This directory contains a dump of the UCSC genome annotation
database for the October 2004 assembly of the Xenopus tropicalis
genome (xenTro1, Oct. 2004) from the US DOE Joint Genome Institute
(JGI).
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=xenTro1
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/xenTro1/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 -
chainDanRer1.txt.gz 2004-11-16 09:43 169M
chainDanRer1Link.txt.gz 2004-11-16 09:50 710M
chainGalGal2.txt.gz 2004-11-16 09:56 11M
chainGalGal2Link.txt.gz 2004-11-16 09:57 63M
gap.txt.gz 2004-11-16 10:03 2.2M
chromInfo.txt.gz 2004-11-16 10:07 131K
cpgIslandExt.txt.gz 2004-11-16 10:07 842K
danRer1_netBlastz.txt.gz 2004-11-16 10:08 9.2M
extFile.txt.gz 2004-11-16 10:08 181
galGal2_netBlastz.txt.gz 2004-11-16 10:08 3.4M
gc5Base.txt.gz 2004-11-16 10:08 6.8M
genscanPep.txt.gz 2004-11-16 10:09 11M
gold.txt.gz 2004-11-16 10:09 3.3M
hg17_netBlastz.txt.gz 2004-11-16 10:09 3.6M
mm5_netBlastz.txt.gz 2004-11-16 10:09 3.6M
mostConserved.txt.gz 2004-11-16 10:09 7.8M
multiz5way.txt.gz 2004-11-16 10:10 25M
netDanRer1.txt.gz 2004-11-16 10:10 24M
netGalGal2.txt.gz 2004-11-16 10:10 6.9M
phastCons5.txt.gz 2004-11-16 10:11 14M
rmsk.txt.gz 2004-11-16 10:11 26M
simpleRepeat.txt.gz 2004-11-16 10:12 15M
blatFr1.txt.gz 2004-11-18 12:20 43M
genscan.txt.gz 2005-01-09 05:38 3.0M
blastHg17KG.txt.gz 2005-03-05 05:28 3.2M
jgiFilteredModels.txt.gz 2005-03-20 05:03 1.8M
chainHg18Link.txt.gz 2006-04-15 06:36 253M
netHg18.txt.gz 2006-04-15 06:38 5.9M
chainHg18.txt.gz 2006-04-15 06:39 57M
netMm8.txt.gz 2006-05-05 06:29 6.0M
chainMm8Link.txt.gz 2006-05-05 06:32 216M
chainMm8.txt.gz 2006-05-05 06:35 26M
gbDelete_tmp.sql 2009-08-19 15:45 1.3K
gbDelete_tmp.txt.gz 2009-08-19 15:45 157K
history.sql 2010-07-04 19:18 1.6K
history.txt.gz 2010-07-04 19:18 494
blastHg17KG.sql 2013-10-01 12:48 1.3K
blatFr1.sql 2013-10-01 12:48 1.3K
chainDanRer1.sql 2013-10-01 12:48 886
chainDanRer1Link.sql 2013-10-01 12:48 585
chainGalGal2.sql 2013-10-01 12:48 886
chainGalGal2Link.sql 2013-10-01 12:48 585
chainHg18.sql 2013-10-01 12:48 880
chainHg18Link.sql 2013-10-01 12:48 579
chainMm8.sql 2013-10-01 12:48 812
chainMm8Link.sql 2013-10-01 12:48 577
chromInfo.sql 2013-10-01 12:48 396
cpgIslandExt.sql 2013-10-01 12:48 751
danRer1_netBlastz.sql 2013-10-01 12:48 675
extFile.sql 2013-10-01 12:48 445
galGal2_netBlastz.sql 2013-10-01 12:48 675
gap.sql 2013-10-01 12:48 722
gc5Base.sql 2013-10-01 12:48 888
genscan.sql 2013-10-01 12:48 748
genscanPep.sql 2013-10-01 12:48 330
gold.sql 2013-10-01 12:48 799
hg17_netBlastz.sql 2013-10-01 12:48 669
jgiFilteredModels.sql 2013-10-01 12:48 768
mm5_netBlastz.sql 2013-10-01 12:48 667
mostConserved.sql 2013-10-01 12:48 650
multiz5way.sql 2013-10-01 12:48 661
netDanRer1.sql 2013-10-01 12:48 1.3K
netGalGal2.sql 2013-10-01 12:48 1.3K
netHg18.sql 2013-10-01 12:48 1.3K
netMm8.sql 2013-10-01 12:48 1.3K
phastCons5.sql 2013-10-01 12:48 894
rmsk.sql 2013-10-01 12:48 1.1K
simpleRepeat.sql 2013-10-01 12:48 1.1K
grp.sql 2014-03-02 04:18 1.4K
grp.txt.gz 2014-03-02 04:18 223
cpgIslandExtUnmasked.sql 2014-06-01 20:17 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 20:17 906K
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.4M
intronEst.sql 2016-05-15 11:44 2.1K
intronEst.txt.gz 2016-05-15 11:44 32M
all_est.sql 2016-05-15 11:45 2.1K
all_est.txt.gz 2016-05-15 11:45 57M
estOrientInfo.sql 2016-05-15 11:45 1.8K
estOrientInfo.txt.gz 2016-05-15 11:45 16M
cytoBandIdeo.sql 2018-05-13 08:39 1.5K
cytoBandIdeo.txt.gz 2018-05-13 08:39 130K
mgcFullMrna.sql 2020-03-01 09:23 2.1K
mgcFullMrna.txt.gz 2020-03-01 09:23 957K
mgcGenes.sql 2020-03-01 09:23 1.9K
mgcGenes.txt.gz 2020-03-01 09:23 792K
all_mrna.sql 2020-05-11 17:36 2.1K
all_mrna.txt.gz 2020-05-11 17:36 2.0M
mrnaOrientInfo.sql 2020-05-11 17:36 1.8K
mrnaOrientInfo.txt.gz 2020-05-11 17:36 380K
gbLoaded.sql 2020-09-03 10:13 1.6K
gbLoaded.txt.gz 2020-09-03 10:13 42K
xenoRefFlat.sql 2020-09-03 10:13 1.7K
xenoRefFlat.txt.gz 2020-09-03 10:13 32M
xenoRefGene.sql 2020-09-03 10:13 2.0K
xenoRefGene.txt.gz 2020-09-03 10:13 35M
xenoRefSeqAli.sql 2020-09-03 10:13 2.1K
xenoRefSeqAli.txt.gz 2020-09-03 10:13 34M
trackDb.sql 2023-03-28 13:54 2.1K
trackDb.txt.gz 2023-03-28 13:54 30K
hgFindSpec.sql 2023-03-28 13:54 1.8K
hgFindSpec.txt.gz 2023-03-28 13:54 712
tableDescriptions.sql 2024-11-16 02:04 1.4K
tableDescriptions.txt.gz 2024-11-16 02:04 5.6K
tableList.sql 2024-11-17 03:33 1.6K
tableList.txt.gz 2024-11-17 03:33 3.3K
bigFiles.sql 2024-11-17 03:33 1.4K
bigFiles.txt.gz 2024-11-17 03:33 33