This directory contains a dump of the UCSC genome annotation database for
the Oct. 2010 (CGSC 2.1.3/panTro3) assembly of the chimp genome
(panTro3, CGSC 2.1.3 (GCA_000001515.3)) from the
Chimp Genome Sequencing Consortium. The annotations were generated
by UCSC and collaborators worldwide.
This assembly was produced by the Chimpanzee Sequencing and Analysis Consortium.
For more information on the chimp genome, see the project website:
http://genome.wustl.edu/genomes/view/pan_troglodytes/
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
To see descriptions of the tables underlying Genome Browser annotation
tracks, select the table in the Table Browser:
http://genome.ucsc.edu/cgi-bin/hgTables?db=panTro3
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
---------------------------------------------------------------
If you plan to download a large file or multiple files from this
directory, we recommend you use ftp rather than downloading the files
via our website. To do so, ftp to hgdownload.cse.ucsc.edu, then go to
the directory goldenPath/panTro3/database/. To download multiple
files, use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Alternate methods to ftp access.
Using an rsync command to download the entire directory:
rsync -avzP rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/panTro3/database/gc5BaseBw.txt.gz'
-O gc5BaseBw.txt.gz
Please note that some files contents, such as this example gc5BaseBw.txt.gz,
will point to the data being hosted in another /gbdb/ location, which
refers to ftp://hgdownload.cse.ucsc.edu/gbdb/
To uncompress the *.txt.gz files:
gunzip <table>.txt.gz
The tables can be loaded directly from the .txt.gz compressed file.
It is not necessary to uncompress them to load into a database,
as shown in the example below.
To load one of the tables directly into your local mirror database,
for example the table chromInfo:
## create table from the sql definition
$ hgsql panTro3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql panTro3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
##############################################################################
The chimpanzee sequence is made freely available before scientific
publication with the following understanding:
1. The data may be freely downloaded, used in analyses, and repackaged
in databases.
2. Users are free to use the data in scientific papers analyzing
particular genes and regions if the providers of these data are
properly acknowledged. See http://genome.ucsc.edu/goldenPath/credits.html
for credit information.
3. The centers producing the data reserve the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
chainMonDom5Link.txt.gz 2011-11-14 03:09 1.2G
chainEquCab2Link.txt.gz 2011-05-03 13:59 1.0G
chainCanFam2Link.txt.gz 2011-05-30 01:13 524M
chainDanRer7Link.txt.gz 2011-03-15 09:15 524M
chainMm9Link.txt.gz 2011-05-24 00:24 520M
chainMonDom5.txt.gz 2011-11-14 03:19 341M
xenoMrna.txt.gz 2020-08-22 18:48 321M
chainEquCab2.txt.gz 2011-05-03 14:41 258M
chainCalJac3Link.txt.gz 2011-05-24 00:37 235M
multiz12way.txt.gz 2011-08-21 03:58 209M
chainPonAbe2Link.txt.gz 2011-05-03 13:32 175M
chainRheMac2Link.txt.gz 2011-05-24 00:41 162M
chainDanRer7.txt.gz 2011-03-15 09:02 160M
rmsk.txt.gz 2011-02-25 17:29 137M
chainHg19Link.txt.gz 2011-02-25 17:19 124M
chainGalGal3Link.txt.gz 2011-05-03 13:25 114M
chainGorGor3Link.txt.gz 2011-11-27 14:04 108M
phyloP12way.txt.gz 2011-08-21 04:00 86M
phyloP12wayPrimate.txt.gz 2011-08-21 03:56 82M
phastCons12wayPrimate.txt.gz 2011-08-21 03:57 80M
phastCons12way.txt.gz 2011-08-21 03:59 77M
netCanFam2.txt.gz 2011-05-30 01:20 77M
netMm9.txt.gz 2011-05-24 00:32 73M
netEquCab2.txt.gz 2011-05-03 13:41 70M
chainMm9.txt.gz 2011-05-24 00:34 67M
netCalJac3.txt.gz 2011-05-24 00:33 45M
chainCanFam2.txt.gz 2011-05-30 01:19 43M
xenoRefGene.txt.gz 2020-08-22 18:57 33M
xenoRefSeqAli.txt.gz 2020-08-22 19:12 31M
netMonDom5.txt.gz 2011-11-14 03:18 31M
xenoRefFlat.txt.gz 2020-08-22 19:12 30M
chainGorGor3.txt.gz 2011-11-27 14:05 28M
chainHg19.txt.gz 2011-02-25 17:11 28M
simpleRepeat.txt.gz 2011-02-25 17:13 26M
netRheMac2.txt.gz 2011-05-24 00:30 26M
chainPonAbe2.txt.gz 2011-05-03 13:29 26M
multiz12waySummary.txt.gz 2011-08-21 03:57 23M
chainGalGal3.txt.gz 2011-05-03 13:44 21M
netPonAbe2.txt.gz 2011-05-03 14:50 20M
nestedRepeats.txt.gz 2011-02-25 17:10 18M
multiz12wayFrames.txt.gz 2011-08-21 03:57 17M
netGorGor3.txt.gz 2011-11-27 14:04 16M
chainCalJac3.txt.gz 2011-05-24 00:35 15M
phastConsElements12way.txt.gz 2011-08-21 03:56 14M
netGalGal3.txt.gz 2011-05-03 13:45 12M
chainRheMac2.txt.gz 2011-05-24 00:40 11M
netHg19.txt.gz 2011-02-25 17:18 10M
netDanRer7.txt.gz 2011-03-15 09:36 8.1M
nscanPep.txt.gz 2011-06-26 14:55 6.1M
phastConsElements12wayPrimate.txt.gz 2011-08-21 03:57 3.2M
gold.txt.gz 2011-02-25 17:09 3.0M
ctgPos2.txt.gz 2011-02-25 17:10 2.5M
gap.txt.gz 2011-02-25 17:24 2.3M
augustusGene.txt.gz 2015-07-26 17:21 2.2M
nscanGene.txt.gz 2011-06-26 14:55 2.2M
cpgIslandExtUnmasked.txt.gz 2014-06-01 18:26 1.0M
all_est.txt.gz 2016-07-17 10:50 875K
intronEst.txt.gz 2016-07-17 10:52 677K
cpgIslandExt.txt.gz 2011-02-25 17:14 627K
microsat.txt.gz 2015-08-23 23:47 349K
all_mrna.txt.gz 2020-05-08 18:29 302K
refSeqAli.txt.gz 2020-08-22 19:12 224K
estOrientInfo.txt.gz 2016-07-17 10:52 221K
refGene.txt.gz 2020-08-22 18:57 217K
refFlat.txt.gz 2020-08-22 18:57 200K
chromInfo.txt.gz 2011-02-25 17:10 138K
chromAlias.txt.gz 2016-09-15 18:01 134K
mrnaOrientInfo.txt.gz 2020-08-22 19:12 109K
trackDb.txt.gz 2023-03-28 13:52 46K
gbLoaded.txt.gz 2020-08-22 19:12 41K
tRNAs.txt.gz 2012-04-23 09:16 12K
tableDescriptions.txt.gz 2024-11-23 02:03 7.1K
tableList.txt.gz 2024-11-24 03:28 4.5K
xenoRefSeqAli.sql 2020-08-22 19:12 2.1K
refSeqAli.sql 2020-08-22 19:12 2.1K
xenoMrna.sql 2020-08-22 18:48 2.1K
all_mrna.sql 2020-05-08 18:29 2.1K
intronEst.sql 2016-07-17 10:52 2.1K
all_est.sql 2016-07-17 10:50 2.1K
trackDb.sql 2023-03-28 13:52 2.1K
netRheMac2.sql 2011-05-24 00:30 2.0K
netPonAbe2.sql 2011-05-03 14:49 2.0K
netMonDom5.sql 2011-11-14 03:18 2.0K
netGorGor3.sql 2011-11-27 14:04 2.0K
netGalGal3.sql 2011-05-03 13:44 2.0K
netEquCab2.sql 2011-05-03 13:39 2.0K
netDanRer7.sql 2011-03-15 09:36 2.0K
netCanFam2.sql 2011-05-30 01:19 2.0K
netCalJac3.sql 2011-05-24 00:32 2.0K
netHg19.sql 2011-02-25 17:17 2.0K
netMm9.sql 2011-05-24 00:31 2.0K
xenoRefGene.sql 2020-08-22 18:57 2.0K
refGene.sql 2020-08-22 18:57 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
nestedRepeats.sql 2011-02-25 17:10 1.9K
simpleRepeat.sql 2011-02-25 17:13 1.9K
nscanGene.sql 2011-06-26 14:55 1.9K
mrnaOrientInfo.sql 2020-08-22 19:12 1.8K
rmsk.sql 2011-02-25 17:28 1.8K
estOrientInfo.sql 2016-07-17 10:52 1.8K
hgFindSpec.sql 2023-03-28 13:52 1.8K
xenoRefFlat.sql 2020-08-22 19:12 1.7K
refFlat.sql 2020-08-22 18:57 1.7K
phastCons12wayPrimate.sql 2011-08-21 03:56 1.7K
phyloP12wayPrimate.sql 2011-08-21 03:56 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 18:26 1.7K
phastCons12way.sql 2011-08-21 03:59 1.7K
phyloP12way.sql 2011-08-21 03:59 1.7K
tRNAs.sql 2012-04-23 09:16 1.7K
multiz12wayFrames.sql 2011-08-21 03:57 1.7K
chainRheMac2.sql 2011-05-24 00:40 1.6K
chainPonAbe2.sql 2011-05-03 13:29 1.6K
chainMonDom5.sql 2011-11-14 03:18 1.6K
chainGorGor3.sql 2011-11-27 14:05 1.6K
chainGalGal3.sql 2011-05-03 13:43 1.6K
chainEquCab2.sql 2011-05-03 14:38 1.6K
chainDanRer7.sql 2011-03-15 09:00 1.6K
chainCanFam2.sql 2011-05-30 01:18 1.6K
chainCalJac3.sql 2011-05-24 00:35 1.6K
chainHg19.sql 2011-02-25 17:11 1.6K
chainMm9.sql 2011-05-24 00:34 1.6K
cpgIslandExt.sql 2011-02-25 17:14 1.6K
gbLoaded.sql 2020-08-22 19:12 1.6K
gold.sql 2011-02-25 17:09 1.6K
tableList.sql 2024-11-24 03:28 1.6K
gap.sql 2011-02-25 17:24 1.5K
multiz12waySummary.sql 2011-08-21 03:57 1.5K
phastConsElements12wayPrimate.sql 2011-08-21 03:57 1.5K
history.sql 2011-02-25 17:11 1.5K
phastConsElements12way.sql 2011-08-21 03:56 1.5K
microsat.sql 2015-08-23 23:47 1.5K
chainRheMac2Link.sql 2011-05-24 00:40 1.5K
chainPonAbe2Link.sql 2011-05-03 13:30 1.5K
chainMonDom5Link.sql 2011-11-14 03:05 1.5K
chainGorGor3Link.sql 2011-11-27 14:04 1.5K
chainGalGal3Link.sql 2011-05-03 13:23 1.5K
chainEquCab2Link.sql 2011-05-03 13:45 1.5K
chainDanRer7Link.sql 2011-03-15 09:08 1.5K
chainCanFam2Link.sql 2011-05-30 01:12 1.5K
chainCalJac3Link.sql 2011-05-24 00:35 1.5K
ctgPos2.sql 2011-02-25 17:10 1.5K
chainHg19Link.sql 2011-02-25 17:18 1.5K
chainMm9Link.sql 2011-05-24 00:21 1.5K
multiz12way.sql 2011-08-21 03:57 1.5K
chromAlias.sql 2016-09-15 18:01 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
bigFiles.sql 2024-11-24 03:28 1.4K
extFile.sql 2011-08-21 03:59 1.4K
grp.sql 2014-03-02 04:14 1.3K
chromInfo.sql 2011-02-25 17:10 1.3K
nscanPep.sql 2011-06-26 14:55 1.3K
gc5BaseBw.sql 2011-02-25 17:35 1.2K
hgFindSpec.txt.gz 2023-03-28 13:52 637
grp.txt.gz 2014-03-02 04:14 234
history.txt.gz 2011-02-25 17:11 147
extFile.txt.gz 2011-08-21 03:59 81
bigFiles.txt.gz 2024-11-24 03:28 68
gc5BaseBw.txt.gz 2011-02-25 17:35 63