This directory contains a dump of the UCSC genome annotation database for
the Apr. 2009 (Broad/oryCun2) assembly of the rabbit genome (oryCun2, Broad Institute oryCun2 (NCBI project 12819, AAGW00000000)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Broad Institute of MIT and Harvard.
For more information on the rabbit genome, see the project website:
http://www.broadinstitute.org/science/projects/mammals-models/rabbit/rabbit-genome-sequencing-project
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=oryCun2
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/oryCun2/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/oryCun2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/oryCun2/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 oryCun2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql oryCun2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
The Rabbit sequence is made freely available before scientific publication
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 these data (The Broad Institute) is
properly acknowledged.
3. The center producing the data reserves the right to publish the initial
large-scale analyses of the data set, including large-scale identification
of regions of evolutionary conservation and large-scale genomic assembly.
Large-scale refers to regions with size on the order of a chromosome (that
is, 30 Mb or more).
4. Any redistribution of the data should carry this notice. 1. The data may
be freely downloaded, used in analyses, and repackaged in databases.
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
xenoRefSeqAli.txt.gz 2020-08-19 23:41 35M
xenoRefSeqAli.sql 2020-08-19 23:41 2.1K
xenoRefGene.txt.gz 2020-08-19 23:41 34M
xenoRefGene.sql 2020-08-19 23:41 2.0K
xenoRefFlat.txt.gz 2020-08-19 23:41 31M
xenoRefFlat.sql 2020-08-19 23:41 1.7K
xenoMrna.txt.gz 2020-08-19 23:14 347M
xenoMrna.sql 2020-08-19 23:14 2.1K
ucscToINSDC.txt.gz 2013-09-15 17:23 27K
ucscToINSDC.sql 2013-09-15 17:23 1.4K
ucscToEnsembl.txt.gz 2011-11-14 02:33 15K
ucscToEnsembl.sql 2011-11-14 02:33 1.3K
trackDb.txt.gz 2024-01-31 15:13 55K
trackDb.sql 2024-01-31 15:13 2.1K
tableList.txt.gz 2024-11-17 03:15 4.4K
tableList.sql 2024-11-17 03:15 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 7.3K
tableDescriptions.sql 2024-11-16 02:03 1.5K
tRNAs.txt.gz 2012-04-23 07:55 13K
tRNAs.sql 2012-04-23 07:55 1.7K
simpleRepeat.txt.gz 2010-04-26 16:56 21M
simpleRepeat.sql 2010-04-26 16:56 2.0K
seqNcbiRefSeq.txt.gz 2020-05-10 03:28 662K
seqNcbiRefSeq.sql 2020-05-10 03:28 1.5K
rmsk.txt.gz 2010-04-26 16:18 118M
rmsk.sql 2010-04-26 16:18 2.0K
refSeqAli.txt.gz 2020-08-19 23:41 146K
refSeqAli.sql 2020-08-19 23:41 2.1K
refGene.txt.gz 2020-08-19 23:41 139K
refGene.sql 2020-08-19 23:41 1.9K
refFlat.txt.gz 2020-08-19 23:41 128K
refFlat.sql 2020-08-19 23:41 1.7K
quality.txt.gz 2010-04-26 16:15 45M
quality.sql 2010-04-26 16:15 1.9K
netRn6.txt.gz 2017-03-27 20:01 48M
netRn6.sql 2017-03-27 20:00 2.1K
netMonDom5.txt.gz 2010-04-26 16:57 15M
netMonDom5.sql 2010-04-26 16:57 2.0K
netMm39.txt.gz 2020-11-25 04:28 49M
netMm39.sql 2020-11-25 04:28 2.1K
netMm10.txt.gz 2013-10-27 19:28 49M
netMm10.sql 2013-10-27 19:28 2.1K
netHg19.txt.gz 2010-04-26 16:54 58M
netHg19.sql 2010-04-26 16:53 2.3K
netCavPor3.txt.gz 2010-04-26 16:54 64M
netCavPor3.sql 2010-04-26 16:54 2.0K
nestedRepeats.txt.gz 2010-04-26 16:34 13M
nestedRepeats.sql 2010-04-26 16:34 2.0K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:28 3.3M
ncbiRefSeqPsl.sql 2020-05-10 03:28 2.1K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:28 2.6M
ncbiRefSeqPredicted.sql 2020-05-10 03:28 2.0K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:28 8.8M
ncbiRefSeqPepTable.sql 2020-05-10 03:28 1.4K
ncbiRefSeqOther.txt.gz 2020-05-10 03:28 75
ncbiRefSeqOther.sql 2020-05-10 03:28 1.3K
ncbiRefSeqLink.txt.gz 2020-05-10 03:28 1.3M
ncbiRefSeqLink.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:28 121K
ncbiRefSeqCurated.sql 2020-05-10 03:28 2.0K
ncbiRefSeqCds.txt.gz 2020-05-10 03:28 264K
ncbiRefSeqCds.sql 2020-05-10 03:28 1.3K
ncbiRefSeq.txt.gz 2020-05-10 03:28 2.7M
ncbiRefSeq.sql 2020-05-10 03:28 1.9K
mrnaOrientInfo.txt.gz 2020-08-19 23:41 82K
mrnaOrientInfo.sql 2020-08-19 23:41 1.8K
microsat.txt.gz 2015-08-23 22:48 595K
microsat.sql 2015-08-23 22:48 1.5K
intronEst.txt.gz 2016-05-15 10:55 718K
intronEst.sql 2016-05-15 10:55 2.1K
history.txt.gz 2010-04-26 16:52 828
history.sql 2010-04-26 16:52 1.6K
hgFindSpec.txt.gz 2024-01-31 15:13 1.4K
hgFindSpec.sql 2024-01-31 15:13 1.8K
grp.txt.gz 2014-03-02 04:14 208
grp.sql 2014-03-02 04:14 1.4K
gold.txt.gz 2010-04-26 16:56 1.4M
gold.sql 2010-04-26 16:56 1.7K
genscan.txt.gz 2013-12-10 03:29 3.5M
genscan.sql 2013-12-10 03:29 1.7K
geneid.txt.gz 2015-11-22 19:57 2.4M
geneid.sql 2015-11-22 19:57 1.9K
gc5Base.txt.gz 2010-04-26 16:55 11M
gc5Base.sql 2010-04-26 16:55 1.9K
gbLoaded.txt.gz 2020-08-19 23:41 110K
gbLoaded.sql 2020-08-19 23:41 1.6K
gap.txt.gz 2010-04-26 16:19 1.1M
gap.sql 2010-04-26 16:19 1.6K
extNcbiRefSeq.txt.gz 2020-05-10 03:28 91
extNcbiRefSeq.sql 2020-05-10 03:28 1.4K
estOrientInfo.txt.gz 2016-05-15 10:55 416K
estOrientInfo.sql 2016-05-15 10:55 1.8K
ensemblToGeneName.txt.gz 2021-05-25 14:41 207K
ensemblToGeneName.sql 2021-05-25 14:41 1.4K
ensemblSource.txt.gz 2021-05-25 14:43 159K
ensemblSource.sql 2021-05-25 14:43 1.4K
ensPep.txt.gz 2021-05-25 14:43 14M
ensPep.sql 2021-05-25 14:43 1.3K
ensGtp.txt.gz 2021-05-25 14:41 519K
ensGtp.sql 2021-05-25 14:41 1.4K
ensGene.txt.gz 2021-05-25 14:41 2.9M
ensGene.sql 2021-05-25 14:41 1.9K
cytoBandIdeo.txt.gz 2013-04-28 19:40 18K
cytoBandIdeo.sql 2013-04-28 19:40 1.5K
ctgPos2.txt.gz 2010-04-26 16:44 36K
ctgPos2.sql 2010-04-26 16:44 1.5K
cpgIslandExtUnmasked.txt.gz 2017-07-16 06:16 2.1M
cpgIslandExtUnmasked.sql 2017-07-16 06:16 1.7K
cpgIslandExt.txt.gz 2017-07-16 06:16 1.4M
cpgIslandExt.sql 2017-07-16 06:16 1.7K
chromInfo.txt.gz 2010-04-26 16:57 18K
chromInfo.sql 2010-04-26 16:57 1.3K
chromAlias.txt.gz 2018-08-05 08:35 17K
chromAlias.sql 2018-08-05 08:35 1.4K
chainRn6Link.txt.gz 2017-03-27 19:40 507M
chainRn6Link.sql 2017-03-27 19:34 1.5K
chainRn6.txt.gz 2017-03-27 19:32 81M
chainRn6.sql 2017-03-27 19:31 1.7K
chainMonDom5Link.txt.gz 2010-04-26 16:39 948M
chainMonDom5Link.sql 2010-04-26 16:37 1.5K
chainMonDom5.txt.gz 2010-04-26 16:17 330M
chainMonDom5.sql 2010-04-26 16:16 1.6K
chainMm39Link.txt.gz 2020-11-25 04:25 437M
chainMm39Link.sql 2020-11-25 04:25 1.6K
chainMm39.txt.gz 2020-11-25 04:22 64M
chainMm39.sql 2020-11-25 04:22 1.7K
chainMm10Link.txt.gz 2013-10-27 19:26 481M
chainMm10Link.sql 2013-10-27 19:26 1.5K
chainMm10.txt.gz 2013-10-27 19:26 78M
chainMm10.sql 2013-10-27 19:25 1.7K
chainHg19Link.txt.gz 2010-04-26 16:48 673M
chainHg19Link.sql 2010-04-26 16:47 1.5K
chainHg19.txt.gz 2010-04-26 16:15 126M
chainHg19.sql 2010-04-26 16:14 1.8K
chainCavPor3Link.txt.gz 2010-04-26 16:23 1.9G
chainCavPor3Link.sql 2010-04-26 16:19 1.5K
chainCavPor3.txt.gz 2010-04-26 16:45 515M
chainCavPor3.sql 2010-04-26 16:44 1.6K
blastHg18KG.txt.gz 2010-05-02 15:15 4.2M
blastHg18KG.sql 2010-05-02 15:15 2.1K
bigFiles.txt.gz 2024-11-17 03:15 73
bigFiles.sql 2024-11-17 03:15 1.4K
augustusGene.txt.gz 2015-07-26 17:21 2.3M
augustusGene.sql 2015-07-26 17:21 1.9K
all_mrna.txt.gz 2020-08-19 23:14 259K
all_mrna.sql 2020-08-19 23:14 2.1K
all_est.txt.gz 2016-05-15 10:55 1.3M
all_est.sql 2016-05-15 10:55 2.1K