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 -
UMassInput.sql 2011-11-06 09:43 1.7K
UMassInput.txt.gz 2011-11-06 09:43 2.4M
UMassME1.sql 2011-11-06 09:43 1.7K
UMassME1.txt.gz 2011-11-06 09:43 2.6M
UMassME1Hotspot.sql 2011-11-06 09:43 1.5K
UMassME1Hotspot.txt.gz 2011-11-06 09:43 560K
UMassME1Peak.sql 2011-11-06 09:43 1.7K
UMassME1Peak.txt.gz 2011-11-06 09:43 750K
UMassME3.sql 2011-11-06 09:43 1.7K
UMassME3.txt.gz 2011-11-06 09:43 1.5M
UMassME3Hotspot.sql 2011-11-06 09:43 1.5K
UMassME3Hotspot.txt.gz 2011-11-06 09:43 408K
UMassME3Peak.sql 2011-11-06 09:43 1.7K
UMassME3Peak.txt.gz 2011-11-06 09:43 565K
affyTargetZonWildType.sql 2007-10-15 09:56 1.9K
affyTargetZonWildType.txt.gz 2007-10-15 09:56 1.7M
affyZebrafishConsensus.sql 2007-10-15 09:56 2.2K
affyZebrafishConsensus.txt.gz 2007-10-15 09:56 1.1M
affyZebrafishTarget.sql 2007-10-15 09:56 2.2K
affyZebrafishTarget.txt.gz 2007-10-15 09:57 717K
affyZonWildType.sql 2007-10-15 09:57 1.8K
affyZonWildType.txt.gz 2007-10-15 09:57 1.9M
all_est.sql 2017-11-26 06:44 2.1K
all_est.txt.gz 2017-11-26 06:44 85M
all_mrna.sql 2020-08-21 08:49 2.1K
all_mrna.txt.gz 2020-08-21 08:49 2.6M
augustusGene.sql 2015-07-26 11:52 1.9K
augustusGene.txt.gz 2015-07-26 11:52 2.8M
bigFiles.sql 2024-12-22 03:16 1.4K
bigFiles.txt.gz 2024-12-22 03:16 33
blastHg18KG.sql 2009-12-20 10:59 2.3K
blastHg18KG.txt.gz 2009-12-20 11:00 3.0M
chainFr2.sql 2007-10-15 10:00 1.6K
chainFr2.txt.gz 2007-10-15 10:00 15M
chainFr2Link.sql 2007-10-15 10:01 1.4K
chainFr2Link.txt.gz 2007-10-15 10:03 93M
chainHg19.sql 2009-10-04 07:34 1.8K
chainHg19.txt.gz 2009-10-04 07:34 10M
chainHg19Link.sql 2009-10-04 07:34 1.5K
chainHg19Link.txt.gz 2009-10-04 07:34 65M
chainMm9.sql 2007-10-15 10:05 1.6K
chainMm9.txt.gz 2007-10-15 10:05 9.1M
chainMm9Link.sql 2007-10-15 10:05 1.4K
chainMm9Link.txt.gz 2007-10-15 10:07 67M
chainMonDom5.sql 2009-09-27 08:01 1.8K
chainMonDom5.txt.gz 2009-09-27 08:01 19M
chainMonDom5Link.sql 2009-09-27 08:01 1.5K
chainMonDom5Link.txt.gz 2009-09-27 08:01 95M
chainOryLat2.sql 2008-11-16 07:51 1.7K
chainOryLat2.txt.gz 2008-11-16 07:52 62M
chainOryLat2Link.sql 2008-11-16 07:52 1.4K
chainOryLat2Link.txt.gz 2008-11-16 07:54 317M
chainTetNig1.sql 2007-10-15 10:25 1.7K
chainTetNig1.txt.gz 2007-10-15 10:25 11M
chainTetNig1Link.sql 2007-10-15 10:25 1.4K
chainTetNig1Link.txt.gz 2007-10-15 10:26 63M
chromInfo.sql 2007-10-15 10:27 1.2K
chromInfo.txt.gz 2007-10-15 10:27 28K
ctgPos2.sql 2007-10-15 10:27 1.4K
ctgPos2.txt.gz 2007-10-15 10:27 835K
ensGene.sql 2009-09-27 08:00 2.0K
ensGene.txt.gz 2009-09-27 08:00 2.5M
ensGtp.sql 2009-09-27 08:00 1.4K
ensGtp.txt.gz 2009-09-27 08:00 364K
ensPep.sql 2009-09-27 08:01 1.3K
ensPep.txt.gz 2009-09-27 08:01 7.4M
estOrientInfo.sql 2017-11-26 06:44 1.8K
estOrientInfo.txt.gz 2017-11-26 06:44 20M
extFile.sql 2007-10-15 10:28 1.3K
extFile.txt.gz 2007-10-15 10:28 129
gap.sql 2007-10-15 10:28 1.5K
gap.txt.gz 2007-10-15 10:28 538K
gbLoaded.sql 2020-08-21 09:14 1.6K
gbLoaded.txt.gz 2020-08-21 09:14 43K
gc5Base.sql 2007-10-15 10:34 1.7K
gc5Base.txt.gz 2007-10-15 10:34 5.6M
gold.sql 2007-10-15 10:34 1.6K
gold.txt.gz 2007-10-15 10:34 86K
grp.sql 2014-03-02 03:40 1.4K
grp.txt.gz 2014-03-02 03:40 208
hgFindSpec.sql 2023-03-28 13:48 1.8K
hgFindSpec.txt.gz 2023-03-28 13:48 1.4K
history.sql 2007-10-15 10:34 1.4K
history.txt.gz 2007-10-15 10:34 907
intronEst.sql 2017-11-26 06:44 2.1K
intronEst.txt.gz 2017-11-26 06:44 54M
mgcFullMrna.sql 2020-03-01 05:36 2.1K
mgcFullMrna.txt.gz 2020-03-01 05:36 1.5M
mgcGenes.sql 2020-03-01 05:36 1.9K
mgcGenes.txt.gz 2020-03-01 05:36 1.2M
microsat.sql 2015-08-23 13:18 1.5K
microsat.txt.gz 2015-08-23 13:18 1.1M
mrnaOrientInfo.sql 2020-08-21 09:12 1.8K
mrnaOrientInfo.txt.gz 2020-08-21 09:12 827K
nestedRepeats.sql 2007-10-15 10:37 1.9K
nestedRepeats.txt.gz 2007-10-15 10:38 11M
netFr2.sql 2007-10-15 10:38 2.2K
netFr2.txt.gz 2007-10-15 10:38 11M
netHg19.sql 2009-10-04 07:34 2.3K
netHg19.txt.gz 2009-10-04 07:34 8.2M
netMm9.sql 2007-10-15 10:39 2.2K
netMm9.txt.gz 2007-10-15 10:39 7.5M
netMonDom5.sql 2009-09-27 08:01 2.3K
netMonDom5.txt.gz 2009-09-27 08:01 8.3M
netOryLat2.sql 2008-11-16 07:56 2.2K
netOryLat2.txt.gz 2008-11-16 07:56 16M
netTetNig1.sql 2007-10-15 10:40 2.2K
netTetNig1.txt.gz 2007-10-15 10:40 10M
refFlat.sql 2020-08-21 08:59 1.7K
refFlat.txt.gz 2020-08-21 08:59 1.5M
refGene.sql 2020-08-21 08:56 1.9K
refGene.txt.gz 2020-08-21 08:56 1.7M
refSeqAli.sql 2020-08-21 09:12 2.1K
refSeqAli.txt.gz 2020-08-21 09:12 1.7M
rmsk.sql 2007-10-15 10:41 1.9K
rmsk.txt.gz 2007-10-15 10:43 87M
seq.sql 2007-10-15 10:45 1.4K
seq.txt.gz 2007-10-15 10:45 365K
simpleRepeat.sql 2007-10-15 10:45 1.9K
simpleRepeat.txt.gz 2007-10-15 10:46 25M
tRNAs.sql 2012-04-22 21:08 1.7K
tRNAs.txt.gz 2012-04-22 21:08 268K
tableDescriptions.sql 2024-12-21 02:04 1.4K
tableDescriptions.txt.gz 2024-12-21 02:04 6.6K
tableList.sql 2024-12-22 03:16 1.6K
tableList.txt.gz 2024-12-22 03:16 4.6K
trackDb.sql 2023-03-28 13:48 2.1K
trackDb.txt.gz 2023-03-28 13:48 36K
vegaGene.sql 2007-10-15 10:46 1.9K
vegaGene.txt.gz 2007-10-15 10:46 1.0M
vegaInfoZfish.sql 2007-10-15 10:47 1.5K
vegaInfoZfish.txt.gz 2007-10-15 10:47 339K
vegaPep.sql 2007-10-15 10:47 1.1K
vegaPep.txt.gz 2007-10-15 10:47 2.1M
vegaPseudoGene.sql 2007-10-15 10:47 1.9K
vegaPseudoGene.txt.gz 2007-10-15 10:47 3.5K
vegaToCloneId.sql 2007-10-15 10:47 1.2K
vegaToCloneId.txt.gz 2007-10-15 10:47 56K
xenoMrna.sql 2016-02-21 12:56 2.1K
xenoMrna.txt.gz 2016-02-21 12:56 213M
xenoRefFlat.sql 2020-08-21 08:59 1.7K
xenoRefFlat.txt.gz 2020-08-21 08:59 20M
xenoRefGene.sql 2020-08-21 08:59 2.0K
xenoRefGene.txt.gz 2020-08-21 08:59 22M
xenoRefSeqAli.sql 2020-08-21 09:14 2.1K
xenoRefSeqAli.txt.gz 2020-08-21 09:14 19M