This directory contains a dump of the UCSC genome annotation database for
the Jul. 2007 Zv7 assembly of the zebrafish genome (danRer5) obtained from
the Wellcome Trust Sanger Institute. The annotations were generated by UCSC
and collaborators worldwide.
This assembly was produced by a collaboration between the
Wellcome Trust Sanger Institute in Cambridge, UK, the Max Planck Institute
for Developmental Biology in Tuebingen, Germany, the Netherlands Institute
for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands
and Yi Zhou and Leonard Zon from the Children's Hospital in Boston,
Massachusetts.
For more information on the zebrafish genome, see the project website:
http://www.sanger.ac.uk/Projects/D_rerio/
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=danRer5
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/danRer5/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/danRer5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer5/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 danRer5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer5 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Zv7 zebrafish sequence data were produced by the Zebrafish Sequencing
Group at the Sanger Institute and can be obtained directly from
ftp://ftp.ensembl.org/pub/assembly/zebrafish/Zv7release/. All sequence
data are made available before scientific publication with the understanding
that the groups involved in generating the data intend to publish the
initial large-scale analyses of the dataset. This will include a summary
detailing the data that have beeen generated and key features of the
genome identified from genomic assembly and clone mapping/sequencing. 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 -
xenoRefSeqAli.txt.gz 2020-08-21 09:14 19M
xenoRefSeqAli.sql 2020-08-21 09:14 2.1K
xenoRefGene.txt.gz 2020-08-21 08:59 22M
xenoRefGene.sql 2020-08-21 08:59 2.0K
xenoRefFlat.txt.gz 2020-08-21 08:59 20M
xenoRefFlat.sql 2020-08-21 08:59 1.7K
xenoMrna.txt.gz 2016-02-21 12:56 213M
xenoMrna.sql 2016-02-21 12:56 2.1K
vegaToCloneId.txt.gz 2007-10-15 10:47 56K
vegaToCloneId.sql 2007-10-15 10:47 1.2K
vegaPseudoGene.txt.gz 2007-10-15 10:47 3.5K
vegaPseudoGene.sql 2007-10-15 10:47 1.9K
vegaPep.txt.gz 2007-10-15 10:47 2.1M
vegaPep.sql 2007-10-15 10:47 1.1K
vegaInfoZfish.txt.gz 2007-10-15 10:47 339K
vegaInfoZfish.sql 2007-10-15 10:47 1.5K
vegaGene.txt.gz 2007-10-15 10:46 1.0M
vegaGene.sql 2007-10-15 10:46 1.9K
trackDb.txt.gz 2023-03-28 13:48 36K
trackDb.sql 2023-03-28 13:48 2.1K
tableList.txt.gz 2024-11-17 03:26 4.6K
tableList.sql 2024-11-17 03:26 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.6K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tRNAs.txt.gz 2012-04-22 21:08 268K
tRNAs.sql 2012-04-22 21:08 1.7K
simpleRepeat.txt.gz 2007-10-15 10:46 25M
simpleRepeat.sql 2007-10-15 10:45 1.9K
seq.txt.gz 2007-10-15 10:45 365K
seq.sql 2007-10-15 10:45 1.4K
rmsk.txt.gz 2007-10-15 10:43 87M
rmsk.sql 2007-10-15 10:41 1.9K
refSeqAli.txt.gz 2020-08-21 09:12 1.7M
refSeqAli.sql 2020-08-21 09:12 2.1K
refGene.txt.gz 2020-08-21 08:56 1.7M
refGene.sql 2020-08-21 08:56 1.9K
refFlat.txt.gz 2020-08-21 08:59 1.5M
refFlat.sql 2020-08-21 08:59 1.7K
netTetNig1.txt.gz 2007-10-15 10:40 10M
netTetNig1.sql 2007-10-15 10:40 2.2K
netOryLat2.txt.gz 2008-11-16 07:56 16M
netOryLat2.sql 2008-11-16 07:56 2.2K
netMonDom5.txt.gz 2009-09-27 08:01 8.3M
netMonDom5.sql 2009-09-27 08:01 2.3K
netMm9.txt.gz 2007-10-15 10:39 7.5M
netMm9.sql 2007-10-15 10:39 2.2K
netHg19.txt.gz 2009-10-04 07:34 8.2M
netHg19.sql 2009-10-04 07:34 2.3K
netFr2.txt.gz 2007-10-15 10:38 11M
netFr2.sql 2007-10-15 10:38 2.2K
nestedRepeats.txt.gz 2007-10-15 10:38 11M
nestedRepeats.sql 2007-10-15 10:37 1.9K
mrnaOrientInfo.txt.gz 2020-08-21 09:12 827K
mrnaOrientInfo.sql 2020-08-21 09:12 1.8K
microsat.txt.gz 2015-08-23 13:18 1.1M
microsat.sql 2015-08-23 13:18 1.5K
mgcGenes.txt.gz 2020-03-01 05:36 1.2M
mgcGenes.sql 2020-03-01 05:36 1.9K
mgcFullMrna.txt.gz 2020-03-01 05:36 1.5M
mgcFullMrna.sql 2020-03-01 05:36 2.1K
intronEst.txt.gz 2017-11-26 06:44 54M
intronEst.sql 2017-11-26 06:44 2.1K
history.txt.gz 2007-10-15 10:34 907
history.sql 2007-10-15 10:34 1.4K
hgFindSpec.txt.gz 2023-03-28 13:48 1.4K
hgFindSpec.sql 2023-03-28 13:48 1.8K
grp.txt.gz 2014-03-02 03:40 208
grp.sql 2014-03-02 03:40 1.4K
gold.txt.gz 2007-10-15 10:34 86K
gold.sql 2007-10-15 10:34 1.6K
gc5Base.txt.gz 2007-10-15 10:34 5.6M
gc5Base.sql 2007-10-15 10:34 1.7K
gbLoaded.txt.gz 2020-08-21 09:14 43K
gbLoaded.sql 2020-08-21 09:14 1.6K
gap.txt.gz 2007-10-15 10:28 538K
gap.sql 2007-10-15 10:28 1.5K
extFile.txt.gz 2007-10-15 10:28 129
extFile.sql 2007-10-15 10:28 1.3K
estOrientInfo.txt.gz 2017-11-26 06:44 20M
estOrientInfo.sql 2017-11-26 06:44 1.8K
ensPep.txt.gz 2009-09-27 08:01 7.4M
ensPep.sql 2009-09-27 08:01 1.3K
ensGtp.txt.gz 2009-09-27 08:00 364K
ensGtp.sql 2009-09-27 08:00 1.4K
ensGene.txt.gz 2009-09-27 08:00 2.5M
ensGene.sql 2009-09-27 08:00 2.0K
ctgPos2.txt.gz 2007-10-15 10:27 835K
ctgPos2.sql 2007-10-15 10:27 1.4K
chromInfo.txt.gz 2007-10-15 10:27 28K
chromInfo.sql 2007-10-15 10:27 1.2K
chainTetNig1Link.txt.gz 2007-10-15 10:26 63M
chainTetNig1Link.sql 2007-10-15 10:25 1.4K
chainTetNig1.txt.gz 2007-10-15 10:25 11M
chainTetNig1.sql 2007-10-15 10:25 1.7K
chainOryLat2Link.txt.gz 2008-11-16 07:54 317M
chainOryLat2Link.sql 2008-11-16 07:52 1.4K
chainOryLat2.txt.gz 2008-11-16 07:52 62M
chainOryLat2.sql 2008-11-16 07:51 1.7K
chainMonDom5Link.txt.gz 2009-09-27 08:01 95M
chainMonDom5Link.sql 2009-09-27 08:01 1.5K
chainMonDom5.txt.gz 2009-09-27 08:01 19M
chainMonDom5.sql 2009-09-27 08:01 1.8K
chainMm9Link.txt.gz 2007-10-15 10:07 67M
chainMm9Link.sql 2007-10-15 10:05 1.4K
chainMm9.txt.gz 2007-10-15 10:05 9.1M
chainMm9.sql 2007-10-15 10:05 1.6K
chainHg19Link.txt.gz 2009-10-04 07:34 65M
chainHg19Link.sql 2009-10-04 07:34 1.5K
chainHg19.txt.gz 2009-10-04 07:34 10M
chainHg19.sql 2009-10-04 07:34 1.8K
chainFr2Link.txt.gz 2007-10-15 10:03 93M
chainFr2Link.sql 2007-10-15 10:01 1.4K
chainFr2.txt.gz 2007-10-15 10:00 15M
chainFr2.sql 2007-10-15 10:00 1.6K
blastHg18KG.txt.gz 2009-12-20 11:00 3.0M
blastHg18KG.sql 2009-12-20 10:59 2.3K
bigFiles.txt.gz 2024-11-17 03:26 33
bigFiles.sql 2024-11-17 03:26 1.4K
augustusGene.txt.gz 2015-07-26 11:52 2.8M
augustusGene.sql 2015-07-26 11:52 1.9K
all_mrna.txt.gz 2020-08-21 08:49 2.6M
all_mrna.sql 2020-08-21 08:49 2.1K
all_est.txt.gz 2017-11-26 06:44 85M
all_est.sql 2017-11-26 06:44 2.1K
affyZonWildType.txt.gz 2007-10-15 09:57 1.9M
affyZonWildType.sql 2007-10-15 09:57 1.8K
affyZebrafishTarget.txt.gz 2007-10-15 09:57 717K
affyZebrafishTarget.sql 2007-10-15 09:56 2.2K
affyZebrafishConsensus.txt.gz 2007-10-15 09:56 1.1M
affyZebrafishConsensus.sql 2007-10-15 09:56 2.2K
affyTargetZonWildType.txt.gz 2007-10-15 09:56 1.7M
affyTargetZonWildType.sql 2007-10-15 09:56 1.9K
UMassME3Peak.txt.gz 2011-11-06 09:43 565K
UMassME3Peak.sql 2011-11-06 09:43 1.7K
UMassME3Hotspot.txt.gz 2011-11-06 09:43 408K
UMassME3Hotspot.sql 2011-11-06 09:43 1.5K
UMassME3.txt.gz 2011-11-06 09:43 1.5M
UMassME3.sql 2011-11-06 09:43 1.7K
UMassME1Peak.txt.gz 2011-11-06 09:43 750K
UMassME1Peak.sql 2011-11-06 09:43 1.7K
UMassME1Hotspot.txt.gz 2011-11-06 09:43 560K
UMassME1Hotspot.sql 2011-11-06 09:43 1.5K
UMassME1.txt.gz 2011-11-06 09:43 2.6M
UMassME1.sql 2011-11-06 09:43 1.7K
UMassInput.txt.gz 2011-11-06 09:43 2.4M
UMassInput.sql 2011-11-06 09:43 1.7K