were determined by aligning
human and/or mouse reference cDNA sequences with each species' assembled genomic
sequence. Any splice-site consensus, exon structure, or protein translation
errors encountered were manually inspected and corrected.
-- |
Display conventions:
This track uses the display conventions for gene prediction tracks. As with other
tracks in this category, it may be necessary to zoom in to
display entries in full display mode due to the 300 line display
limit. |
-- |
Track details:
Clicking on an item in full mode provides position, size, and score
information, and a link to dsplay the DNA sequence associated with this
feature. |
-- |
Table details:
To view a text version of the data set, select the
pjt_gene positional table in the Table Browser. To view the table
definition, click here. |
Gene Bounds
This track shows the boundaries of genes and the direction of transcription as
deduced from clustering spliced ESTs and mRNAs against the genome. When there
are many spliced variants of the same gene, this track shows the variant that
spans the greatest distance in the genome.
-- |
Display conventions:
This track uses the display conventions for EST tracks. As with other
tracks in this category, it may be necessary to zoom in to
display entries in full display mode due to the 300 line display
limit. |
-- |
Track details:
Clicking on an item in full mode provides position, size, and score
information, and a link to dsplay the DNA sequence associated with this
feature. |
-- |
Table details:
To view a text version of the data set, select the
rnaCluster positional table in the Table Browser. To view the table
definition, click here. |
Geneid Gene Predictions
This track shows gene predictions from the geneid program, which is
being developed at the Grup de Recerca en Informatica Biomedica at IMIM
in Barcelona. Geneid uses information from sequence signals involved in
genes specification, as well as coding coding statistics, to define exons
and genes.
-- |
Display conventions:
This track uses the display conventions for gene predictions tracks. |
-- |
Track details:
Clicking on an entry in full display mode brings up basic track
information, plus links to the translated protein, predicted mRNA, and
genomic sequences. |
-- |
Table details:
To view a text version of the data set, select the
geneid positional table in the Table Browser. To view the table
definition, click here. |
GenMapDB Clones
This track shows BAC clones from the
GenMapDB
database placed on the draft sequence using BAC end sequence information and
confirmed using STS markers by Vivian Cheung's lab at the Department of
Pediatrics, University of Pennsylvania.
-- |
Display conventions:
The clone positions are shown in black. |
-- |
Track details:
Clicking on an entry in full display mode brings up basic position
information and additional information about the clones and STS markers.
|
-- |
Table details:
To view a text version of the data set, select the
genMapDb positional table in the Table Browser. To view the table
definition, click here. |
Genoscope GAZE (Tetraodon)
This track shows Genoscope gene model annotations from the GAZE program
written by Kevin Howe. These annotaions were computed using GAZE with a i
custom-designed gene model. GAZE integrates information from Geneid,
Genscan, Exofish (Human, Mouse and Fugu), Genewise (Human and Mouse) and
Tetraodon cDNAs.
-- |
Display conventions:
This track uses the display conventions for gene prediction tracks.
|
-- |
Track configuration:
The track description page contains a control that can be used to turn
on codon coloring. |
-- |
Track details:
Clicking on a track feature in full display mode shows position
information and provides links to the translated protein, predicted mRNA,
and genome sequences. |
-- |
Table details:
To view a text version of the data set, select the
gaze positional table in the Table Browser. To view the table
definition, click here. |
Genscan Genes
This track shows gene predictions from
GenScan. These predictions are based on transcriptional, translational,
and donor and acceptor splicing signals, plus length and compositional
distributions of exons, introns and intergenic regions. The program does not
use similarity to known proteins like
GenomeScan. For a description of the Genscan program and the model that
underlies it, refer to Burge, C. and Karlin, S. (1997)
Prediction of complete gene structures in human genomic
DNA. J. Mol. Biol. 268(1):78-94.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
-- |
Track details:
Clicking on an entry in full display mode will show basic track
information, plus links to the translated protein, predicted mRNA, and
genomic sequences. |
-- |
Table details:
To view a text version of the data set, select the
genscan positional table in the Table Browser. To view the table
definition, click here. |
Genscan Genes (Zoo)
This track shows gene predictions from the
GenScan program written by Chris Burge.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
-- |
Track details:
Clicking on an entry in full display mode shows basic track
information and provides a link to view the underlying genomic sequence. |
-- |
Table details:
To view a text version of the data set, select the
pjt_genscan positional table in the Table Browser. To view the table
definition, click here. |
GNF Atlas 2
This track shows expression data from the GNF (The Genomics Institute of the
Novartis Research Foundation) Gene Expression Atlas 2. The data contains 2
replicates each of 61 mouse tissues and 79 human tissues run over Affymetrix
microarrays. For more
information about the experiments, refer to the description page for this track.
-- |
Display conventions:
This track uses display conventions similar to those for PSL alignment tracks. |
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment.
| -- |
Table details:
To view a text version of the data set, select the
gnfAtlas2 positional table in the Table Browser. To view the table
definition, click here. |
GNF Ratio
This track shows expression data from GNF (The Genomics Institute of the
Novartis Research Foundation) using Affymetrix GeneChips. For more
information about the experiments, refer to the description page for this track.
-- |
Display conventions:
In dense display mode, the track color denotes the average signal over
all experiments on a log base 2 scale. Lighter colors correspond
to lower signals and darker colors correspond to higher signals.
In full display mode, the color of each item represents the log base 2 ratio
of the signal of that particular experiment to the median signal of all
experiments for that probe. |
-- |
Track configuration:
The track description page contains options to change the display mode,
group the displayed results, and change the display colors.
|
-- |
Table details:
To view a text version of the data set, select the
affyRatio positional table in the Table Browser. To view the table
definition, click here. |
GNF U74A
This track shows expression data from GNF using the Affymetrix U74A chip.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyGnfU74A positional table in the Table Browser. To view the table
definition, click here. |
GNF U74B
This track shows expression data from GNF using the Affymetrix U74B chip.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyGnfU74B positional table in the Table Browser. To view the table
definition, click here. |
GNF U74C
This track shows expression data from GNF using the Affymetrix U74C chip.
-- |
Display conventions:
This track follows display conventions similar to PSL alignment tracks.
|
-- |
Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
-- |
Table details:
To view a text version of the data set, select the
affyGnfU74C positional table in the Table Browser. To view the table
definition, click here. |
Haplotype Blocks (chr21)
See the description for Perlegen.
Haplotype Blocks (chr22)
This track shows haplotype blocks on Chromosome 22 from The University of
Oxford and The Wellcome Trust Sanger Institute, as described in
Dawson E. et. al. (2002),
"A first-generation linkage disequilibrium map of human
chromosome 22", Nature 418:544-8.
-- |
Display conventions:
The location of each haplotype block is represented by a blue horizontal
line with tall vertical blue bars at the first and last SNPs of
the block. Blocks are displayed as starting at the first SNP and ending
at the last SNP of the block. Individual SNPs are denoted
by smaller black vertical bars. At multi-megabase resolution in dense
display mode, clusters of tall blue bars may indicate hotspots
for recombination. |
-- |
Track details:
Clicking on an entry in full display mode will show basic position
information, SNP information for the block, and a link to sequence
information for the feature. |
-- |
Table details:
To view a text version of the data set, select the
haplotype positional table in the Table Browser. To view the table
definition, click here. |
H-Inv
This track shows alignments of full-length cDNAs used as the basis of the
H-Invitational Gene Database (HInv-DB). Entries in this track include
gene structures, functions, functional domains, metabolic pathways, and many
other entities.
-- |
Display conventions:
This track uses the display conventions for PSL alignment tracks. |
-- |
Track details:
Clicking on an entry in full display mode provides gene ID, cluster
ID, and cDNA accession information and a link to sequence
information for the feature. |
-- |
Table details:
To view a text version of the data set, select the
HInvGeneMrna positional table in the Table Browser. To view the table
definition, click here. |
HOX Genes (Tetraodon chr2, 8, 9, 17, 21, and un_random only)
This track shows HOX genes annotated using information on
sequence similarity between Tetraodon vs. human, mouse and zebrafish HOX
protein and nucleotide sequences.
-- |
Display conventions:
This track uses the display conventions for gene prediction tracks.
|
-- |
Track details:
Clicking on an entry in full display mode provides position, size, and
CDS information, and links to the related translated protein, predicted
mRNA, and genomic sequences. |
-- |
Table details:
To view a text version of the data set, select the
hoxGenes positional table in the Table Browser. To view the table
definition, click here. |
Human Best
This track displays best-in-genome alignments of the specified human draft
assembly to the selected genome baed on the associated alignment net, i.e. the
best chain for every part of the human genome. See the track description page
for the Human Net track for more information about the methods used to generate
this track.
-- |
Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
-- |
Track details:
Clicking on an entry in full display mode will show position information
for the human alignment and the selected genome, alignment details, and
a link to a detailed view of parts of the alignment.
|
-- |
Table details:
To view a text version of the data set, select the
axtNetHgX positional table in the Table Browser, where
X is the assembly version in which you're interested.
To view the table definition, click here. |
Human Blat
This track displays translated BLAT alignments of the human genome
vs. the mouse genome.
The alignments were done with BLAT in translated protein mode using the
parameters -q=dnax -t=dnax and otherwise the default settings. Both
genomes were masked with RepeatMasker and Tandem Repeats Finder before
running BLAT. Places where more than 250 alignments occurred
over the same place were filtered out. Beware of alignments of greater
than 97% identity: these may reflect mouse contamination in the human
genome or human contamination in the mouse genome.
-- |
Display conventions:
This track uses the display conventions for a BLAT alignment track. |
-- |
Track details:
Clicking on an entry in full display mode will show basic track
information and a link to sequence information for the alignment. |
-- |
Table details:
To view a text version of the data set, select the
blatHuman positional table in the Table Browser. To view the table
definition, click here. |
Human Chain
This track shows human genomic alignment to the selected genome using blastz and
axtChain.
-- |
Display conventions:
This track uses the display conventions for chain tracks. |
-- |
Track details:
Clicking on an item in full display mode shows position information
in the mouse and the selected genome, the chain ID and score, and
provides links to view details of parts of the chain or to open the
mouse browser to the corresponding position. |
-- |
Table details:
To view a text version of the data set, select the
chainX positional table in the Table Browser, where X
is the assembly version in which you're interested, e.g. Hg16. To view
the table definition, click here. |
Human Cons
This track displays the conservation between the mouse and human genomes for
50bp windows in the mouse genome that have at least 15bp aligned to human. The
score for a window reflects the probability that the level of observed
conservation in that 50bp region would occur by chance under neutral evolution.
It is given on a logarithmic scale, and thus it is called the "L-score". An
L-score of 1 means there is a 1/10 probability that the observed conservation
level would occur by chance, an L-score of 2 means a 1/100 probability, an
L-score of 3 means a 1/1000 probability, etc. The L-scores display as
"mountain ranges".
-- |
Display conventions:
This track uses the display conventions for wiggle tracks.
|
-- |
Track configuration:
The track description page contains options to configure
several of the graph characteristics. To read more information
about each option, click the "Graph configuration help" link.
|
-- |
Track details:
Clicking on one of the peaks in the track when in full display mode will
show human genome
position information for the window, as well as position information for
the corresponding region in the human genome. The details page provides
links to the underlying sequence for the alignment and to the sequence
underlying the individual alignment windows. In full mode in
a zoomed-out display, detailed information may not be accessible for an
individual feature. In this case, zoom in and try again. |
-- |
Table details:
To view a text version of the data set, select the
musHumL positional table in the Table Browser. To view the table
definition, click here. |
Human Deletions
This track displays regions of the chimp assembly that are deleted in the
human assembly. Only regions of between 80 and 12000 bases are included.
The name of each deletion is a unique pointer to that deletion followed by an
underscore and then its length. A similar track, showing chimp deletions in the
human assembly, appears in the human Genome Browser.
-- |
Display conventions:
Deletions are indicated by thin vertical lines. |
-- |
Track details:
Clicking on a deletion in full display mode provides the item name,
position, genomic size, and a link to the DNA underlying the feature.
|
-- |
Table details:
To view a text version of the data set, select the
humanDels positional table in the Table Browser. To view the table
definition, click here. |
Human Ecores
This track shows human evolutionary conserved regions (ecores) computed against
the selected assembly by the Exofish program at Genoscope.
-- |
Display conventions:
This track uses display conventions similar to PSL alignment tracks. Each
singleton block corresponds to an ecore. Blocks connected by a
line correspond to an "ecotig", a set of colinear ecores in a
syntenic region. |
-- |
Track details:
Clicking on an entry in full display mode will show positional
information,
a link to the Exofish browser, and a link to display the DNA sequence.
|
-- |
Table details:
To view a text version of the data set, select the
ecores positional table in the Table Browser, where
X is the assembly version in which you're interested (e.g.
hg16).
To view the table definition, click here. |
Human ESTs
This track shows alignments between Expressed Sequence Tags (ESTs) -
spliced and unspliced - in GenBank and the genome. ESTs are single read
(typically approximately 500 base) sequences
that usually represent fragments of transcribed genes.
To view only spliced ESTs, see the Spliced EST track.
This track was generated by aligning human ESTs from GenBank against the
genome using the BLAT program. Note that the maximum intron length
allowed by BLAT is 500,000 bases, which may eliminate some ESTs with
very long introns that might otherwise align. When a single EST aligns
in multiple places, the alignment having the highest base identity is
found. Only alignments that have a base identity level within 1% of the
best are kept. Alignments must also have at least 93% base identity to be
kept.
-- |
Display conventions:
This track uses the display conventions for EST tracks. Hatch marks on the
introns indicate the direction of transcription. In the December 2001
assembly and later, this direction is taken by looking at the splice sites.
In previous assemblies, the direction of transcription was taken from the
GenBank annotations, which frequently were inaccurate; these should be
verified in the details page alignment on the basis of the GT-AG splice
donor/acceptor rule. As with otherEST tracks, it may be necessary to zoom
in to display entries in full display mode due to the 300 line display
limit. |
-- |
Track configuration:
The track description page contains a filter to restrict the display to
only those entries that match certain keywords and to change the color
of the selected entries. |
-- |
Track details:
Clicking on an individual EST entry will show basic track information,
the accession number, GenBank highlights, and links to EST/Genomic
Alignments. |
-- |
Table details:
To view a text version of the data set, select the
all_est positional table in the Table Browser. To view the table
definition, click here. |
Human mRNAs
This track shows alignments between mRNAs from the current assembly in GenBank
and the genome. The mRNAs are aligned against the genome using the BLAT
program. When a single mRNA aligns
in multiple places, the alignment having the highest base identity is found.
Only alignments that have a base identity level within 1% of the best
are kept. Alignments must also have at least 95% base identity
to be kept.
-- |
Display conventions:
This track follows the display conventions for PSL alignment tracks. |
-- |
Track configuration:
The track description page contains a filter to restrict the display to
only those entries that match certain keywords and to change the color
of the selected entries. |
-- |
Track details:
Clicking on an entry in full display mode will show a summary of the GenBank
entry on that mRNA, convenient hyperlinks to major databases, and base-by-base
mRNA/genomic alignments. |
-- |
Table details:
To view a text version of the data set, select the
all_mrna positional table in the Table Browser. To view the table
definition, click here. |
Human Net
This track shows the best human chain for every part of the selected genome.
-- |
Display conventions:
This track uses the display conventions for net tracks. |
-- |
Track details:
In full display mode, clicking on a box shows details information about
the chain as a whole, while clicking on a line shows information
about the gap. The detailed information is useful in determining the
cause of the gap or, for lower level chains, the genomic
rearrangement. |
-- |
Table details:
To view a text version of the data set, select the
netX positional table in the Table Browser, where X
is the assembly version in which you're interested, e.g. Hg16. To view
the table definition, click here. |
Human Proteins
This track shows tBLASTn alignments of the peptides from the predicted and
known genes indentified in the specified Known Genes track.
-- |
Display conventions:
This track follows the display conventions for PSL alignment tracks. |
-- |
Track configuration:
The track description page contains options to configure the information shown
in the track element labels.
|
-- |
Track details:
Clicking on an entry in full display mode will show position information,
external links to human mRNA and UniProtKB information, and links to the alignment
and peptide sequences.
|
-- |
Table details:
To view a text version of the data set, select the
blastHg16KG positional table in the Table Browser. To view the table
definition, click here. |
Human Synteny
This track shows syntenous (corresponding) regions between mouse and human
chromosomes. The track was created by passing a 100k non-overlapping window over
the genome and using the blastz best in human genome alignments to look for
high-scoring regions where at least 40% of the bases aligned with the same
region in mouse. 100k segments were joined together if they agreed in direction
and were within 500kb of each other in the mouse genome and within 4mb of each
other in the human. Gaps were joined between syntenic anchors if the bases
between two flanking regions agreed with synteny (direction and human location).
The syntenic block was extended to include these areas.
-- |
Display conventions:
This track uses the display conventions for synteny tracks. |
-- |
Track details:
Clicking on an item in full display mode shows details of the
mouse-human correspondence and provides a link to the genomic sequence
for this feature. |
-- |
Table details:
To view a text version of the data set, select the
syntenyHuman positional table in the Table Browser. To view the table
definition, click here. |
Human Tight
This track displays Blastz alignments of the human
assembly to the current genome, filtered by axtBest and
subsetAxt with very stringent constraints. See the track's description
page for more details.
-- |
Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
-- |
Track details:
Clicking on an entry in full display mode will show position information
for the human and the current genome, alignment details, and a link to
a detailed view of parts of the alignment. |
-- |
Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
-- |
Table details:
To view a text version of the data set, select the
blastzTightHg positional table in the Table Browser, where
X is the number of the assembly. To view the table
definition, click here. |
JGI Genes (C. intestinalis)
This track contains alignments of predicted transcripts from the DOE Joint Genome Institute
(JGI) to the C. intestinalis genome.
-- |
Display conventions:
This track uses the display conventions for gene predictions tracks. |
-- |
Track details:
Clicking on an entry in full display mode brings up basic track
information, plus links to the translated protein, predicted mRNA, and
genomic sequences. |
-- |
Table details:
To view a text version of the data set, select the
jgiGene positional table in the Table Browser. To view the table
definition, click here. |
Known Genes
The Known Genes track shows known protein coding genes based on proteins from
UniProtKB the corresponding mRNAs from GenBank.
Features are colored according to origin and review status:
-
Black: Feature has a corresponding entry in the Protein Data Bank (PDB).
-
Dark blue: Feature has a corresponding protein in UniProtKB or a corresponding
NCBI Reference Sequence mRNA with a "Reviewed" status.
-
Lighter blue: Feature has a corresponding NCBI Reference
Sequence mRNA with "Provisional" status.
-
Lightest blue: All other features.
All mRNAs of a species are aligned against the genome using the BLAT program.
When a single mRNA aligns in multiple places, only the best alignments with at
least 98% sequence identity are kept. The set of alignments is further reduced
by keeping only those mRNAs that are referenced by a protein in UniProtKB.
When a single protein references multiple mRNAs, the best
mRNA is chosen based on a quality score that depends on its length, how good its
translation matches the protein sequence, and its release date. The resulting
list of mRNA and protein pairs is trimmed by removing short invalid entries and
consolidating entries with identical CDS regions. Finally, RefSeq entries
derived from DNA sequences instead of mRNA sequences are added.
-- |
Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. See above description of color coding conventions.
|
-- |
Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, microarray expression data,
protein structure information, homology information and related links to
several tools and databases. |
-- |
Table details:
To view a text version of the data set, select the
knownGene positional table in the Table Browser. To view the table
definition, click here. |
Map Contigs
This track shows the locations of contigs of clones on the physical map.
In assembly versions prior to the August 6 2001 assembly, this track was
based on the Washington University accession map, which in turn was
based on a fingerprint contig (FPC) map described in
'A physical map of the human genome' in Nature volume 409 pages 934-941.
Starting with the August 6 2001 assembly, this track is based on tiling path
fingerprint (TPF) maps curated by the sequencing centers responsible for each
chromosome. The TPF maps are merged with the FPC map,
favoring the TPF map where conflicts occur. This step increases the
clone coverage substantially over that in the TPF maps. The clone contigs in
this merged map are shown in this track.
-- |
Display conventions:
The clone contigs are represented by blocks that indicate their location
on the assembly sequence. |
-- |
Track details:
Clicking on an item in full display mode will show a brief description of the
extent and number of clones in contig, and the DNA sequence. |
-- |
Table details:
To view a text version of the data set, select the
ctgPos positional table in the Table Browser. To view the table
definition, click here. |
Mapped Human (X. tropicalis)
This track contains tBLASTn alignments of the peptides from the predicted
and known genes identified in the specified version of the Known Genes track.
-- |
Display conventions:
This track follows the display conventions for BLAT tracks. |
-- |
Track details:
Clicking on an item in full display mode shows positional information,
related mRNA and UniProtKB links, the protein length, and links to the
alignment an peptide sequences.
|
-- |
Table details:
To view a text version of the data set, select the
blastHg17KG positional table in the Table Browser. To view the
table definition, click here. |
MCS Binomial (Zoo)
This track shows Multi-Species Conserved Sequences (MCSs) defined using a
conservation score threshold from the binomial-based method
that selects the top 5% most conserved sequence.
-- |
Display conventions:
Sequence positions are depicted by blocks. |
-- |
Track details:
Clicking on an item in full display mode shows position and size
information, and provides a link to the underlying DNA sequence.
|
-- |
Table details:
To view a text version of the data set, select the
mcs_b positional table in the Table Browser. To view the
table definition, click here. |
MCS Inter (Zoo)
This track shows Multi-Species Conserved Sequences (MCSs) found by intersecting
the sequences generated using the binomial-based and parsimony p-value-based
methods (see the MCS Binomial and MCS ParsPVal track descriptions).
-- |
Display conventions:
Sequence positions are depicted by blocks. |
-- |
Track details:
Clicking on an item in full display mode shows position and size
information, and provides a link to the underlying DNA sequence.
|
-- |
Table details:
To view a text version of the data set, select the
intersectingMCS positional table in the Table Browser. To view the
table definition, click here. |
MCS InterMerged (Zoo)
Same as MCS Inter, but regions less than 10 bp apart have been merged into one
region.
-- |
Display conventions:
Sequence positions are depicted by blocks. |
-- |
Track details:
Clicking on an item in full display mode shows position and size
information, and provides a link to the underlying DNA sequence.
|
-- |
Table details:
To view a text version of the data set, select the
intersectingMergedMCS positional table in the Table Browser. To
view the table definition, click here. |
MCS ParsPVal (Zoo)
This track shows Multi-Species Conserved Sequences (MCSs) defined using a
conservation score threshold from the parsimony p-value method
that selects the top 5% most conserved sequence.
-- |
Display conventions:
Sequence positions are depicted by blocks. |
-- |
Track details:
Clicking on an item in full display mode shows position and size
information, and provides a link to the underlying DNA sequence.
|
-- |
Table details:
To view a text version of the data set, select the
mcs_p positional table in the Table Browser. To view the
table definition, click here. |
MGC Genes
This track displays alignments between Mammalian Gene Collection (MGC) human mRNAs with full-length ORFs and the human genome.
-- |
Display conventions:
This track uses the display conventions for gene predictions tracks. |
-- |
Track details:
Clicking on an entry in full display mode will show basic track
information and links to the mRNA, genomic, and comparative sequences. |
-- |
Track configuration:
The track description page offers configuration options that can be used to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
|
-- |
Table details:
To view a text version of the data set, select the
mgcGenes positional table in the Table Browser. To view the table
definition, click here. |
Microsatellites
This track contains all perfect microsatellite repeats with between 2 and 10 bp
repeat units and 10 or more perfect copies. Over 90% of the items will be
multi-allelic polymorphisms. This track was created by using three programs:
Tandyman, display_VNTR and Primeleftright. See the track description page for
more information.
-- |
Display conventions:
Microsatellite locations are indicated by thin grey vertical lines.
|
-- |
Track details:
Clicking on an item in full display mode shows position information,
details about the repeat, and a link to the DNA sequence associated with
the feature. |
-- |
Table details:
To view a text version of the data set, select the
vntr positional table in the Table Browser. To view the table
definition, click here. |
miRNA
This track shows microRNAs from the
miRNA Registry
at the Wellcome Trust Sanger Institute.
-- |
Display conventions:
Mature miRNAs (miRs) are represented by thick lines; the predicted
stem-loop portions of the primary transcripts are indicated by thinner
lines. miRNAs in the sense orientation are shown in black; those in the
reverse orientation are colored grey. When a single precursor produces
two mature miRs from its 5' and 3' parts, it is displayed twice with the
two different positions of the mature miR. |
-- |
Track details:
Clicking in full mode displays positional information and
a link to item's entry in the miRNA registry. |
-- |
Table details:
To view a text version of the data set, select the
miRNA positional table in the Table Browser. To view the table
definition, click here. |
Most Conserved
This track shows predictions of conserved elements produced by the phastCons program.
Predictions are based on a phylogenetic hidden Markov model (phylo-HMM), a type of
probabilistic model that describes both the process of DNA substitution at each site in
a genome and the way this process changes from one site to the next. For more
information on the methods used to produce this track, see the track's description
page.
-- |
Display conventions:
Rectangular blocks indicate the positions of conserved elements.
|
-- |
Track details:
Clicking on an entry in full display mode will show position information and
a list of the top-scoring elements in the window. |
-- |
Table details:
To view a text version of the data set, select the phastConsElements
positional table from the Table Browser. To view the table definition, click
here.
|
Mouse Blat
This track displays alignments of mouse genome to human. The mouse genomic
DNA is from the Arachne assembly of mouse whole genome shotgun reads available
at the Trace Repository.
The alignments were done with BLAT in translated protein mode requiring 2 nearby
4-mer matches to trigger a detailed alignment. The human genome was masked with
RepeatMasker
and Tandem Repeats Finder
prior to running BLAT. Regions with more than 300 aligned reads were assumed novel
repeat elements and filtered out. Alignments of greater than 97% identity may represent
mouse contamination of human or vice versa.
-- |
Display conventions:
This track follows the display conventions for BLAT tracks. |
-- |
Track details:
Clicking on an item will show details on mouse sequence fragment and
alignment details. |
-- |
Table details:
To view a text version of the data set, select the
blatMouse positional table in the Table Browser. To view the table
definition, click here. |
Mouse Chain
This track shows mouse genomic alignment to the selected genome using blastz and
axtChain. See the Human Chain track description for more information.
Mouse Cons
This track displays the conservation between the human and mouse genomes for
50bp windows in the human genome that have at least 15bp aligned to mouse. The
score for a window reflects the probability that the level of observed
conservation in that 50bp region would occur by chance under neutral evolution.
It is given on a logarithmic scale, and thus it is called the "L-score". An
L-score of 1 means there is a 1/10 probability that the observed conservation
level would occur by chance, an L-score of 2 means a 1/100 probability, an
L-score of 3 means a 1/1000 probability, etc. The L-scores display as
"mountain ranges".
-- |
Display conventions:
This track uses the display conventions for wiggle tracks.
|
-- |
Track configuration:
The track description page contains options to configure
several of the graph characteristics. To read more information
about each option, click the "Graph configuration help" link.
|
-- |
Track details:
Clicking on one of the peaks in the track when in full display mode will
show human genome
position information for the window, as well as position information for
the corresponding region in the mouse genome. The details page provides
links to the underlying sequence for the alignment and to the sequence
underlying the individual alignment windows. In full mode in
a zoomed-out display, detailed information may not be accessible for an
individual feature. In this case, zoom in and try again. |
-- |
Table details:
To view a text version of the data set, select the
humMusL positional table in the Table Browser. To view the table
definition, click here. |
Mouse Ecores
This track shows Mouse evolutionary conserved regions (ecores) computed against
the selected assembly genome by the Exofish program at Genoscope. For
information on this track, see the Human Ecores track description.
Mouse ESTs
This track shows alignments between mouse Expressed Sequence Tags (ESTs) -
spliced and unspliced - in GenBank and the genome. This track was generated by
aligning mouse ESTs from GenBank against the
genome using the BLAT program. Note that the maximum intron length
allowed by BLAT is 500,000 bases, which may eliminate some ESTs with
very long introns that might otherwise align. When a single EST aligns
in multiple places, the alignment having the highest base identity is
found. Only alignments that have a base identity level within 1% of the
best are kept. Alignments must also have at least 93% base identity to be
kept.
-- |
Display conventions:
This track uses the display conventions for EST tracks. As with other
EST tracks, it may be necessary to zoom in to display entries in full
display mode due to the 300 line display limit. |
-- |
Track details:
Clicking on an individual EST entry will show basic track information,
the accession number, GenBank highlights, and links to EST/Genomic
Alignments. |
-- |
Table details:
To view a text version of the data set, select the
all_est positional table in the Table Browser. To view the table
definition, click here. |
Mouse mRNAs
See the description for Human mRNAs.
Mouse Net
This track shows the best mouse chain for every part of the selected genome.
See the Human Net track description for more information.
Mouse Synteny (hg13+)
This track shows syntenous (corresponding) regions between human and mouse
chromosomes. The track was created by passing a 100k non-overlapping window over
the genome and using the blastz best in mouse genome alignments to look for
high-scoring regions where at least 40% of the bases aligned with the same
region in mouse. 100k segments were joined together if they agreed in direction
and were within 500kb of each other in the human genome and within 4mb of each
other in the mouse. Gaps were joined between syntenic anchors if the bases
between two flanking regions agreed with synteny (direction and mouse location).
The syntenic block was extended to include these areas.
-- |
Display conventions:
This track uses the display conventions for synteny tracks. |
-- |
Track details:
Clicking on an item in full display mode shows details of the
mouse-human correspondence and provides a link to the genomic sequence
for this feature. |
-- |
Table details:
To view a text version of the data set, select the
syntenyMouse positional table in the Table Browser. To view the table
definition, click here. |
Mouse Synteny (hg12 only)
This track shows orthologous (syntenic) regions between mouse and human chromosomes based on data from Michael Kamal at the Whitehead Institute.
-- |
Display conventions:
This track uses the display conventions for synteny tracks. |
Track details:
Clicking on an item in full display mode will show details of the
mouse-human correspondence, as well links to genomic dotplots,
additional information, and an alternative synteny map based on
orthologous genes.
-- |
Table details:
To view a text version of the data set, select the
mouseSynWhd positional table in the Table Browser. To view the table
definition, click here. |
Multiz Yeast
This track displays multiz multiple alignments of seven species of the genus
Saccharomyces. The graphic display shows the alignment projected onto
S. cerevisiae.
-- |
Display conventions:
In full display mode, the track displays pairwise alignments of several
species aligned to the S. cerevisiae genome. The pairwise
alignments
are displayed in standard UCSC browser "dense" mode using a grey-scale
density gradient. When zoomed-in to the base-display level, the track
shows the base composition of each alignment. The numbers and symbols on
the "hidden gap" line indicate the lengths of gaps in the S.
cerevisiae sequence
at those alignment positions. If the gap size is greater than 9, the
"+" symbol is displayed. The track must be zoomed-in to 30,000
or fewer bases to access detailed information about the
alignments at a specific position.
|
-- |
Track details:
Clicking on an entry in full display mode will show detailed alignment
information for each of the organisms. |
-- |
Table details:
To view a text version of the data set, select the
multizYeast positional table in the Table Browser. To view the
table definition, click here. |
NIA Genes
This track displays alignments of the National Institute on Aging (NIA) Mouse
Gene Index (Version 3) against the mouse genome.
-- |
Display conventions:
This track uses the display conventions for Blat alignment tracks.
|
-- |
Track details:
Clicking on an individual track item in full mode displays a page
with alignment details and a link to the corresponding NIA Mouse Gene
Index entry. |
-- |
Table details:
To view a text version of the data set, select the
NIAGene positional table in the Table Browser. To view the table
definition, click here. |
NCI60
This track displays cDNA expression data for a micro-array of 8,000 genes for
60 cell lines used in an NCI
cancer drug screen.
-- |
Display conventions:
To understand the track, experiment with it set to
full mode but other tracks (except known genes) hidden, while reading its
filter page. Each column of colored boxes represents variation in
transcript levels for a given cDNA across array experiments; each row
represents the measured transcript levels for all genes in a single sample.
The saturation of a color corresponds to the magnitude of transcript
variation. Black indicates an undetectable change in expression; gray shows
missing data. |
-- |
Track configuration:
The track description page contains a filter to limit the tissue types
displayed and change the color scheme of the display. |
Track details:
Clicking on an individual track item in full mode opens a rich details
page. The exon probe and experiment selected are highlighted in blue
under item name.
-- |
Table details:
To view a text version of the data set, select the
nci60 positional table in the Table Browser. To view the table
definition, click here. |
Non-A. gambiae mRNAs
See the description for Non-Human mRNAs.
Non-A. mel. mRNAs
mRNAs of organisms other than A. mellifera. See the description for Non-Human
mRNAs.
Non-Chicken mRNAs
See the description for Non-Human mRNAs.
Non-Chicken RefSeq
This track shows known protein-coding genes from organisms other than chicken, taken from
the mRNA reference sequences collection (RefSeq) compiled at NCBI. See the Non-Dog RefSeq
track for more information.
Non-Chimp ESTs
See the description for Non-Human ESTs.
Non-Chimp mRNAs
See the description for Non-Human mRNAs.
Non-C. intestinalis mRNAs
See the description for Non-Human mRNAs.
Non-Ciona mRNAs
See the description for Non-Human mRNAs.
Non-Ciona RefSeq
This track shows known protein-coding genes from organisms other than
C. intestinalis, taken from the mRNA reference sequences collection (RefSeq)
compiled at NCBI. See the Non-Dog RefSeq track for more information.
Non-Dog RefSeq
This track shows known protein-coding genes from organisms other than dog, taken from
the mRNA reference sequences collection (RefSeq) compiled at NCBI.
-- |
Display conventions:
This track uses the display conventions for gene
predictions tracks. |
-- |
Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, and related links to
external databases. |
-- |
Track configuration:
The track description page contains configuration options to
change the feature label to display the gene name (default), the
accession name, both the gene and accession names, or no label at all.
|
-- |
Table details:
To view a text version of the data set, select the
xenoRefGene positional table in the Table Browser. To view the table
definition, click here. |
Non-D. anan. mRNAs
mRNAs of organisms other than D. ananassae. See the description for Non-Human
mRNAs.
Non-D. anan. RefSeq
This track shows known protein-coding genes from organisms other than D.
ananassae, taken from the mRNA reference sequences collection (RefSeq) compiled
at NCBI. See the description for Non-Human mRNAs.
Non-D. melanogaster mRNAs
See the description for Non-Human mRNAs.
Non-D. moj. mRNAs
mRNAs of organisms other than D. mojavensis. See the description for Non-Human
mRNAs.
Non-D. moj. RefSeq
This track shows known protein-coding genes from organisms other than D.
mojavensis, taken from the mRNA reference sequences collection (RefSeq) compiled
at NCBI. See the description for Non-Human mRNAs.
Non-D. pseudo. mRNAs
mRNAs of organisms other than D. pseudoobscura. See the description for
Non-Human mRNAs.
Non-D. pseudo. RefSeq
This track shows known protein-coding genes from organisms other than D.
pseudoobscura, taken from the mRNA reference sequences collection (RefSeq) compiled
at NCBI. See the description for Non-Human mRNAs.
Non-D. vir. mRNAs
mRNAs of organisms other than D. virilis. See the description for
Non-Human mRNAs.
Non-D. vir. RefSeq
This track shows known protein-coding genes from organisms other than D.
virilis, taken from the mRNA reference sequences collection (RefSeq) compiled
at NCBI. See the description for Non-Human mRNAs.
Non-D. yakuba mRNAs
See the description for Non-Human mRNAs.
Non-Fugu mRNAs
See the description for Non-Human mRNAs.
Non-Human ESTs
This track displays translated BLAT alignments of non-human vertebrate
ESTs from GenBank. The alignments were passed through a piecewise
near-best-in-genome filter. In cases where ESTs align to multiple places in the
genome, only the near-best are retained. Matches help validate human exon
identification.
-- |
Display conventions:
This track uses the display conventions for EST tracks. As with other
EST tracks, it may be necessary to zoom in to
display entries in full display mode due to the 300 line display
limit. |
-- |
Track details:
Clicking on an item in full display will show a summary of the GenBank
entry, a hyperlink to the full record, PubMed links by gene name,
product, and author, and mRNA/genomic alignment information. |
-- |
Table details:
To view a text version of the data set, select the
xenoEst positional table in the Table Browser. To view the table
definition, click here. |
Non-Human mRNAs
This track displays translated BLAT alignments of vertebrate and invertebrate
mRNA (other than that from the selected genome) from GenBank. The alignments
were passed through a near-best-in-genome
filter. Some mRNAs align to multiple places but only the near-best are retained.
For a distant vertebrate, alignment requires a fairly slowly evolving gene.
Matches are often plausible ortholog candidates.
-- |
Display conventions:
This track uses the display conventions for PSL alignment tracks. |
-- |
Track configuration:
The track description page contains a filter to restrict the display to
only those entries that match certain keywords and to change the color
of the selected entries. |
-- |
Track details:
Clicking on an entry in full display mode will show a summary of the GenBank
entry on that mRNA, convenient hyperlinks to major databases, and
base-by-base mRNA/genomic alignments. |
-- |
Table details:
To view a text version of the data set, select the
xenoMrna positional table in the Table Browser. To view the table
definition, click here. |
Non-Mouse ESTs
See the description for Non-Human ESTs.
Non-Mouse mRNAs
See the description for Non-Human mRNAs.
Non-Opossum mRNAs
See the description for Non-Human mRNAs.
Non-Rat ESTs
See the description for Non-Human ESTs.
Non-Rat mRNAs
See the description for Non-Human mRNAs.
Non-Tetraodon mRNAs
See the description for Non-Human mRNAs.
Non-Zebrafish mRNAs
See the description for Non-Human mRNAs.
Opossum Chain
This track shows opossum genomic alignments to the selected genome using
blastz and axtChain. See the Human Chain track description for more information.
Opossum mRNAs
See the description for Human mRNAs.
Opossum Net
This track shows the best opossum chain for every part of the selected
genome. See the Human Net track description for more information.
Overlap SNPs (older archived versions only)
This track shows single nucleotide polymorphisms found on overlapping contigs.
Overlap SNPs are useful markers in mapping genes and diseases. This data was provided
by the SNP Consortium.
-- |
Display conventions:
SNP locations are indicated by thin grey vertical lines. |
-- |
Track details:
Clicking in full mode brings up a location description and
dbSNP link. |
-- |
Table details:
To view a text version of the data set, select the
snpNih positional table in the Table Browser. To view the table
definition, click here. |
Parsimony P-Values (Zoo)
This track displays the level of conservation of Zoo sequences at any given
position. More precisely, it computes the p-value of observing a certain
parsimony score for a given column of the multiple alignment under the null
model of neutral evolution.
-- |
Display conventions:
This track uses the display conventions for wiggle tracks.
|
-- |
Track configuration:
The track description page contains options to configure
several of the graph characteristics. To read more information
about each option, click the "Graph configuration help" link.
|
-- |
Track details:
Clicking on one of the peaks in the track when in full display mode will
show genome position information for the window and a link to the
underlying DNA sequence. In full mode in
a zoomed-out display, detailed information may not be accessible for an
individual feature. In this case, zoom in and try again. |
-- |
Table details:
To view a text version of the data set, select the
parsPValues positional table in the Table Browser. To view the
table definition, click here. |
Perlegen (chr21 only)
This track shows haplotype blocks derived from common single nucleotide
polymorphisms (SNPs) on Chromosome 21 by Perlegen Sciences, as
described in Patil N et. al. (2001),
"Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning",
Science 294:1719-1723. General information on the blocks is available
from Perlegen's Chromosome 21 Haplotype Browser.
-- |
Display conventions:
The location of each haplotype block is represented by a blue horizontal
line with tall vertical blue bars at the first and last SNPs of
the block. Blocks are displayed as starting at the first SNP and ending
at the last SNP of the block. This is slightly different from the
representation on the Perlegen web site in which blocks are stretched
until they abut each other. The shade of the blue indicates the
minimum number of SNPs required to discriminate between haplotype
patterns that account for at least 80% of genotyped
chromosomes. Darker colors indicate fewer SNPs are necessary. Individual
SNPs are denoted by smaller black vertical bars. At
multi-megabase resolution in dense display mode, clusters of tall blue
bars may indicate hotspots for recombination. |
-- |
Track details:
Clicking on an entry in full display mode will show basic position
information, SNP information for the block, and a link to sequence
information for the feature. To view additional information on a
particular block, click on Outside Link on the item's details
page. |
-- |
Table details:
To view a text version of the data set, select the
perlegen positional table in the Table Browser. To view the table
definition, click here. |
QTL
This track shows approximate positions of quantititive trait loci (QTL) based on
reported peak LOD scores taken from Jackson Lab's
Mouse Genome Informatics (MGI) Database.
-- |
Display conventions:
QTL locations are indicated by thin vertical bars. |
-- |
Track details:
Clicking on an item in full mode provides a link to the MGI record for the selected QTL,
information about the QTL, and position information. |
-- |
Table details:
To view a text version of the data set, select the
jaxQTL positional table in the Table Browser. To view the table
definition, click here. |
Quality Scores
This track shows the sequencing quality score (between 0 and 100)
of each base in the assembly.
-- |
Display conventions:
The height at each position of the track indicates the quality of the
base. When zoomed out to a large range, the heights reflect the averaged
scores. Scores of 40 or higher reflect high confidence in the sequence
(with an error rate of less than 1/10,000); scores of 20 or higher
reflect reasonable confidence (of working draft quality). |
-- |
Table details:
To view a text version of the data set, select the
quality positional table in the Table Browser.
To view the table definition, click here. |
Radiation Hybrid Map (Zebrafish)
This track shows alignments between zebrafish Radiation Hybrid (RH) map sequences
(consisting of ESTs and other genetic markers) and the genome.
-- |
Display conventions:
This track uses the display conventions for EST tracks.
|
-- |
Track details:
Clicking in full display mode provides a link to the genomic alignment.
|
-- |
Table details:
To view a text version of the data set, select the
rhMap positional table in the Table Browser.
To view the table definition, click here. |
Random SNPs (older archived versions only)
This track displays single nucleotide polymorphisms (SNPs)found by random
sequencing. Random SNPs are useful markers in mapping genes and complex traits.
Because these SNPs are detected from random reads, they are useful for
evolutionary studies. This data was provided by the SNP
Consortium.
-- |
Display conventions:
SNP locations are indicated by thin grey vertical lines. |
-- |
Track details:
Clicking in full mode brings up a location description
and dbSNP link. |
-- |
Table details:
To view a text version of the data set, select the
snpTsc positional table in the Table Browser. To view the table
definition, click here. |
Rat Chain
This track shows rat genomic alignment to the selected genome using blastz and
axtChain. See the Human Chain track description for more information.
Rat Ecores
This track shows rat evolutionary conserved regions (ecores) computed against
the selected assembly genome by the Exofish program at Genoscope. For
information on this track, see the Human Ecores track description.
Rat ESTs
See the description for the Human ESTs track.
Rat mRNAs
See the description for the Human mRNAs track.
Rat Net
This track shows the best rat chain for every part of the selected genome. See
the Human Net track description for more information.
Rat Synteny
This track shows syntenous (corresponding) regions between human and rat
chromosomes. The track was created by passing a 100k non-overlapping window over
the genome and using the blastz best in mouse genome alignments to look for
high-scoring regions where at least 40% of the bases aligned with the same
region in rat. 100k segments were joined together if they agreed in direction
and were within 500kb of each other in the human genome and within 4mb of each
other in the rat. Gaps were joined between syntenic anchors if the bases
between two flanking regions agreed with synteny (direction and rat location).
The syntenic block was extended to include these areas.
-- |
Display conventions:
This track uses the display conventions for synteny tracks. |
-- |
Track details:
Clicking on an item in full display mode shows details of the
rat-human correspondence and provides a link to the genomic sequence
for this feature. |
-- |
Table details:
To view a text version of the data set, select the
syntenyRat positional table in the Table Browser. To view the table
definition, click here. |
Recomb Rate
This track shows calculated sex-averaged rates of recombination based on either
the deCODE, Marshfield, or Genethon genetic maps. The deCODE map rates are
displayed by default.
-- |
Display conventions:
Each 1Mb window represents the average recombination rate of the bases
contained within that window. Darker shades of gray correspond to higher
recombination rates.
| -- |
Track configuration:
The track description page contains a filter to map distances
(sex-averaged distance, female distance, or male distance) for the 3
different types of maps. |
-- |
Track details:
Clicking in full mode shows position information
and a list of all the recombination rate values for that 1Mb window. |
-- |
Table details:
To view a text version of the data set, select the
recombRate positional table in the Table Browser. To view the table
definition, click here. |
RefSeq Genes
The RefSeq Gene track shows known protein coding genes taken from the mRNA
reference sequences collection (RefSeq) compiled at NCBI. Refseq mRNAs are aligned
against the genome using the BLAT program. When a single mRNA aligns in multiple places,
only the best alignments are kept. Alignments must also have at least 98% sequence
identity to be kept.
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. Non-coding RNA genes have their own track in some
assemblies. The color shading indicates the level of review that the
RefSeq record has undergone: predicted (light), provisional (medium),
reviewed (dark). |
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Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, and related links to
outside databases. |
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Track configuration:
The track description page contains configuration options to
change the feature label to display the gene name (default), the
accession name, both the gene and accession names, or no label at all.
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Table details:
To view a text version of the data set, select the
refGene positional table in the Table Browser. To view the table
definition, click here. |
Reg. CHIP/CHIP
This track shows the location of the probes spotted on a slide in the chromatin
immunoprecipitation/microarray hybridization (CHIP/CHIP) experiments described in
Harbison, C.T. et al.,
Transcriptional regulatory code of a eukaryotic genome.
Nature 431(7004), 99-104 (2004). See also the "Regulatory Code" track
for the position of the individual motifs.
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Display conventions:
Black boxes indicate the probe locations.
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Track details:
Clicking on an entry in full display mode shows position information, as well as
which transcription factors pulled down DNA that is enriched for the probe
sequence, which transcription factor binding site motifs are present in the
probe, and whether these motifs are conserved in related yeast species.
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Table details:
To view a text version of the data set, select the
transRegCodeProbe positional table in the Table Browser. To view
the table definition, click here. |
Regulatory Code
This track shows putative regulatory elements in S. cerevisiae that are
supported by cross-species evidence, as described in (Harbison, C.T. et al.,
Transcriptional regulatory code of a eukaryotic genome.
Nature 431(7004), 99-104 (2004)). The authors performed a genome-wide
location analysis with 203 known DNA-binding transcriptional regulators (some under
multiple environmental conditions) and identified 11,000 high-confidence interactions
between regulators and promoter regions. They then compiled a compendium of motifs for
102 transcriptional regulators based on a combination of their experimental results,
cross-species conservation data for four species of yeast, and motifs from the literature,
and finally, they mapped these motifs to the S. cerevisiae genome. This track
shows positions at which these motifs matched the genome with high confidence and at
which the matching sequence was well conserved across yeast species. See the
"Reg. CHIP/CHIP" track for additional related information.
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Display conventions:
Regulatory elements are represented by rectangular blocks. The darker the shade
of the block, the stronger the evidence supporting it. |
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Track details:
Clicking on an entry in full display mode shows the sequence at that site
compared to the position-specific probability matrix for the associated
transcriptional regulator (shown as both a table and a graphical logo). It also
indicates whether the binding site is supported by experimental (CHIP/CHIP)
results and the number of other yeast species in which it is conserved. |
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Track configuration:
The user can set the minimum unnormalized score criteria that data must
meet to be displayed in the track.
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Table details:
To view a text version of the data set, select the
tranRegCode positional table in the Table Browser. To view
the table definition, click here. |
Regulatory Module
This track shows predicted transcription factor binding sites based on sequence
similarities upstream of coordinately expressed genes.
Clicking on a particular predicted binding site brings up a page which indicates the sequence motif associated with the predicted transcription factor, and the sequence at the predicted binding site. Where known motifs have been identified by this method, they are named, otherwise they are assigned a Motif_ number.
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Display conventions:
In dense display mode, gold areas indicate the extent of the area
searched for binding sites; black boxes indicate the actual binding
sites. In fuller display modes, the gold areas disappear and only the
binding sites are displayed. |
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Track details:
Clicking on an entry in full display mode provides positional and
score information about the item, and a link to display the DNA
underlying the feature. |
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Track configuration:
The user can set the minimum unnormalized score criteria that data must
meet to be displayed in the track.
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Table details:
To view a text version of the data set, select the
esRegGeneToMotif positional table in the Table Browser. To view
the table definition, click here. |
RepeatMasker
The track shows dispersed repeats as determined by
RepeatMasker
using the
Repbase Update
library of repetitive sequences from the Genetic Information Research
Institute.
These elements include SINE, LINE, LTR, DNA, simple, low complexity,
micro-satellite, tRNA, and other repeat families.
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Display conventions:
Darker gray boxes indicates a more recent age (as dated by alignment to a
canonical repeat). In dense mode for large chromosomal regions, the black
boxes representing repeats may merge into misleading single blocks in the
display. Full display mode shows 9 tracks representing the major repeat
classes. |
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Table details:
To view a text version of the data set, select the
rmsk positional table in the Table Browser. To view the table
definition, click here. |
Retroposed Genes
This track shows processed mRNAs that have been inserted back into the genome after the
mouse/human split. Retrogenes can be functional genes that have acquired a promoter
from a neighboring gene, non-functional pseudogenes, or transcribed pseudogenes.
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Display conventions:
This track follows the display conventions used by gene prediction tracks.
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Track details:
Clicking on an entry in full display mode will show detailed information
about the pseudogene's characteristics, alignment links, and Genome Browser
annotation links for the gene locus that spawned the retrogene.
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Table details:
To view a text version of the data set, select the
pseudoGeneLink positional table in the Table Browser. To view the table
definition, click here. |
RGD ESTs
This track shows alignments expressed sequence tags (ESTs) from the Rat Genome
Database (RGD).
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Display conventions:
This track uses the display conventions for EST tracks. As with other
EST tracks, it may be necessary to zoom in to display entries in full
display mode due to the 300 line display limit. |
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Track details:
Clicking on an individual EST entry will show basic track information,
the accession number, GenBank highlights, links to EST/genomic
alignments, and an external link to the RGD EST report. |
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Table details:
To view a text version of the data set, select the
rgdEst positional table in the Table Browser. To view the table
definition, click here. |
RGD Genes
This track shows RefSeq genes curated by the Rat Genome Database (RGD).
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Display conventions:
This track follows the display conventions used by gene prediction tracks.
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Track details:
Clicking on an entry in full display mode will display position
information, links to sequence displays, and links to outside sources
showing additional information. |
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Track configuration:
The track description page contains a filter that can be used to turn
on codon coloring for the track. Click the "Codon coloring help"
link on the page for more information about this feature.
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Table details:
To view a text version of the data set, select the
rgdGene positional table in the Table Browser. To view the table
definition, click here. |
RGD QTL
This track shows quantitative trait loci (QTLs) curated by the Rat Genome
Database (RGD).
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Display conventions:
Loci positions are represented by blocks. |
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Track details:
Clicking on an entry in full display mode will display genomic
information and a link to the corresponding entry in the RGD. |
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Table details:
To view a text version of the data set, select the
rgdQtl positional table in the Table Browser. To view the table
definition, click here. |
RGD SSLP
This track shows simple sequence length polymorphisms (SSLPs), also known as
microsatellite DNA, from the Rat Genome Database (RGD). SSLPs consist of
1 - 6 simple nucleotide repeat sequences, highly polymorphic in repeat length
among strains. They are often used as genetic markers for genotyping.
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Display conventions:
SSLP positions are represented by thin blocks. |
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Track details:
Clicking on an entry in full display mode will display genomic
information and a link to the corresponding entry in the RGD. |
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Table details:
To view a text version of the data set, select the
rgdSslp positional table in the Table Browser. To view the table
definition, click here. |
Rinn Sex Exp
This track shows gene expression differences between adult male and female tissues as
described in Rinn, JL et al. (2004)
Major Molecular Differences between Mammalian Sexes Are Involved in Drug
Metabolism and Renal Function. Developmental Cell 6:791-800.
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Display conventions:
This track follows display conventions similar to PSL alignment tracks.
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Track details:
In dense or packed display mode, the track shows averages of related
tissues. In full display mode, all tissues are displayed. Click on an
individual tissue entry to show a gene expression map for all tissues in
the experiment. |
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Table details:
To view a text version of the data set, select the
rinnSex positional table in the Table Browser. To view the table
definition, click here. |
RNA Genes
This track shows human non-protein-coding RNA genes and RNA pseudogenes. This
includes tRNAs, rRNAs, SRPs, methylation guide snoRNAs, U2-U6 RNA-like, and
similar elements both known and predicted (by tRNAscanSE etc). The density of
these elements can range from 1-4 per million bp in some chromosomes. Protein
coding genes are displayed elsewhere in the RefSeq Genes track.
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Display conventions:
RNA genes are represented by light-colored blocks. Pseudogenes are
represented by darker blocks. |
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Track details:
Clicking on an entry in full display mode will display feature
classification, method of prediction, location, reliability score, and
a link to DNA sequence for the feature. |
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Table details:
To view a text version of the data set, select the
rnaGene positional table in the Table Browser. To view the table
definition, click here. |
Rosetta
This track displays microarray tissue
expression data provided by Rosetta Inpharmatics.
It helps catalogue genes and transcriptome, complements computational gene
predictions, and seeks to define gene boundaries via co-regulated expression
of nearby exons.
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Display conventions:
The data is stratified by various tissue and disease-specific
conditions of gene expression. Confirmed and predicted exons are placed in
separate tracks. Click on the mini-button to the left of the track to
display a track description page containing more information. |
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Track configuration:
The track description page contains a filter to fine-tune the track
display. The following display options are configurable:
o Reference Sample: Determines which of the 69 different
experiments are displayed, based on the reference sample
used.
o Exons Shown: Determines whether data is shown for probes
corresponding to confirmed, predicted, or all exons.
o Color Scheme: Data are presented using two color false display.
The default colors can be changed for those who are colorblind. Gray
values indicate missing data.
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Track details:
Clicking on a Rosetta exon in full display mode will show an averaged display
that can be expanded via checkboxes to a graph of actual intensities for an
individual experiment. |
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Table details:
To view a text version of the data set, select the
rosetta positional table in the Table Browser. To view the table
definition, click here. |
Sanger 22 and Sanger 22 Pseudo
These tracks contain the Sanger Centre annotations of chromosome 22.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on the track while in full display mode will show details of
the methods used to construct this track as well as the contributors. |
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Table details:
To view a text version of the data set, select the
sanger22 positional table in the Table Browser. To view the table
definition, click here. |
S. cerevisiae ESTs
See the Human ESTs track description.
S. cerevisiae mRNAs
See the Human mRNAs track description.
Scaffolds (Chimp)
This track shows the chromosome-based version of the November 2003 Arachne chimp assembly
(panTro1) from the Chimp Genome Sequencing Consortium.
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Display conventions:
In dense display mode, this track depicts in alternating gold and brown the
individual scaffolds used to create the assembled sequence.
Where gaps exist in the path, spaces are shown between the gold and brown blocks.
Relative order and orientation of the scaffolds, as determined from the human/chimp
alignments, is implied for the non-random chromosomes. The display must be
sufficiently zoomed in to view the gap features. |
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Track details:
Clicking on an item in full display mode will show information about the
scaffold fragment and bases and position information. |
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Table details:
To view a text version of the data set, select the
gold positional table in the Chimp Table Browser. To view the table
definition, click here. |
Scaffolds (Fugu, Zebrafish, Tetraodon)
This track shows the draft and finished clones that comprise the assembly.
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Display conventions:
In dense display mode, this track depicts in alternating gold and brown the
individual clones used to create the assembled sequence.
Where gaps exist in the path, spaces are shown between the gold and brown blocks.
If the relative order and orientation of the contigs between the two blocks is
known, a line is drawn to bridge the blocks. The display must be
sufficiently zoomed in to view the gap features. |
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Track details:
Clicking on an item in full display mode will show contig and position information.
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Table details:
To view a text version of the data set, select the
gold positional table in the Fugu or Zebrafish Table Browser. To view
the table definition, click here. |
Segmental Duplications
This track shows regions detected as putative genomic duplications within the
golden path.
For a description of the 'fuguization' detection method,
see Bailey JA et. al. (2001).
"Segmental duplications: organization and impact within the current human genome
project assembly". Genome Res 11:1005-17.
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Display conventions:
Orange, yellow, dark-light gray represent
similarities of greater than 99%, 99-98% and 98-90% respectively. Duplications
greater than 98% similarity that lack sufficient SDD evidence (likely
missed overlaps) are shown as red. Cut off values were at least 1 kb of
total sequence aligned (containing at least 500 bp non-RepeatMasked
sequence) and at least 90% sequence identity. |
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Track details:
Clicking on an entry in full display mode provides position, filter,
and alignment information as well as links to the corresponding genomic
sequence. |
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Table details:
To view a text version of the data set, select the
genomicSuperDups positional table in the Table Browser. To view the table
definition, click here. |
Self Chain
This track shows alignments of the selected genome with itself using blastz and
axtChain.
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Display conventions:
This track uses the display conventions for chain tracks. |
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Track details:
Clicking on an item in full display mode shows position information, the
chain ID and score, and provides
links to view details of parts of the chain or to open the browser
to the corresponding aligning position. |
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Table details:
To view a text version of the data set, select the
chainSelf positional table in the Table Browser. To view the
table definition, click here. |
SGD Genes
This track shows annotated genes and open reading frames (ORFs) of
Saccharomyces cerevisiae obtained from the Saccharomyces Genome
Database (SGD).
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. |
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Track details:
Clicking on an entry in full display mode provides a wealth of
genomic, mRNA, and protein information about the gene as well as
links to several associated external sites. |
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Table details:
To view a text version of the data set, select the
sgdGene positional table in the Table Browser. To view the table
definition, click here. |
SGD Other
This track shows a variety of features in the Saccharomyces cerevisiae
genome, including tRNAs, transposons, centromeres, and open reading frames (ORFs) classified as dubious.
The data was downloaded from the Saccharomyces Genome Database
(SGD).
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. |
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Track details:
Clicking on an entry in full display mode provides genomic information
and a link to view the DNA underlying the track. |
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Table details:
To view a text version of the data set, select the
sgdOther positional table in the Table Browser. To view the table
definition, click here. |
SGP Genes
This track shows gene predictions from the SGP program, which is being developed
at the Grup de Recerca en Informàtica Biomèdica (GRIB) at Institut Municipal
d'Investigació Mèdica (IMIM) in Barcelona. To predict genes in a genomic query,
SGP combines geneid predictions with tblastx comparisons of the genomic query
against other genomic sequences.
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. |
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Track details:
Clicking on an entry in full display mode provides position information
as well as links to the corresponding protein, mRNA, genomic, and
comparative sequences. |
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Table details:
To view a text version of the data set, select the
sgpGene positional table in the Table Browser. To view the table
definition, click here. |
Short Match
This track shows all occurrences of a selected short motif within the displayed
position range of the assembly sequence. It is useful for finding
oligonucleotides, restriction sites, or other recurring short sequences within
the assembly.
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Display conventions:
Perfect matches are indicated by a solid rectangle. In full display mode,
each occurrence is labeled by the strand on which the match is located,
followed by the starting coordinate of the match. In cases where the
input motif sequence is identical to its reverse complement, only the
match on the "+" strand is shown.
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Track details:
Clicking on an entry in full display mode provides position information
about the match. |
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Track configuration:
The track may be configured to search for any short sequence of 2-30
bases in length. To change the sequence, type a new sequence into the
text box at the top of the track description page.
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Table details:
Unlike most annotations in the Genome Browser, this track is not
table-based. |
Simple Repeats
This track displays simple tandem repeats (possibly imperfect) located by
Tandem Repeats Finder,
which is specialized to this purpose. These repeats can occur within coding regions of
genes and may be quite polymorphic. Repeat expansions are sometimes associated with
specific diseases.
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Display conventions:
Repeats are represented by block boxes that indicate location in the
assembly. |
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Track details:
Clicking on an item in full display mode will show the simple repeat
sequence, copy number, and quality of match statistics. |
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Table details:
To view a text version of the data set, select the
simpleRepeats positional table in the Table Browser. To view the table
definition, click here. |
Slam Human, Slam Mouse, Slam Rat
These tracks predict coding exons and conserved noncoding regions in a pair of
homologous DNA sequences, incorporating both statistical sequence properties and
the degree of conservation in making the predictions. The model is symmetric: the
same gene structure (with possibly different exon lengths) is predicted in both
sequences.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode will show basic track
information, plus links to the predicted mRNA,
genomic sequence, and comparative sequence. |
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Table details:
To view a text version of the data set, select the appropriate
slam positional table in the Table Browser (e.g. slamHuman,
slamMouse, slamRat). To view the table
definition, click here. |
SlamHumanNonCoding, SlamMouseNonCoding, SlamRatNonCoding
These tables show slam predictions of conserved noncoding regions in homologous
DNA sequences.
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Display conventions:
The data in these tables are displayed as part of the Slam Human,
Slam Mouse, and Slam Rat tracks. See the track descriptions for these
tracks for display information. |
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Table details:
To view a text version of the data set, select the appropriate
slamNonCoding positional table in the Table Browser (e.g. slamHumanNonCoding,
slamMouseNonCoding, slamRatNonCoding). To view the table
definition, click here. |
SNAP Genes (C. intestinalis)
This track shows gene predictions determined by SNAP (Semi-HMM-based Nucleic Acid Parser),
a general purpose gene-finding program written by Ian Korf. SNAP is suitable for both
eukaryotic and prokaryotic genomes. For this set of gene predictions, it was trained on
gene annotations from the DOE Joint Genome Institute (JGI).
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode brings up basic track
information, plus links to the translated protein, predicted mRNA, and
genomic sequences. |
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Table details:
To view a text version of the data set, select the
snapGene positional table in the Table Browser. To view the table
definition, click here. |
Sno/miRNA
This track displays positions of four different types of RNA in the human genome:
microRNAs from the miRNA Registry at the Wellcome Trust Sanger Institute, small nucleolar
RNAs (C/D box and H/ACA box snoRNAs) and Cajal body-specific RNAs (scaRNAs) from the
snoRNA-LBME-DB maintained at the Laboratoire de Biologie Moléculaire Eucaryote. C/D box
and H/ACA box snoRNAs are guides for the 2'O-ribose methylation and the pseudouridilation,
respectively, of rRNAs and snRNAs, although many of them have no documented target RNA.
The scaRNAs guide modifications of the spliceosomal snRNAs transcribed by RNA polymerase
II, and often contain both C/D and H/ACA domains.
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Display conventions:
Mature miRNAs (miRs) are represented by thick red blocks; the predicted stem-loop
portions of the primary transcripts are indicated by thinner blocks. When a
single precursor produces two mature miRs from its 5' and 3' parts, both positions
of the mature miRNA are individually displayed. C/D box, H/ACA box snoRNAs and
scaRNAs are represented by blue, green and magenta blocks, respectively. At a
zoomed-in resolution, arrows superimposed on the blocks indicate the sense
orientation of the snoRNAs. |
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Track details:
Clicking on an entry in full display mode provides a link to the miRNA
Registry, the RNA type, position information, and a link to the DNA sequence
associated with the feature. |
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Table details:
To view a text version of the data set, select the
wgRna positional table in the Table Browser. To view the table
definition, click here. |
SNPs (Human assemblies hg17 and later)
This track displays all the known Simple Nucleotide Polymorphisms (SNPs) that
can be mapped against the current genome assembly. These data were obtained from
dbSNP and
commercially-available genotyping arrays and include known point
mutations (Single Nucleotide Polymorphisms), insertions, deletions, multiple
See the track description page for more information about the SNP
classifications.
These data were provided by the SNP Consortium and
Affymetric, Inc..
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Display conventions:
Variants are drawn a single tick marks at most zoom levels.
When viewing the track at or near base-level resolution, the displayed
width of the SNP corresponds to the width of the variant in the
reference sequence. Insertions are indicated by a single tick mark
displayed between two nucleotides, single nucleotide polymorphisms are
displayed as the width of a single base, and multiple nucleotide
variants are represented by a block that spans two or more bases.
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Track details:
Clicking in full mode brings up position information about the reference
sequence, detailed information about the variant, and a link to the
record in dbSNP. |
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Track configuration:
The colors of variants may be changed to highlight their source,
molecule type, variant class, validation status, or functional
classification. Variants can be excluded from the display based on
these same criteria or if they fall below the user-specified minimum
average heterozygosity. |
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Table details:
To view a text version of the data set, select the
snp positional table in the Table Browser. To view the table
definition, click here. |
SNPs (Human assemblies prior to hg17)
This track displays all the known Simple Nucleotide Polymorphisms (SNPs) that
can be mapped against the current genome assembly. These include known point
mutations (Single Nucleotide Polymorphisms), insertions, deletions, and
segmental mutations from the current build of dbSnp (shown in the Genome
Browser release log). See the track
description page for more information about major cases that are not mapped.
These data were provided by the SNP
Consortium.
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Display conventions:
SNP locations are indicated by thin grey vertical lines. |
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Track details:
Clicking in full mode brings up a location description
and dbSNP link. |
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Table details:
To view a text version of the data set, select the
snpMap positional table in the Table Browser. To view the table
definition, click here. |
Spliced ESTs
The Spliced EST track displays the subset of Expressed Sequence Tags (ESTs)
from GenBank that show signs of splicing when aligned against
the genome. ESTs are single read (typically approximately 500 base) sequences
that usually represent fragments of transcribed genes. By requiring splicing,
the level of contamination in the EST databases is drastically reduced at the
expense of eliminating many genuine 3' ESTs. This track may also suggest
alternate splices. The GT-AG splice donor/acceptor rule has not been applied.
For a display of all ESTs (including unspliced), see the Human EST
track.
This track was generated by aligning human ESTs from GenBank against the
genome using the BLAT program. Note that the maximum intron length
allowed by BLAT is 500,000 bases, which may eliminate some ESTs with
very long introns that might otherwise align. When a single EST aligns
in multiple places, the alignment having the highest base identity is
found. Only alignments that have a base identity level within 1% of the
best are kept. Alignments must also have at least 93% base identity to be
kept.
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Display conventions:
This track uses the display conventions for EST tracks
As with other EST tracks, it may be necessary to zoom in to
display entries in full display mode due to the 300 line display
limit. |
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Track details:
Clicking on an individual EST entry will show basic track information,
the accession number, GenBank highlights, and links to translated
protein, predicted mRNA, and genomic sequences. |
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Table details:
To view a text version of the data set, select the
intronEst positional table in the Table Browser. To view the table
definition, click here. |
STS Markers (human)
This track shows the locations of Sequence Tagged Site (STS) markers along
the draft assembly. The STS markers have been mapped using either
genetic (Genethon and Marshfield maps), radiation hybridization (the Stanford,
Whitehead RH, and GeneMap99 maps) or YAC mapping (the Whitehead YAC map)
techniques. In releases prior to August 2001, this track also shows the
approximate position of FISH mapped clones. Starting with the August 2001 assembly,
the FISH clones have been moved into a separate track.
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Display conventions:
Genetic map markers are shown in blue, and radiation hybrid
map markers are shown in black. When a marker maps to multiple
positions in the genome, it is shown in a lighter color. |
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Track details:
Clicking on a specific marker in full display mode will show synonyms,
position information, primers, YAC map position, and uniSTS and GDB links. |
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Table details:
To view a text version of the data set, select the
stsMap positional table in the Table Browser. To view the table
definition, click here. |
STS Markers (mouse)
This track shows the locations of Sequence Tagged Site (STS) markers
along the draft assembly of the mouse genome. These STS markers appear on the MGI consensus
mouse genetic map. Information about the genetic map and STS marker
primer sequences are provided by the Mouse Genome Informatics database group at The Jackson
Laboratory.
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Display conventions:
Genetic map markers are shown as thin black boxes. |
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Track details:
Clicking on a specific marker in full display mode will show position
information, primers, genetic map position, genomic alignments, and MGI
links. |
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Table details:
To view a text version of the data set, select the
stsMapMouse positional table in the Table Browser. To view the table
definition, click here. |
STS Markers (rat)
This track shows locations of Sequence Tagged Site (STS) markers along the draft
assembly of the rat genome. These STSs have been mapped using either
genetic (rat FHH x ACI F2 intercross genetic map, rat SHRSP x BN F2 intercross genetic map) or radiation hybridization (RH
map.2.2).
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Display conventions:
Genetic map markers are shown as thin black boxes. |
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Track details:
Clicking on a specific marker in full display mode will show position
information, primers, genetic map position, and links to the corresponding
UniSTS and RGD entries.
|
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Table details:
To view a text version of the data set, select the
stsMapRat positional table in the Table Browser. To view the table
definition, click here. |
Superfamily
The Superfamily track shows proteins having homologs with known structures or
functions. Each entry in the track shows the coding region of a gene (based on
Ensembl gene prediction). The label, shown in Full mode at the left
hand side of each entry, consists of the names of all known protein domains
coded by this gene. This usually contains structural and/or function descriptions
that provide valuable information for getting a quick grasp of the biological
significance for the gene.
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Display conventions:
Coding regions are indicated by red blocks. |
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Track details:
Clicking on an entry in full display mode will show the Superfamily
domains of the corresponding protein and provide a link to the Superfamily database entry. |
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Table details:
To view a text version of the data set, select the
superfamily positional table in the Table Browser. To view the table
definition, click here. |
Tetraodon Chain
This track shows Tetraodon genomic alignments to the selected
genome using blastz and axtChain. See the Human Chain track description for
more information.
Tetraodon Ecores
This track shows Tetraodon evolutionary conserved regions (ecores) computed
against the selected assembly genome by the Exofish program at Genoscope. For
information on this track, see the Human Ecores track description.
Tetraodon Net
This track shows the best Tetraodon chain for every part of the selected genome.
See the Human Net track description for more information.
TFBS Conserved
This tracks shows the location and score of transcription factor binding sites
(TFBSs) conserved in a multiple species alignment. A binding site is considered
to be conserved across the alignment if its score meets the threshold score for
that binding site in all aligned species. The score and threshold are computed
with the Transfac Matrix Database created by Biobase. The data are purely
computational, and as such not all binding sites listed here are biologically
functional binding sites.
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Display conventions: TFBSs are represented by thin blocks.
The darker the shading, the better the match of the binding site.
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Track details:
Clicking on a block in full display mode will show the the entry's
Transfac ID, positional information, and a link to its Transfac Matrix
(free registration with Transfac is required).
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Table details:
To view a text version of the data set, select the
tfbsCons positional table in the Table Browser. To view the table
definition, click here. |
Tight Mouse
This track displays Blastz alignments of the specified mouse
draft assembly to the human genome, filtered by axtBest and
subsetAxt with very stringent constraints. See the track's description
page for more details.
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Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
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Track details:
Clicking on an entry in full display mode will show human and
mouse position information, alignment details, and a link to a detailed
view of parts of the alignment. |
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Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
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Table details:
To view a text version of the data set, select the
blastzTightMouse positional table in the Table Browser. To view the table
definition, click here. |
Tight Rat
This track displays Blastz alignments of the Nov. 2002 rat
draft assembly to the mouse genome, filtered by axtBest and
subsetAxt with very stringent constraints. See the track's description
page for more details.
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Display conventions:
This track uses the display conventions for cross-species synteny
tracks. |
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Track details:
Clicking on an entry in full display mode will show mouse and
rat position information, alignment details, and a link to a detailed
view of parts of the alignment. |
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Track configuration:
The track description page contains a filter that can be used to turn
on the chromosome color track or to filter the display output by
chromosome. |
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Table details:
To view a text version of the data set, select the
blastzTightRat positional table in the Table Browser. To view the table
definition, click here. |
Tigr Gene Index
This track displays alignments of the
TIGR Gene Index (TGI)
against the human genome. The TGI is based largely on assemblies of EST
sequences from the public databases and TIGR. Entries are
actual assemblies providing a consensus sequence, not simply clusters of
overlapping sequences, but generally don't predict whole genes. Gene
indices for mouse, rat, cow, and pig also contribute to this track.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode will show basic track
information, links to the predicted mRNA and
genomic sequences, and a link to supporting information in the TIGR
Human Gene Index. |
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Table details:
To view a text version of the data set, select the
tigrGeneIndex positional table in the Table Browser. To view the table
definition, click here. |
Transcriptome
This track shows transcriptome data for chromosomes 21 and 22 from Affymetrix,
as described in "Large-Scale Transcriptional Activity in Chromosomes 21 and 22",
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S, Strausberg, R. L.,
Fodor, S.P.A. and Gingeras, T.R.. In general, the data presented is the perfect
match - mismatch value. Different experiments were normalized by setting the
average value to be the same for each chip.
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Display conventions:
This track uses the display conventions for wiggle tracks. To present a
more interpretable display when zoomed out, averages have been
precalculated over the chromosome at two different resolutions in
addition to the raw data. For example, when zoomed out, there may appear
to be a peak at the center of a gene rather than a signal at every exon.
Zooming in will reveal the raw data for that region.
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Track details:
In dense mode (or at the top of the track in full mode), the
transcriptome wiggle track displays the maximum value over all
experiments for that probe, the idea
being to paint as many transcribed regions as possible. In full mode,
the track displays a separate wiggle track for each cell type, showing
the data produced by averaging together replicates for that cell type.
Clicking on an individual data point will show positional information and
a link to view the sequence for the feature.
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Table details:
To view a text version of the data set, select the
affyTranscriptome positional table in the Table Browser. To view the table
definition, click here. |
Twinscan Gene Predictions
This track displays Twinscan gene predictions. Twinscan predicts genes in a
manner similar to Genscan, except that Twinscan takes advantage of genome
comparison to improve gene prediction accuracy. More information and a web
server can be found at the Washington University St. Louis
Twinscan web page.
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Display conventions:
This track uses the display conventions for gene predictions tracks. |
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Track details:
Clicking on an entry in full display mode will show basic track
information, links to the predicted protein, predicted mRNA,
genomic sequence, and comparative sequence. |
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Table details:
To view a text version of the data set, select the
twinscan positional table in the Table Browser. To view the table
definition, click here. |
UCSC Synteny (hg12)
See description for Mouse Synteny (hg13+).
UniGene
This track shows UniGene
clusters of ESTs aligned to the genome using BLAT. This data imperfectly
indicates exon/intron boundaries and to a lesser extent genes. The Serial
Analysis of Gene Expression
(SAGE) project at NCBI - a quantitative measurement of gene expression in
various tissues and disease states - mapped small 10bp bar-coded expression
markers onto these UniGene clusters in the SageMap project. The Genome Browser
uses this mapping to provide access to the SAGE data associated with the
UniGene track in the assembled and annotated genome.
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Display conventions:
This track uses the display conventions for PSL alignment tracks. |
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Track details:
Clicking on a UniGene feature will show an elaborate display of tabular and
graphical data from the SAGE project relevant to that cluster. |
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Table details:
To view a text version of the data set, select the
uniGene positional table in the Table Browser. To view the table
definition, click here. |
Vega Genes (selected human chromosomes only)
This track shows genes from the Vertebrate Genome Annotation (VEGA) database, a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centers, Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.
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Display conventions:
This track uses the display conventions for gene prediction tracks. |
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Track details:
Clicking on an entry in full display mode will show basic track
information, a link to the Vega web page for the item, and links to the
predicted protein, predicted mRNA,
genomic sequence, and comparative sequence. |
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Table details:
To view a text version of the data set, select the
vegaGene positional table in the Table Browser. To view the table
definition, click here. |
Vega Pseudogenes (selected human chromosomes only)
This track shows annotated pseudogenes and immunoglobulin segments from the Vertebrate Genome Annotation (VEGA) database, a central repository for manual annotation of different vertebrate finished genome sequence. In collaboration with the genome sequencing centers, Vega attempts to present consistent high-quality curation of the published chromosome sequences. Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against DNA and protein databases as well as a series of ab initio gene predictions (GENSCAN, Fgenes). In addition, comparative analysis using vertebrate datasets such as the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores (Evolutionary Conserved Regions) are used for novel gene discovery.
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Display conventions:
This track uses the display conventions for gene prediction tracks. |
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Track details:
Clicking on an entry in full display mode will show basic track
information, a link to the Vega web page for the item, and links to the
predicted mRNA, genomic sequence, and comparative sequence. |
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Table details:
To view a text version of the data set, select the
vegaPseudoGene positional table in the Table Browser. To view the table
definition, click here. |
WashU Clones
This track displays the location of clones (mostly lambda and cosmid clones)
from Washington University in St. Louis using the names assigned by that group.
The data was downloaded from the Saccharomyces Genome Database
(SGD).
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Display conventions:
The clone positions are shown in black. |
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Track details:
Clicking on an entry in full display mode brings up genomic
information and a link to the American Type Culture Collection (ATCC)
website.
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Table details:
To view a text version of the data set, select the
sgdClone positional table in the Table Browser. To view the table
definition, click here. |
WormBase Genes
This track shows Sanger Gene predictions from the Wormbase files
downloaded from the Sanger Institute FTP site. The data shown is the subset
annotated with "curated", "DNA", or "RNA" followed by one of these strings:
"intron", "exon", "cds", "sequence", or "transcri".
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Display conventions:
This track uses the display conventions for gene prediction tracks.
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Track details:
Clicking on an entry in full display mode will show a wealth of
information about the gene and its associated mRNA and protein, as
well as links to many related external sites.
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Track configuration:
The track description page contains a filter that can be used to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
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Table details:
To view a text version of the data set, select the
sangerGene positional table in the Table Browser. To view
the table definition, click here. |
WormBase Genefinder
This track shows Sanger Gene predictions from the Wormbase files
downloaded from the Sanger Institute FTP site. The data shown is the subset
annotated with the string "Genefinder" and found by the gene prediction
program, Genefinder.
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Display conventions:
This track uses the display conventions for gene prediction tracks.
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Track details:
Clicking on an entry in full display mode will show genomic
information and links to the
translated protein, predicted mRNA, genomic sequence. |
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Track configuration:
The track description page contains a filter that can be used to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
|
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Table details:
To view a text version of the data set, select the
sangerGenefinder positional table in the Table Browser. To view
the table definition, click here. |
WSSD Coverage
This track represents coverage of clones that were assayed for segmental duplications
using high-depth Celera reads. Absent regions were not assessed by this version of the
Segmental Duplication Database (SDD). For a description of the whole-genome shotgun
sequence detection (WSSD) "fuguization" method, see Bailey, JA. et al.,
Segmental duplications: organization and impact within the current human
genome project assembly, Genome Res. 11(6), 1005-17 (2001).
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Display conventions:
Rectangular blocks indicate the positions of clones.
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Track details:
Clicking on an entry in full display mode will show position information and a
link to the underlying DNA for the feature.
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Table details:
To view a text version of the data set, select the
celeraCoverage positional table in the Table Browser. To view
the table definition, click here. |
WSSD Duplication
High-depth sequence reads from the Celera project were used to detect paralogy in the
human genome reference sequence. This track shows confirmed segmental duplications,
defined as having similarity to sequences in the Segmental Duplication Database (SDD)
of greater than 90% over more than 250 bp of repeatmasked sequence. For a description
of the whole-genome shotgun sequence detection (WSSD) 'fuguization' method, see
Bailey, JA. et al.,
Segmental duplications: organization and impact within the current human
genome project assembly, Genome Res. 11(6), 1005-17 (2001).
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Display conventions:
Rectangular blocks indicate the positions of duplications.
|
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Track details:
Clicking on an entry in full display mode will show the WSSD ID number,
position information, and a link to the underlying DNA for the feature.
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Table details:
To view a text version of the data set, select the
celeraDupPositive positional table in the Table Browser. To view
the table definition, click here. |
WSSD Overlay
This track shows regions detected as overlays of Celera whole-genome shotgun sequence
assembly on the public human assembly.
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Display conventions:
Regions are represented by rectangular blocks. |
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Track details:
Clicking on an entry in full display mode will show position information and a
link to the underlying DNA for the feature.
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Table details:
To view a text version of the data set, select the
celeraOverlay positional table in the Table Browser. To view
the table definition, click here. |
X. tropicalis Chain
This track shows X. tropicalis genomic alignments to the selected
genome using blastz and axtChain. See the Human Chain track description for
more information.
X. tropicalis ESTs
See the description for the Human ESTs track.
X. tropicalis mRNAs
See the description for the Human mRNAs track.
X. tropicalis Net
This track shows the best X. tropicalis chain for every part of the selected genome. See
the Human Net track description for more information.
Yale Pseudo
This track shows pseudogenes identified in the
Yale Pseudogene
Database.
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Display conventions:
This track uses the display conventions for gene prediction tracks.
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Track details:
Clicking on an entry in full display mode will show genomic
information, a link to the corresponding pseudogene entry in the
Yale Pseudogene Database, and links to predicted mRNA and genomic
sequence. |
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Track configuration:
The track description page provides an option to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
|
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Table details:
To view a text version of the data set, select the
pseudoYale positional table in the Table Browser. To view
the table definition, click here. |
Zebrafish Chain
This track shows zebrafish genomic alignments to the selected
genome using blastz and axtChain. See the Human Chain track description for
more information.
Zebrafish ESTs
See the Human ESTs track description.
Zebrafish mRNAs
See the Human mRNAs track description.
Zebrafish Net
This track shows the best Zebrafish chain for every part of the selected genome.
See the Human Net track description for more information.
Zfish WZ EST Clusters (Zebrafish)
This track shows alignments between zebrafish WZ expressed sequence tags (ESTs) from
WashU-Zebrafish Genome Resources and the genome. These WZ ESTs are compiled to produce
longer reads by clustering together ESTs that originate from the same transcript.
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Display conventions:
This track uses the display conventions for EST tracks. Hatch marks on the
introns indicate the direction of transcription.
As with otherEST tracks, it may be necessary to zoom
in to display entries in full display mode due to the 300 line display
limit. |
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Track details:
Clicking on an individual EST entry displays a link to the genomic alignment.
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Table details:
To view a text version of the data set, select the
wz_ests positional table in the Table Browser. To view the table
definition, click here. |
ZGC Genes (Zebrafish)
This track shows alignments to the genome of zebrafish mRNAs from the Mammalian Gene
Collection (MGC) having full-length open reading frames (ORFs).
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Display conventions:
This track uses the display conventions for known genes and gene
predictions tracks. |
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Track details:
Clicking on an entry in full display provides links to the
corresponding protein, mRNA, and genomic sequences, and related links to
outside databases. |
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Track configuration:
The track description page offers configuration options that can be used to turn
on codon coloring for the track. Click the "Codon coloring
help" link on the page for more information about this feature.
|
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Table details:
To view a text version of the data set, select the
mgcGenes positional table in the Table Browser. To view the table
definition, click here. |
ZooSeq (Zoo)
This track displays the level of conservation for each zoo species based on
blastz pair-wise alignments.
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Display conventions:
This track uses the display conventions for wiggle tracks.
Gray horizontal bars denote a mapping/sequencing gap. Percent identities
of less than 50% are not shown because they fall below the minimum
y-axis value. |
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Track configuration:
The track description page contains options to configure
several of the graph characteristics. To read more information
about each option, click the "Graph configuration help" link.
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Track details:
Clicking on an entry in full display mode will show basic track
information, a link to the Vega web page for the item, and links to the
predicted mRNA, genomic sequence, and comparative sequence. |
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Table details:
To view a text version of the data set, select the
zoo positional table in the Table Browser. To view the table
definition, click here. |
Last updated on 3 Mar. 2005.
Questions and feedback welcome.
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