This directory contains a dump of the UCSC genome annotation
database for the assembly of the Xenopus tropicalis genome
from the US DOE Joint Genome Institute (JGI) (xenTro2, Aug. 2005,
JGI v4.1).
Files included in this directory (updated nightly):
- *.sql files: the MySQL commands used to create the tables.
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=xenTro2
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
- *.txt.gz files: the database tables in a tab-delimited format
compressed with gzip.
---------------------------------------------------------------
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/xenTro2/database/. To download multiple files,
use the "mget" command:
mget <filename1> <filename2> ...
- or -
mget -a (to download all the files in the directory)
Preliminary drafts of the X. tropicalis sequence are made freely available
before scientific publication by the JGI and the X. tropicalis Genome
Consortium, 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 provider of this data
(DOE Joint Genome Institute) is properly acknowledged.
3. Additional shotgun sequencing is ongoing, and future assembly
releases will be made in a timely fashion. We expect to publish an
initial analysis of a high quality draft X. tropicalis genome sequence
in 2005 (with submission targeted for the spring of 2005) which will
include descriptions of the large scale organization of the frog
genome as well as genome-scale comparisons of the frog sequence and
gene set with those of other animals. Others who would like to
coordinate other genome-wide analysis with this work should contact
Paul Richardson (pmrichardson@lbl.gov), JGI. We welcome a coordinated
approach to describing this community resource.
4. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
bigFiles.txt.gz 2024-11-10 03:15 33
extFile.txt.gz 2014-10-19 15:46 85
grp.txt.gz 2014-03-02 04:18 223
history.txt.gz 2010-07-04 19:18 732
hgFindSpec.txt.gz 2023-03-28 13:54 889
chromInfo.sql 2006-06-13 07:20 1.2K
ensPep.sql 2011-03-15 13:13 1.3K
microsat.sql 2006-08-03 07:52 1.3K
ensGtp.sql 2011-03-15 13:14 1.4K
chainRn4Link.sql 2006-06-13 07:14 1.4K
grp.sql 2014-03-02 04:18 1.4K
bigFiles.sql 2024-11-10 03:15 1.4K
multiz7way.sql 2006-06-21 08:48 1.4K
chainGalGal3Link.sql 2006-08-06 19:49 1.4K
chainMonDom4Link.sql 2006-08-11 12:23 1.4K
phastConsElements7way.sql 2006-06-21 08:50 1.4K
genscanSubopt.sql 2006-06-13 07:21 1.4K
chainMm9Link.sql 2007-11-06 18:28 1.4K
tableDescriptions.sql 2024-11-09 02:04 1.4K
multiz7waySummary.sql 2006-06-21 08:49 1.4K
extFile.sql 2014-10-19 15:46 1.5K
gap.sql 2006-06-13 07:13 1.5K
chainAnoCar2Link.sql 2011-10-16 04:00 1.5K
chainDanRer7Link.sql 2011-03-24 09:31 1.5K
multiz7wayFrames.sql 2006-06-21 08:49 1.5K
chainHg19Link.sql 2009-10-04 12:59 1.5K
genscan.sql 2006-06-13 07:21 1.5K
gold.sql 2006-06-13 07:21 1.6K
history.sql 2010-07-04 19:18 1.6K
tableList.sql 2024-11-10 03:15 1.6K
cpgIslandExt.sql 2006-06-13 07:20 1.6K
gbLoaded.sql 2020-09-03 10:13 1.6K
chainRn4.sql 2006-06-13 07:13 1.6K
chainGalGal3.sql 2006-08-06 19:48 1.6K
chainMonDom4.sql 2006-08-11 12:18 1.6K
chainAnoCar2.sql 2011-10-16 03:59 1.6K
chainDanRer7.sql 2011-03-24 09:49 1.6K
chainMm9.sql 2007-11-06 18:41 1.6K
gc5Base.sql 2006-06-13 07:21 1.7K
phastCons7way.sql 2006-06-21 08:49 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 20:18 1.7K
refFlat.sql 2020-09-03 10:13 1.7K
xenoRefFlat.sql 2020-09-03 10:13 1.7K
hgFindSpec.sql 2023-03-28 13:54 1.8K
estOrientInfo.sql 2016-05-15 11:45 1.8K
chainHg19.sql 2009-10-04 12:58 1.8K
mrnaOrientInfo.sql 2020-09-03 10:13 1.8K
rmsk.sql 2006-06-13 07:23 1.8K
ensGene.sql 2011-03-15 13:12 1.9K
pubsBlat.sql 2012-05-09 13:12 1.9K
simpleRepeat.sql 2006-06-13 07:24 1.9K
mgcGenes.sql 2020-03-01 09:24 1.9K
augustusGene.sql 2015-07-26 17:28 1.9K
refGene.sql 2020-09-03 10:13 1.9K
xenoRefGene.sql 2020-09-03 10:13 2.0K
netAnoCar2.sql 2011-10-16 04:03 2.0K
netDanRer7.sql 2011-03-24 09:55 2.0K
trackDb.sql 2023-03-28 13:54 2.1K
pubsBlatPsl.sql 2012-05-09 13:11 2.1K
all_est.sql 2016-05-15 11:45 2.1K
intronEst.sql 2016-05-15 11:45 2.1K
mgcFullMrna.sql 2020-03-01 09:24 2.1K
all_mrna.sql 2020-05-11 17:36 2.1K
refSeqAli.sql 2020-09-03 10:13 2.1K
xenoRefSeqAli.sql 2020-09-03 10:13 2.1K
netRn4.sql 2006-06-13 07:23 2.2K
netGalGal3.sql 2006-08-06 19:50 2.2K
netMonDom4.sql 2006-08-11 12:45 2.2K
pubsBingBlatPsl.sql 2014-01-26 19:44 2.2K
netMm9.sql 2007-11-06 18:41 2.2K
blastHg18KG.sql 2009-12-20 16:08 2.3K
netHg19.sql 2009-10-04 13:04 2.3K
pubsBingBlat.sql 2014-01-26 19:44 2.4K
tableList.txt.gz 2024-11-10 03:15 4.5K
tableDescriptions.txt.gz 2024-11-09 02:04 7.0K
gbLoaded.txt.gz 2020-09-03 10:13 42K
trackDb.txt.gz 2023-03-28 13:54 43K
chromInfo.txt.gz 2006-06-13 07:20 100K
microsat.txt.gz 2006-08-03 07:52 139K
ensGtp.txt.gz 2011-03-15 13:14 235K
pubsBlat.txt.gz 2012-05-09 13:12 315K
pubsBingBlatPsl.txt.gz 2014-01-26 19:44 461K
pubsBlatPsl.txt.gz 2012-05-09 13:11 464K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:18 481K
mrnaOrientInfo.txt.gz 2020-09-03 10:13 528K
pubsBingBlat.txt.gz 2014-01-26 19:44 544K
mgcGenes.txt.gz 2020-03-01 09:24 788K
refFlat.txt.gz 2020-09-03 10:13 825K
cpgIslandExt.txt.gz 2006-06-13 07:20 858K
refGene.txt.gz 2020-09-03 10:13 901K
refSeqAli.txt.gz 2020-09-03 10:13 943K
mgcFullMrna.txt.gz 2020-03-01 09:24 944K
all_mrna.txt.gz 2020-05-11 17:36 1.9M
ensGene.txt.gz 2011-03-15 13:12 2.0M
gap.txt.gz 2006-06-13 07:13 2.1M
augustusGene.txt.gz 2015-07-26 17:28 2.4M
blastHg18KG.txt.gz 2009-12-20 16:08 2.6M
genscan.txt.gz 2006-06-13 07:21 2.8M
gold.txt.gz 2006-06-13 07:21 3.1M
genscanSubopt.txt.gz 2006-06-13 07:21 4.6M
ensPep.txt.gz 2011-03-15 13:13 5.7M
multiz7wayFrames.txt.gz 2006-06-21 08:49 6.0M
netGalGal3.txt.gz 2006-08-06 19:50 6.3M
gc5Base.txt.gz 2006-06-13 07:21 6.4M
multiz7waySummary.txt.gz 2006-06-21 08:49 6.5M
phastConsElements7way.txt.gz 2006-06-21 08:50 6.8M
netRn4.txt.gz 2006-06-13 07:23 7.0M
netMonDom4.txt.gz 2006-08-11 12:45 7.0M
netMm9.txt.gz 2007-11-06 18:41 8.8M
netDanRer7.txt.gz 2011-03-24 09:55 9.2M
netHg19.txt.gz 2009-10-04 13:04 9.3M
netAnoCar2.txt.gz 2011-10-16 04:03 9.6M
phastCons7way.txt.gz 2006-06-21 08:50 14M
simpleRepeat.txt.gz 2006-06-13 07:24 15M
estOrientInfo.txt.gz 2016-05-15 11:45 15M
chainGalGal3.txt.gz 2006-08-06 19:48 17M
multiz7way.txt.gz 2006-06-21 08:49 21M
xenoRefFlat.txt.gz 2020-09-03 10:13 23M
xenoRefSeqAli.txt.gz 2020-09-03 10:13 24M
xenoRefGene.txt.gz 2020-09-03 10:13 26M
intronEst.txt.gz 2016-05-15 11:45 32M
chainRn4.txt.gz 2006-06-13 07:14 44M
rmsk.txt.gz 2006-06-13 07:23 46M
chainMm9.txt.gz 2007-11-06 18:42 46M
chainAnoCar2.txt.gz 2011-10-16 04:00 51M
all_est.txt.gz 2016-05-15 11:45 55M
chainGalGal3Link.txt.gz 2006-08-06 19:49 79M
chainHg19.txt.gz 2009-10-04 12:58 126M
chainMonDom4.txt.gz 2006-08-11 12:21 219M
chainDanRer7.txt.gz 2011-03-24 09:51 224M
chainAnoCar2Link.txt.gz 2011-10-16 04:01 253M
chainRn4Link.txt.gz 2006-06-13 07:17 283M
chainMm9Link.txt.gz 2007-11-06 18:34 291M
chainHg19Link.txt.gz 2009-10-04 13:01 494M
chainDanRer7Link.txt.gz 2011-03-24 09:36 652M
chainMonDom4Link.txt.gz 2006-08-11 12:34 771M