This directory contains a dump of the UCSC genome annotation database for the
Sep. 2014 (GRCz10/danRer10) assembly of the zebrafish genome
(danRer10, Genome Reference Consortium Zebrafish Build 10) .
The annotations were generated by UCSC and collaborators worldwide.
For more information about this assembly, please note the NCBI resources:
http://www.ncbi.nlm.nih.gov/genome/50
http://www.ncbi.nlm.nih.gov/genome/assembly/210611
http://www.ncbi.nlm.nih.gov/bioproject/13922
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=danRer10
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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/danRer10/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/danRer10/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/danRer10/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 danRer10 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer10 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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GenBank Data Usage
The GenBank database is designed to provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. Therefore, NCBI places no restrictions on the use
or distribution of the GenBank data. However, some submitters may claim
patent, copyright, or other intellectual property rights in all or a
portion of the data they have submitted. NCBI is not in a position to
assess the validity of such claims, and therefore cannot provide comment
or unrestricted permission concerning the use, copying, or distribution
of the information contained in GenBank.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
gc5BaseBw.txt.gz 2015-04-01 15:08 67
crisprAllTargets.txt.gz 2023-11-06 10:50 70
ncbiRefSeqOther.txt.gz 2018-04-08 05:49 76
grcIncidentDb.txt.gz 2018-05-13 04:55 78
extNcbiRefSeq.txt.gz 2018-04-08 05:49 92
bigFiles.txt.gz 2024-04-14 03:07 145
grp.txt.gz 2015-04-01 15:06 213
history.txt.gz 2015-04-01 15:06 441
gc5BaseBw.sql 2015-04-01 15:08 1.3K
grcIncidentDb.sql 2018-05-13 04:55 1.3K
ncbiRefSeqOther.sql 2018-04-08 05:49 1.3K
ensPep.sql 2018-02-04 06:19 1.3K
crisprAllTargets.sql 2023-11-06 10:50 1.3K
hgFindSpec.txt.gz 2023-12-05 13:51 1.3K
hgFindSpec_pushedout.txt.gz 2023-12-05 13:51 1.3K
ncbiRefSeqCds.sql 2018-04-08 05:49 1.3K
grp.sql 2015-04-01 15:06 1.3K
ensemblSource.sql 2018-02-04 06:19 1.4K
ncbiRefSeqPepTable.sql 2018-04-08 05:49 1.4K
chromInfo.sql 2015-04-01 15:06 1.4K
ensemblToGeneName.sql 2018-02-04 06:19 1.4K
bigFiles.sql 2024-04-14 03:07 1.4K
ensGtp.sql 2018-02-04 06:19 1.4K
chromAlias.sql 2017-09-03 05:24 1.4K
ucscToINSDC.sql 2015-04-01 15:09 1.4K
ucscToRefSeq.sql 2018-02-18 06:01 1.4K
extNcbiRefSeq.sql 2018-04-08 05:49 1.4K
tableDescriptions.sql 2024-04-13 02:03 1.5K
microsat.sql 2015-08-23 12:56 1.5K
windowmaskerSdust.sql 2015-04-01 15:09 1.5K
cytoBandIdeo.sql 2015-04-01 15:06 1.5K
chainRn6Link.sql 2017-03-26 19:04 1.5K
chainHg38Link.sql 2015-04-01 15:02 1.5K
seqNcbiRefSeq.sql 2018-04-08 05:49 1.5K
chainGalGal5Link.sql 2016-09-18 07:35 1.6K
chainMelGal5Link.sql 2017-03-19 16:58 1.6K
history.sql 2015-04-01 15:06 1.6K
tableList.sql 2024-04-14 03:07 1.6K
gap.sql 2015-04-01 15:06 1.6K
gbLoaded.sql 2020-08-18 21:59 1.6K
gold.sql 2015-04-01 15:06 1.7K
genscan.sql 2015-04-01 15:06 1.7K
mmBlastTab.sql 2018-05-21 16:02 1.7K
cpgIslandExt.sql 2015-04-01 15:06 1.7K
chainRn6.sql 2017-03-26 19:02 1.7K
chainHg38.sql 2015-04-01 15:00 1.7K
chainGalGal5.sql 2016-09-18 07:35 1.7K
chainMelGal5.sql 2017-03-19 16:57 1.7K
cpgIslandExtUnmasked.sql 2015-04-01 15:06 1.7K
refFlat.sql 2020-08-18 21:59 1.7K
xenoRefFlat.sql 2020-08-18 21:59 1.7K
hgFindSpec.sql 2023-12-05 13:51 1.8K
estOrientInfo.sql 2017-11-26 06:39 1.8K
hgFindSpec_pushedout.sql 2023-12-05 13:51 1.8K
mrnaOrientInfo.sql 2020-08-18 21:59 1.8K
rmsk.sql 2015-04-01 15:09 1.9K
ensGene.sql 2018-02-04 06:19 1.9K
mgcGenes.sql 2020-03-01 05:32 1.9K
simpleRepeat.sql 2015-04-01 15:09 1.9K
ncbiRefSeq.sql 2018-04-08 05:49 1.9K
nestedRepeats.sql 2015-04-01 15:06 1.9K
augustusGene.sql 2015-07-26 11:52 1.9K
refGene.sql 2020-08-18 21:59 1.9K
ncbiRefSeqCurated.sql 2018-04-08 05:49 2.0K
xenoRefGene.sql 2020-08-18 21:59 2.0K
ncbiRefSeqPredicted.sql 2018-04-08 05:49 2.0K
ncbiRefSeqLink.sql 2018-04-08 05:49 2.0K
trackDb.sql 2023-12-05 13:51 2.1K
netRn6.sql 2017-03-26 19:16 2.1K
trackDb_pushedout.sql 2023-12-05 13:51 2.1K
netHg38.sql 2015-04-01 15:07 2.1K
netGalGal5.sql 2016-09-18 07:35 2.1K
netMelGal5.sql 2017-03-19 16:57 2.1K
all_est.sql 2017-11-26 06:40 2.1K
intronEst.sql 2017-11-26 06:39 2.1K
mgcFullMrna.sql 2020-03-01 05:32 2.1K
ncbiRefSeqPsl.sql 2018-04-08 05:49 2.1K
all_mrna.sql 2020-08-18 21:22 2.1K
xenoMrna.sql 2020-08-18 21:22 2.1K
refSeqAli.sql 2020-08-18 21:59 2.1K
xenoRefSeqAli.sql 2020-08-18 21:59 2.2K
tableList.txt.gz 2024-04-14 03:07 4.1K
cytoBandIdeo.txt.gz 2015-04-01 15:06 6.3K
chromInfo.txt.gz 2015-04-01 15:06 6.8K
tableDescriptions.txt.gz 2024-04-13 02:03 6.9K
ucscToINSDC.txt.gz 2015-04-01 15:09 8.6K
ucscToRefSeq.txt.gz 2018-02-18 06:01 9.7K
chromAlias.txt.gz 2017-09-03 05:24 12K
trackDb.txt.gz 2023-12-05 13:51 35K
trackDb_pushedout.txt.gz 2023-12-05 13:51 35K
gbLoaded.txt.gz 2020-08-18 21:59 42K
ensemblSource.txt.gz 2018-02-04 06:19 207K
gap.txt.gz 2015-04-01 15:06 244K
cpgIslandExt.txt.gz 2015-04-01 15:06 250K
ncbiRefSeqCds.txt.gz 2018-04-08 05:49 324K
mmBlastTab.txt.gz 2018-05-21 16:02 339K
ensemblToGeneName.txt.gz 2018-02-04 06:19 458K
gold.txt.gz 2015-04-01 15:06 641K
ensGtp.txt.gz 2018-02-04 06:19 706K
mrnaOrientInfo.txt.gz 2020-08-18 21:59 764K
seqNcbiRefSeq.txt.gz 2018-04-08 05:49 844K
cpgIslandExtUnmasked.txt.gz 2015-04-01 15:06 957K
microsat.txt.gz 2015-08-23 12:56 1.0M
mgcGenes.txt.gz 2020-03-01 05:32 1.2M
mgcFullMrna.txt.gz 2020-03-01 05:32 1.5M
refFlat.txt.gz 2020-08-18 21:59 1.5M
ncbiRefSeqCurated.txt.gz 2018-04-08 05:49 1.5M
refSeqAli.txt.gz 2020-08-18 21:59 1.6M
refGene.txt.gz 2020-08-18 21:59 1.7M
ncbiRefSeqLink.txt.gz 2018-04-08 05:49 1.9M
genscan.txt.gz 2015-04-01 15:06 2.4M
all_mrna.txt.gz 2020-08-18 21:22 2.4M
ncbiRefSeqPredicted.txt.gz 2018-04-08 05:49 2.6M
augustusGene.txt.gz 2015-07-26 11:52 2.7M
ncbiRefSeq.txt.gz 2018-04-08 05:49 3.7M
ensGene.txt.gz 2018-02-04 06:19 4.0M
ncbiRefSeqPsl.txt.gz 2018-04-08 05:49 4.5M
netMelGal5.txt.gz 2017-03-19 16:57 4.8M
chainMelGal5.txt.gz 2017-03-19 16:57 5.9M
netGalGal5.txt.gz 2016-09-18 07:35 6.3M
nestedRepeats.txt.gz 2015-04-01 15:06 8.1M
netRn6.txt.gz 2017-03-26 19:16 9.4M
netHg38.txt.gz 2015-04-01 15:07 10M
xenoRefSeqAli.txt.gz 2020-08-18 21:59 11M
xenoRefFlat.txt.gz 2020-08-18 21:59 12M
chainGalGal5.txt.gz 2016-09-18 07:35 12M
ncbiRefSeqPepTable.txt.gz 2018-04-08 05:49 13M
xenoRefGene.txt.gz 2020-08-18 21:59 13M
ensPep.txt.gz 2018-02-04 06:19 13M
estOrientInfo.txt.gz 2017-11-26 06:40 17M
chainMelGal5Link.txt.gz 2017-03-19 16:58 20M
simpleRepeat.txt.gz 2015-04-01 15:09 25M
intronEst.txt.gz 2017-11-26 06:39 51M
chainGalGal5Link.txt.gz 2016-09-18 07:35 55M
chainRn6.txt.gz 2017-03-26 19:02 60M
all_est.txt.gz 2017-11-26 06:40 73M
windowmaskerSdust.txt.gz 2015-04-01 15:09 80M
rmsk.txt.gz 2015-04-01 15:09 93M
xenoMrna.txt.gz 2020-08-18 21:22 131M
chainHg38.txt.gz 2015-04-01 15:00 200M
chainRn6Link.txt.gz 2017-03-26 19:07 291M
chainHg38Link.txt.gz 2015-04-01 15:03 734M