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This page contains links to custom annotation tracks contributed by the UCSC
Genome Bioinformatics group and by the research community. Click on a track to
display it in the UCSC Genome Browser. To access custom annotation tracks built
on archived assemblies, see the Genome Browser
archives. Please check the Genome Browser standard track set for
additional contributed annotation tracks.
For information on how to create a custom annotation track, see
Displaying Your Own Annotations in the Genome Browser. If you would
like to submit your own custom tracks to this list, contact
genome@soe.ucsc.edu.
Human Genome
Alternative conserved exons predicted by ACEScan (hg17).
This track displays human exons (from Known Genes with an exonic alignment
to mouse) that have a positive ACEScan score. For a description of
the methods used to generate this annotation, see Yeo, G.W. et al..
Identification and analysis of alternative splicing events
conserved in human and mouse. Proc. Natl. Acad. Sci. USA
102(8), 2850-2855 (2005). The ACEScan online webtool is available at
http://genes.mit.edu/acescan. Thanks to Gene Yeo and Chris
Burge at MIT for contributing this annotation.
Perfect LINEs identified by
GPS
(hg17). This track displays regions in the chromosome in which all the
components have at least 10% identity to the query (Retroid Agent) and no
frame shifts or stop codons in the gene coding regions.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
20,
22,
X,
Y.
Thanks to Dr. Marcella McClure and Vijay A. Raghavan
at Montana State University for providing this annotation.
DoTS Genes (hg17). Generated using BLAT alignments of DoTS RNAs.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
X,
Y,
M.
Thanks to Y. Thomas Gan for creating this track.
Isochore track (hg17) generated using
IsoFinder, a segmentation algorithm
developed by
Grupo de Bioinformatica, Universidad de Granada, Spain.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
X,
Y.
Thanks to Dr. Jose L. Oliver for contributing this track.
Stanford Human Promoters (hg16). The Stanford Human
Promoters data set was generated by the
Richard M. Myers lab at
Stanford University and is described in
Trinklein, N., Force Aldred, S., Saldanha, A., and Myers, R.M. (2003).
Identification and Functional Analysis of Human Transcriptional
Promoters. Genome Res., 13:308-312. Thanks to
Nathan Trinklein at Stanford School of Medicine for contributing this track, and to Daryl Thomas of UCSC for lifting the data to the hg16 assembly.
DoTS Genes (hg16). Generated using BLAT alignments of DoTS RNAs.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
21,
22,
X,
Y,
M.
Thanks to Y. Thomas Gan for creating this track.
Isochore track (hg16)
generated using IsoFinder, a segmentation algorithm developed
by Grupo de Bioinformatica,
Universidad de Granada, Spain. Click
here for more information about this annotation.
Thanks to Dr. Jose L.
Oliver for contributing this track.
Stanford Human Promoters (hg15). The Stanford Human
Promoters data set was generated by the
Richard M. Myers lab at
Stanford University and is described in
Trinklein, N., Force Aldred, S., Saldanha, A., and Myers, R.M. (2003).
Identification and Functional Analysis of Human Transcriptional
Promoters. Genome Res., 13:308-312. Thanks to
Nathan Trinklein at Stanford School of Medicine for contributing this track, and to Daryl Thomas of UCSC for lifting the data to the hg16 assembly.
Isochore track (hg15).
See the description for the hg17 Isochore track for more information. Thanks to Dr. Jose L. Oliver for contributing this track.
Mouse Genome
Locations of known, suspected, and imputed SNPs generated by BLAT alignment
of 3 million Celera associated sequences to the May 2004 mouse genome
assembly (mm5), provided by The GeneNetwork and WebQTL. Only those SNPs that
distinguish strains C57BL/6J from DBA/2J (1.75 million) or that distinguish
C57BL/6J from A/J (1.80 million) are displayed in the custom track.
Due to the proprietary nature of these data, only low resolution
position data (SNP density per 100,000 to 300,000 bp) are currently provided.
This custom track is available on any PHYSICAL and GENETIC maps in WebQTL for
the BXD and AXB/BXA genetic reference panels simply by clicking on
interval maps.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
X.
Thanks to Celera Genomics (Richard Mural and
Paul Thomas) for this level of access to CDS data and to Christopher
Vincent (Georgia Tech), Alex G. Williams (UCSC); Robert Crowell
(UTHSC and MIT), Gary Churchill and Natalie Blades (The Jackson
Laboratory), and the WebQTL group at UTHSC (Jintao Wang, Yanhua Qu,
Yan Cui, Robert Williams, and Kenneth Manly) for contributing this
track.
BayGenomics mouse
knockout gene tags (mm5), generated using BLAT alignments of sequences derived
from gene-trap vector insertions into thousands of genes in mouse embryonic
stem cells. Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
X,
Y,
M.
Thanks to the BayGenomics
bioinformatics group at UCSF for providing this track.
DoTS Genes (mm5). Generated using BLAT alignments of DoTS RNAs.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
X,
Y,
M.
Thanks to Y. Thomas Gan for creating this track.
Isochore track (mm5) generated using
IsoFinder, a segmentation algorithm
developed by
Grupo de Bioinformatica, Universidad de Granada, Spain.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
X.
Thanks to Dr. Jose L. Oliver for contributing this track.
DoTS Genes (mm4). Generated using BLAT alignments of DoTS RNAs.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
X,
Y,
M.
Thanks to Y. Thomas Gan at the University of Pennsylvania for creating this track.
Isochore track (mm3) generated using IsoFinder, a segmentation
algorithm developed by
Grupo de Bioinformatica,
Universidad de Granada, Spain. Click here for more
information about this annotation.
Thanks to Dr. Jose L. Oliver for contributing this track.
Rat Genome
Isochore track (rn3) generated using
IsoFinder, a segmentation algorithm developed by
Grupo de Bioinformatica, Universidad de Granada, Spain.
Click on the chromosome you wish to display:
1,
2,
3,
4,
5,
6,
7,
8,
9,
10,
11,
12,
13,
14,
15,
16,
17,
18,
19,
20,
X.
Thanks to Dr. Jose L. Oliver for contributing this track.
Isochore track (rn2) generated using IsoFinder, a segmentation
algorithm developed by
Grupo de Bioinformatica,
Universidad de Granada, Spain. Click here for more
information about this annotation. Thanks to Dr. Jose L. Oliver for contributing this track.
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