This directory contains a dump of the UCSC genome annotation database for
the March 2009 (WUGSC 3.2/calJac3) assembly of
the marmoset genome (calJac3, WUSTL 3.2 (GCA_000004665.1)),
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Washington University St. Louis (WUSTL)
School of Medicine Genome Sequencing Center in St. Louis.
For more information on the marmoset genome, see the project website:
For more information on the marmoset genome, see the project website:
http://genome.wustl.edu/genomes/view/callithrix_jacchus/
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=calJac3
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/calJac3/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/calJac3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/calJac3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/calJac3/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 calJac3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql calJac3 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Marmoset sequence is made freely available to the community by the
Genome Sequencing Center, Washington University School of Medicine, 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 these data
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.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
qualityBw.txt.gz 2010-11-07 14:12 61
ncbiRefSeqOther.txt.gz 2020-05-10 03:26 75
extNcbiRefSeq.txt.gz 2020-05-10 03:26 91
bigFiles.txt.gz 2024-12-08 03:32 96
extFile.txt.gz 2011-10-24 16:01 104
grp.txt.gz 2014-03-02 03:40 208
history.txt.gz 2010-05-28 14:04 1.0K
qualityBw.sql 2010-11-07 14:12 1.2K
nscanPep.sql 2010-05-28 13:58 1.3K
ncbiRefSeqOther.sql 2020-05-10 03:26 1.3K
chromInfo.sql 2010-05-28 14:25 1.3K
ensPep.sql 2016-11-20 05:59 1.3K
ncbiRefSeqCds.sql 2020-05-10 03:26 1.3K
grp.sql 2014-03-02 03:40 1.3K
extFile.sql 2011-10-24 16:01 1.4K
ensemblSource.sql 2016-11-20 05:54 1.4K
ucscToEnsembl.sql 2014-10-19 08:20 1.4K
ncbiRefSeqPepTable.sql 2020-05-10 03:26 1.4K
ensemblToGeneName.sql 2018-02-04 06:01 1.4K
hgFindSpec.txt.gz 2024-07-25 09:34 1.4K
bigFiles.sql 2024-12-08 03:32 1.4K
ensGtp.sql 2016-11-20 05:58 1.4K
chromAlias.sql 2018-02-18 05:31 1.4K
ucscToINSDC.sql 2013-09-15 09:31 1.4K
ucscToRefSeq.sql 2018-02-18 05:31 1.4K
extNcbiRefSeq.sql 2020-05-10 03:26 1.4K
bacEndCalJac3Singles.sql 2010-10-31 13:39 1.5K
tableDescriptions.sql 2024-12-07 02:03 1.5K
multiz13way.sql 2011-10-24 16:05 1.5K
chainMm9Link.sql 2010-05-28 14:26 1.5K
chainHg19Link.sql 2010-05-28 13:58 1.5K
chainMm10Link.sql 2012-05-07 09:03 1.5K
ctgPos2.sql 2010-05-28 14:03 1.5K
chainCanFam2Link.sql 2010-05-28 14:09 1.5K
chainGorGor3Link.sql 2011-11-27 08:06 1.5K
chainMonDom5Link.sql 2010-05-28 14:14 1.5K
chainPanTro3Link.sql 2011-05-23 07:59 1.5K
chainPonAbe2Link.sql 2010-05-28 14:23 1.5K
microsat.sql 2015-08-23 11:23 1.5K
phastConsElements13way.sql 2011-10-24 16:13 1.5K
history.sql 2010-05-28 14:04 1.5K
multiz13waySummary.sql 2011-10-24 16:02 1.5K
cytoBandIdeo.sql 2013-04-28 11:15 1.5K
gap.sql 2010-05-28 14:31 1.5K
chainHg38Link.sql 2018-01-07 06:21 1.5K
seqNcbiRefSeq.sql 2020-05-10 03:26 1.5K
chainTarSyr2Link.sql 2015-05-24 21:05 1.5K
chainMicMur1Link.sql 2012-11-11 09:28 1.6K
chainPapHam1Link.sql 2012-11-18 11:15 1.6K
chainRheMac3Link.sql 2012-12-02 11:11 1.6K
tableList.sql 2024-12-08 03:32 1.6K
gold.sql 2010-10-24 13:31 1.6K
gbLoaded.sql 2020-08-18 11:07 1.6K
cpgIslandExt.sql 2010-05-28 14:03 1.6K
chainMm9.sql 2010-05-28 13:53 1.6K
chainHg19.sql 2010-05-28 14:00 1.6K
chainMm10.sql 2012-05-07 08:57 1.6K
chainCanFam2.sql 2010-05-28 14:22 1.6K
chainGorGor3.sql 2011-11-27 08:05 1.6K
chainMonDom5.sql 2010-05-28 14:06 1.6K
chainPanTro3.sql 2011-05-23 07:59 1.6K
chainPonAbe2.sql 2010-05-28 14:31 1.6K
multiz13wayFrames.sql 2011-10-24 16:03 1.7K
genscan.sql 2013-12-09 19:32 1.7K
tRNAs.sql 2012-04-15 16:35 1.7K
gc5Base.sql 2010-05-28 14:13 1.7K
bacEnds.sql 2010-10-31 13:39 1.7K
chainHg38.sql 2018-01-07 06:20 1.7K
phastCons13way.sql 2011-10-24 16:14 1.7K
phyloP13wayAll.sql 2011-10-24 16:17 1.7K
chainTarSyr2.sql 2015-05-24 21:04 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 09:24 1.7K
chainMicMur1.sql 2012-11-11 09:27 1.7K
chainPapHam1.sql 2012-11-18 11:15 1.7K
chainRheMac3.sql 2012-12-02 11:13 1.7K
refFlat.sql 2020-08-18 11:00 1.7K
xenoRefFlat.sql 2020-08-18 11:03 1.7K
estOrientInfo.sql 2016-06-12 06:19 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
rmsk.sql 2010-05-28 13:57 1.8K
mrnaOrientInfo.sql 2020-08-18 11:07 1.8K
nscanGene.sql 2010-05-28 14:14 1.9K
simpleRepeat.sql 2010-05-28 14:02 1.9K
nestedRepeats.sql 2010-05-28 14:25 1.9K
ensGene.sql 2016-11-20 05:59 1.9K
ncbiRefSeq.sql 2020-05-10 03:26 1.9K
augustusGene.sql 2015-07-26 10:54 1.9K
refGene.sql 2020-08-18 10:48 1.9K
ncbiRefSeqCurated.sql 2020-05-10 03:26 2.0K
xenoRefGene.sql 2020-08-18 11:00 2.0K
ncbiRefSeqPredicted.sql 2020-05-10 03:26 2.0K
ncbiRefSeqLink.sql 2020-05-10 03:26 2.0K
netMm9.sql 2010-05-30 13:34 2.0K
netHg19.sql 2010-05-28 14:08 2.0K
netMm10.sql 2012-05-07 08:59 2.0K
netCanFam2.sql 2010-05-28 14:00 2.0K
netGorGor3.sql 2011-11-27 08:06 2.0K
netMonDom5.sql 2010-05-28 13:57 2.0K
netPanTro3.sql 2011-05-23 07:58 2.0K
netPonAbe2.sql 2010-05-28 14:03 2.0K
trackDb.sql 2024-07-25 09:34 2.1K
netHg38.sql 2018-01-07 06:24 2.1K
netTarSyr2.sql 2015-05-24 21:11 2.1K
netMicMur1.sql 2012-11-11 09:31 2.1K
netPapHam1.sql 2012-11-18 11:16 2.1K
netRheMac3.sql 2012-12-02 11:12 2.1K
all_est.sql 2016-06-12 06:20 2.1K
intronEst.sql 2016-06-12 06:19 2.1K
ncbiRefSeqPsl.sql 2020-05-10 03:26 2.1K
all_mrna.sql 2020-05-05 23:50 2.1K
xenoMrna.sql 2020-08-18 10:38 2.1K
refSeqAli.sql 2020-08-18 11:07 2.1K
xenoRefSeqAli.sql 2020-08-18 11:07 2.1K
tableList.txt.gz 2024-12-08 03:32 5.7K
tableDescriptions.txt.gz 2024-12-07 02:03 8.7K
tRNAs.txt.gz 2012-04-15 16:35 9.8K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:26 19K
refFlat.txt.gz 2020-08-18 11:00 19K
refGene.txt.gz 2020-08-18 10:48 20K
refSeqAli.txt.gz 2020-08-18 11:07 22K
mrnaOrientInfo.txt.gz 2020-08-18 11:07 25K
ctgPos2.txt.gz 2010-05-28 14:03 35K
ucscToEnsembl.txt.gz 2014-10-19 08:20 75K
all_mrna.txt.gz 2020-05-05 23:50 75K
trackDb.txt.gz 2024-07-25 09:34 78K
cytoBandIdeo.txt.gz 2013-04-28 11:15 81K
chromInfo.txt.gz 2010-05-28 14:25 85K
gbLoaded.txt.gz 2020-08-18 11:07 113K
ucscToINSDC.txt.gz 2013-09-15 09:31 116K
ucscToRefSeq.txt.gz 2018-02-18 05:31 123K
chromAlias.txt.gz 2018-02-18 05:31 152K
ensemblSource.txt.gz 2016-11-20 05:54 177K
ensemblToGeneName.txt.gz 2018-02-04 06:01 253K
ncbiRefSeqCds.txt.gz 2020-05-10 03:26 315K
microsat.txt.gz 2015-08-23 11:23 450K
ensGtp.txt.gz 2016-11-20 05:58 512K
cpgIslandExt.txt.gz 2010-05-28 14:03 720K
cpgIslandExtUnmasked.txt.gz 2014-06-01 09:24 788K
seqNcbiRefSeq.txt.gz 2020-05-10 03:26 879K
bacEndCalJac3Singles.txt.gz 2010-10-31 13:39 907K
ncbiRefSeqLink.txt.gz 2020-05-10 03:26 1.7M
nscanGene.txt.gz 2010-05-28 14:14 2.1M
bacEnds.txt.gz 2010-10-31 13:39 2.2M
augustusGene.txt.gz 2015-07-26 10:54 2.3M
gap.txt.gz 2010-05-28 14:31 2.5M
genscan.txt.gz 2013-12-09 19:32 3.1M
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:26 3.2M
ncbiRefSeq.txt.gz 2020-05-10 03:26 3.3M
gold.txt.gz 2010-10-24 13:31 3.4M
estOrientInfo.txt.gz 2016-06-12 06:19 3.5M
ensGene.txt.gz 2016-11-20 05:59 3.5M
ncbiRefSeqPsl.txt.gz 2020-05-10 03:26 4.2M
nscanPep.txt.gz 2010-05-28 13:58 6.1M
intronEst.txt.gz 2016-06-12 06:19 8.4M
ensPep.txt.gz 2016-11-20 05:59 9.1M
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:26 9.6M
all_est.txt.gz 2016-06-12 06:20 11M
gc5Base.txt.gz 2010-05-28 14:13 12M
chainRheMac3.txt.gz 2012-12-02 11:13 13M
chainGorGor3.txt.gz 2011-11-27 08:05 13M
chainHg19.txt.gz 2010-05-28 14:00 14M
chainPanTro3.txt.gz 2011-05-23 07:59 15M
phastConsElements13way.txt.gz 2011-10-24 16:13 16M
nestedRepeats.txt.gz 2010-05-28 14:25 16M
chainPapHam1.txt.gz 2012-11-18 11:15 17M
chainPonAbe2.txt.gz 2010-05-28 14:31 17M
netMonDom5.txt.gz 2010-05-28 13:57 18M
multiz13wayFrames.txt.gz 2011-10-24 16:04 20M
simpleRepeat.txt.gz 2010-05-28 14:03 21M
multiz13waySummary.txt.gz 2011-10-24 16:02 28M
xenoRefFlat.txt.gz 2020-08-18 11:03 32M
xenoRefGene.txt.gz 2020-08-18 11:00 36M
netHg38.txt.gz 2018-01-07 06:25 36M
netHg19.txt.gz 2010-05-28 14:09 37M
netPanTro3.txt.gz 2011-05-23 07:58 38M
netGorGor3.txt.gz 2011-11-27 08:06 38M
xenoRefSeqAli.txt.gz 2020-08-18 11:07 39M
chainCanFam2.txt.gz 2010-05-28 14:22 39M
netPonAbe2.txt.gz 2010-05-28 14:03 40M
netRheMac3.txt.gz 2012-12-02 11:12 42M
netPapHam1.txt.gz 2012-11-18 11:16 45M
chainMm9.txt.gz 2010-05-28 13:54 57M
chainMm10.txt.gz 2012-05-07 08:58 64M
netMm9.txt.gz 2010-05-30 13:35 67M
netMm10.txt.gz 2012-05-07 09:01 67M
netTarSyr2.txt.gz 2015-05-24 21:11 67M
netMicMur1.txt.gz 2012-11-11 09:31 68M
netCanFam2.txt.gz 2010-05-28 14:01 73M
phastCons13way.txt.gz 2011-10-24 16:15 73M
phyloP13wayAll.txt.gz 2011-10-24 16:18 83M
rmsk.txt.gz 2010-05-28 13:57 129M
chainHg38.txt.gz 2018-01-07 06:20 181M
multiz13way.txt.gz 2011-10-24 16:07 198M
chainMicMur1.txt.gz 2012-11-11 09:27 209M
chainPapHam1Link.txt.gz 2012-11-18 11:16 215M
chainGorGor3Link.txt.gz 2011-11-27 08:06 215M
chainRheMac3Link.txt.gz 2012-12-02 11:11 219M
chainPanTro3Link.txt.gz 2011-05-23 08:01 231M
chainHg19Link.txt.gz 2010-05-28 13:59 235M
chainPonAbe2Link.txt.gz 2010-05-28 14:23 249M
chainTarSyr2.txt.gz 2015-05-24 21:05 264M
chainMonDom5.txt.gz 2010-05-28 14:07 265M
xenoMrna.txt.gz 2020-08-18 10:38 412M
chainMm9Link.txt.gz 2010-05-28 14:27 460M
chainMm10Link.txt.gz 2012-05-07 09:07 484M
chainCanFam2Link.txt.gz 2010-05-28 14:10 490M
chainMicMur1Link.txt.gz 2012-11-11 09:29 688M
chainHg38Link.txt.gz 2018-01-07 06:22 725M
chainMonDom5Link.txt.gz 2010-05-28 14:16 741M
chainTarSyr2Link.txt.gz 2015-05-24 21:07 1.1G