This directory contains a dump of the UCSC genome annotation database for the
May 2017 (GRCz11/danRer11) assembly of the zebrafish genome
(danRer11, Genome Reference Consortium) .
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/1104621
http://www.ncbi.nlm.nih.gov/bioproject/11776
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=danRer11
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.soe.ucsc.edu, then go to
the directory goldenPath/danRer11/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.soe.ucsc.edu/goldenPath/danRer11/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/danRer11/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 danRer11 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql danRer11 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
-----------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-18 22:14 13M
xenoRefSeqAli.sql 2020-08-18 22:14 2.2K
xenoRefGene.txt.gz 2020-08-18 21:59 16M
xenoRefGene.sql 2020-08-18 21:59 2.0K
xenoRefFlat.txt.gz 2020-08-18 21:59 14M
xenoRefFlat.sql 2020-08-18 21:59 1.7K
xenoMrna.txt.gz 2020-08-18 21:59 153M
xenoMrna.sql 2020-08-18 21:59 2.1K
windowmaskerSdust.txt.gz 2017-11-01 13:03 99M
windowmaskerSdust.sql 2017-11-01 13:03 1.5K
ucscToRefSeq.txt.gz 2017-11-01 13:03 18K
ucscToRefSeq.sql 2017-11-01 13:03 1.4K
ucscToINSDC.txt.gz 2017-11-01 13:03 17K
ucscToINSDC.sql 2017-11-01 13:03 1.4K
ucscToEnsembl.txt.gz 2019-01-13 04:04 9.7K
ucscToEnsembl.sql 2019-01-13 04:04 1.4K
trackDb.txt.gz 2024-07-25 09:34 76K
trackDb.sql 2024-07-25 09:34 2.1K
tableList.txt.gz 2024-11-24 03:06 3.9K
tableList.sql 2024-11-24 03:06 1.6K
tableDescriptions.txt.gz 2024-11-23 02:03 6.9K
tableDescriptions.sql 2024-11-23 02:03 1.4K
simpleRepeat.txt.gz 2017-11-01 12:59 29M
simpleRepeat.sql 2017-11-01 12:59 1.9K
seqNcbiRefSeq.txt.gz 2020-05-10 03:27 922K
seqNcbiRefSeq.sql 2020-05-10 03:27 1.5K
rmsk.txt.gz 2017-11-01 12:58 113M
rmsk.sql 2017-11-01 12:58 1.9K
refSeqAli.txt.gz 2020-08-18 22:14 1.8M
refSeqAli.sql 2020-08-18 22:14 2.1K
refGene.txt.gz 2020-08-18 21:59 1.9M
refGene.sql 2020-08-18 21:59 1.9K
refFlat.txt.gz 2020-08-18 21:59 1.7M
refFlat.sql 2020-08-18 21:59 1.7K
netMm39.txt.gz 2020-11-25 02:50 6.8M
netMm39.sql 2020-11-25 02:50 2.1K
netMm10.txt.gz 2017-11-01 13:03 6.4M
netMm10.sql 2017-11-01 13:03 2.1K
netHg38.txt.gz 2017-11-01 13:03 6.6M
netHg38.sql 2017-11-01 13:03 2.1K
netGalGal6.txt.gz 2019-01-20 08:07 11M
netGalGal6.sql 2019-01-20 08:07 2.1K
nestedRepeats.txt.gz 2017-11-01 13:03 9.8M
nestedRepeats.sql 2017-11-01 13:03 1.9K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:27 5.5M
ncbiRefSeqPsl.sql 2020-05-10 03:27 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:27 3.0M
ncbiRefSeqPredicted.sql 2020-05-10 03:27 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:27 14M
ncbiRefSeqPepTable.sql 2020-05-10 03:27 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:27 76
ncbiRefSeqOther.sql 2020-05-10 03:27 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:27 2.4M
ncbiRefSeqLink.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:27 1.9M
ncbiRefSeqCurated.sql 2020-05-10 03:27 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:27 370K
ncbiRefSeqCds.sql 2020-05-10 03:27 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:27 4.4M
ncbiRefSeq.sql 2020-05-10 03:27 1.9K
mrnaOrientInfo.txt.gz 2020-08-18 22:14 869K
mrnaOrientInfo.sql 2020-08-18 22:14 1.8K
mmBlastTab.txt.gz 2022-07-12 17:09 348K
mmBlastTab.sql 2022-07-12 17:09 1.7K
microsat.txt.gz 2017-11-01 13:02 1.2M
microsat.sql 2017-11-01 13:02 1.5K
intronEst.txt.gz 2017-11-26 06:40 59M
intronEst.sql 2017-11-26 06:40 2.1K
history.txt.gz 2017-11-01 13:05 606
history.sql 2017-11-01 13:05 1.6K
hgFindSpec.txt.gz 2024-07-25 09:34 1.3K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgBlastTab.txt.gz 2022-07-12 17:02 356K
hgBlastTab.sql 2022-07-12 17:02 1.7K
grp.txt.gz 2017-11-01 13:04 213
grp.sql 2017-11-01 13:04 1.3K
grcIncidentDb.txt.gz 2019-09-22 03:19 78
grcIncidentDb.sql 2019-09-22 03:19 1.3K
gold.txt.gz 2017-11-01 13:03 657K
gold.sql 2017-11-01 13:03 1.7K
genscanSubopt.txt.gz 2017-11-01 13:04 3.9M
genscanSubopt.sql 2017-11-01 13:04 1.6K
genscan.txt.gz 2017-11-01 13:04 2.5M
genscan.sql 2017-11-01 13:04 1.7K
gc5BaseBw.txt.gz 2017-11-01 13:04 67
gc5BaseBw.sql 2017-11-01 13:04 1.3K
gbLoaded.txt.gz 2020-08-18 22:17 28K
gbLoaded.sql 2020-08-18 22:17 1.6K
gap.txt.gz 2017-11-01 13:03 196K
gap.sql 2017-11-01 13:03 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:27 92
extNcbiRefSeq.sql 2020-05-10 03:27 1.4K
estOrientInfo.txt.gz 2017-11-26 06:41 20M
estOrientInfo.sql 2017-11-26 06:41 1.8K
ensemblToGeneName.txt.gz 2019-02-10 03:41 451K
ensemblToGeneName.sql 2019-02-10 03:41 1.4K
ensemblSource.txt.gz 2019-02-10 03:41 200K
ensemblSource.sql 2019-02-10 03:41 1.4K
ensemblLift.txt.gz 2019-01-13 04:04 6.8K
ensemblLift.sql 2019-01-13 04:04 1.4K
ensPep.txt.gz 2019-02-10 03:41 15M
ensPep.sql 2019-02-10 03:41 1.3K
ensGtp.txt.gz 2019-02-10 03:41 687K
ensGtp.sql 2019-02-10 03:41 1.4K
ensGene.txt.gz 2019-02-10 03:41 3.8M
ensGene.sql 2019-02-10 03:41 1.9K
cytoBandIdeo.txt.gz 2017-11-01 13:03 13K
cytoBandIdeo.sql 2017-11-01 13:03 1.5K
crisprAllTargets.txt.gz 2023-11-06 10:50 70
crisprAllTargets.sql 2023-11-06 10:50 1.3K
cpgIslandExtUnmasked.txt.gz 2017-11-01 13:03 1.1M
cpgIslandExtUnmasked.sql 2017-11-01 13:03 1.7K
cpgIslandExt.txt.gz 2017-11-01 13:03 287K
cpgIslandExt.sql 2017-11-01 13:03 1.7K
chromInfo.txt.gz 2017-11-01 13:03 14K
chromInfo.sql 2017-11-01 13:03 1.4K
chromAlias.txt.gz 2018-08-05 06:11 20K
chromAlias.sql 2018-08-05 06:11 1.4K
chainMm39Link.txt.gz 2020-11-25 02:49 41M
chainMm39Link.sql 2020-11-25 02:49 1.6K
chainMm39.txt.gz 2020-11-25 02:48 11M
chainMm39.sql 2020-11-25 02:48 1.7K
chainMm10Link.txt.gz 2017-11-01 13:03 83M
chainMm10Link.sql 2017-11-01 13:03 1.5K
chainMm10.txt.gz 2017-11-01 13:02 33M
chainMm10.sql 2017-11-01 13:02 1.7K
chainHg38Link.txt.gz 2017-11-01 13:01 554M
chainHg38Link.sql 2017-11-01 13:00 1.5K
chainHg38.txt.gz 2017-11-01 12:59 239M
chainHg38.sql 2017-11-01 12:59 1.7K
chainGalGal6Link.txt.gz 2019-01-20 08:06 96M
chainGalGal6Link.sql 2019-01-20 08:06 1.6K
chainGalGal6.txt.gz 2019-01-20 08:06 26M
chainGalGal6.sql 2019-01-20 08:06 1.7K
bigFiles.txt.gz 2024-11-24 03:06 145
bigFiles.sql 2024-11-24 03:06 1.4K
augustusGene.txt.gz 2017-11-01 12:58 3.3M
augustusGene.sql 2017-11-01 12:58 1.9K
all_mrna.txt.gz 2020-08-18 21:59 2.8M
all_mrna.sql 2020-08-18 21:59 2.1K
all_est.txt.gz 2017-11-26 06:40 84M
all_est.sql 2017-11-26 06:40 2.1K