This directory contains a dump of the UCSC genome annotation database for
the Mar. 2012 (RGSC 5.0/rn5) assembly of the rat genome
(rn5, RGSC Rnor_5.0 (GCA_000001895.3)) from the
Rat Genome Sequencing 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/73
http://www.ncbi.nlm.nih.gov/genome/assembly/382928
http://www.ncbi.nlm.nih.gov/bioproject/16219
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=rn5
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/rn5/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/rn5/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn5/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 rn5 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rn5 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
------------------------------------------------------------------
These data are made 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 providers of this data (the Rat
Genome Sequencing Consortium) are properly acknowledged.
3. The Centers producing the data reserve the right to publish the
initial large-scale analyses of the dataset, 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. This is in accordance with, and with the understandings in the Fort
Lauderdale meeting discussing Community Resource Projects (see
http://www.wellcome.ac.uk/en/1/awtpubrepdat.html) and the resulting
NHGRI policy statement
(http://www.genome.gov/page.cfm?pageID=10506537).
5. Any redistribution of the data should carry this notice.
Name Last modified Size Description
Parent Directory -
chainMm10Link.txt.gz 2012-06-17 20:59 1.0G
chainPanTro4Link.txt.gz 2014-01-26 18:30 485M
chainRheMac3Link.txt.gz 2012-12-02 21:07 444M
xenoMrna.txt.gz 2020-08-20 08:23 236M
multiz13way.txt.gz 2014-06-22 17:01 207M
chainMm10.txt.gz 2012-06-17 21:30 179M
windowmaskerSdust.txt.gz 2012-06-17 20:43 127M
rmsk.txt.gz 2012-06-17 21:30 123M
phyloP13way.txt.gz 2014-06-22 17:03 72M
phastCons13way.txt.gz 2014-06-22 17:02 65M
netMm10.txt.gz 2012-06-17 20:48 56M
chainPanTro4.txt.gz 2014-01-26 18:29 56M
netPanTro4.txt.gz 2014-01-26 18:32 51M
netRheMac3.txt.gz 2012-12-02 21:09 51M
chainRheMac3.txt.gz 2012-12-02 21:09 51M
all_est.txt.gz 2016-05-15 11:25 46M
simpleRepeat.txt.gz 2012-06-17 21:37 36M
multiz13waySummary.txt.gz 2014-06-22 17:02 30M
xenoRefSeqAli.txt.gz 2020-08-20 08:47 24M
xenoRefGene.txt.gz 2020-08-20 08:47 24M
intronEst.txt.gz 2016-05-15 11:27 24M
multiz13wayFrames.txt.gz 2014-06-22 17:02 23M
xenoRefFlat.txt.gz 2020-08-20 08:47 22M
phastConsElements13way.txt.gz 2014-06-22 17:02 16M
estOrientInfo.txt.gz 2016-05-15 11:26 13M
nestedRepeats.txt.gz 2012-06-17 21:33 11M
ensPep.txt.gz 2015-02-09 04:16 7.5M
genscanSubopt.txt.gz 2012-06-11 07:54 6.6M
all_mrna.txt.gz 2020-08-20 08:23 4.1M
locusName.txt.gz 2016-11-06 09:26 3.4M
genscan.txt.gz 2012-06-17 21:29 3.1M
gap.txt.gz 2012-06-17 21:32 2.9M
ensGene.txt.gz 2015-02-09 04:18 2.4M
augustusGene.txt.gz 2015-07-26 17:21 2.4M
microsat.txt.gz 2015-08-24 01:15 2.2M
gold.txt.gz 2012-06-17 21:33 2.0M
refGene.txt.gz 2020-08-20 08:47 1.9M
refSeqAli.txt.gz 2020-08-20 08:47 1.8M
refFlat.txt.gz 2020-08-20 08:47 1.7M
mrnaOrientInfo.txt.gz 2020-08-20 08:47 1.7M
crisprRanges.txt.gz 2016-11-06 09:26 1.3M
mgcFullMrna.txt.gz 2020-03-01 08:51 666K
mgcGenes.txt.gz 2020-03-01 08:52 614K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:35 447K
cpgIslandExt.txt.gz 2012-06-17 21:34 378K
ensGtp.txt.gz 2015-02-09 04:17 308K
ensemblToGeneName.txt.gz 2015-02-09 04:17 230K
ensemblSource.txt.gz 2015-02-09 04:17 89K
trackDb.txt.gz 2024-07-25 09:34 60K
gbLoaded.txt.gz 2020-08-20 08:47 44K
ucscToINSDC.txt.gz 2013-09-15 19:12 22K
cytoBandIdeo.txt.gz 2013-07-28 06:10 17K
chromInfo.txt.gz 2012-06-17 21:36 16K
tableDescriptions.txt.gz 2024-12-07 02:03 6.7K
tableList.txt.gz 2024-12-08 03:34 3.6K
cytoBand.txt.gz 2013-07-28 06:10 2.3K
xenoRefSeqAli.sql 2020-08-20 08:47 2.1K
refSeqAli.sql 2020-08-20 08:47 2.1K
xenoMrna.sql 2020-08-20 08:23 2.1K
all_mrna.sql 2020-08-20 08:23 2.1K
mgcFullMrna.sql 2020-03-01 08:51 2.1K
intronEst.sql 2016-05-15 11:27 2.1K
all_est.sql 2016-05-15 11:25 2.1K
netRheMac3.sql 2012-12-02 21:09 2.1K
netPanTro4.sql 2014-01-26 18:32 2.1K
trackDb.sql 2024-07-25 09:34 2.1K
netMm10.sql 2012-06-17 20:47 2.0K
xenoRefGene.sql 2020-08-20 08:47 1.9K
refGene.sql 2020-08-20 08:47 1.9K
augustusGene.sql 2015-07-26 17:21 1.9K
mgcGenes.sql 2020-03-01 08:52 1.9K
ensGene.sql 2015-02-09 04:18 1.9K
nestedRepeats.sql 2012-06-17 21:33 1.9K
simpleRepeat.sql 2012-06-17 21:37 1.9K
mrnaOrientInfo.sql 2020-08-20 08:47 1.8K
rmsk.sql 2012-06-17 21:29 1.8K
hgFindSpec.sql 2024-07-25 09:34 1.8K
phastCons13way.sql 2014-06-22 17:02 1.8K
estOrientInfo.sql 2016-05-15 11:26 1.8K
phyloP13way.sql 2014-06-22 17:03 1.8K
xenoRefFlat.sql 2020-08-20 08:47 1.7K
multiz13wayFrames.sql 2014-06-22 17:02 1.7K
refFlat.sql 2020-08-20 08:47 1.7K
chainRheMac3.sql 2012-12-02 21:09 1.7K
cpgIslandExtUnmasked.sql 2014-06-01 19:35 1.7K
chainPanTro4.sql 2014-01-26 18:29 1.7K
chainMm10.sql 2012-06-17 21:29 1.6K
cpgIslandExt.sql 2012-06-17 21:34 1.6K
genscan.sql 2012-06-17 21:29 1.6K
gbLoaded.sql 2020-08-20 08:47 1.6K
gold.sql 2012-06-17 21:33 1.6K
tableList.sql 2024-12-08 03:34 1.6K
multiz13waySummary.sql 2014-06-22 17:02 1.6K
phastConsElements13way.sql 2014-06-22 17:02 1.6K
chainRheMac3Link.sql 2012-12-02 21:07 1.5K
chainPanTro4Link.sql 2014-01-26 18:29 1.5K
multiz13way.sql 2014-06-22 17:01 1.5K
gap.sql 2012-06-17 21:32 1.5K
cytoBandIdeo.sql 2013-07-28 06:10 1.5K
cytoBand.sql 2013-07-28 06:10 1.5K
history.sql 2012-06-17 21:29 1.5K
genscanSubopt.sql 2012-06-11 07:53 1.5K
locusName.sql 2016-11-06 09:26 1.5K
microsat.sql 2015-08-24 01:15 1.5K
chainMm10Link.sql 2012-06-17 20:52 1.5K
tableDescriptions.sql 2024-12-07 02:03 1.5K
chromAlias.sql 2016-09-15 18:03 1.4K
windowmaskerSdust.sql 2012-06-17 20:45 1.4K
crisprRanges.sql 2016-11-06 09:26 1.4K
ensGtp.sql 2015-02-09 04:17 1.4K
ucscToINSDC.sql 2013-09-15 19:12 1.4K
extFile.sql 2014-06-22 17:01 1.4K
bigFiles.sql 2024-12-08 03:34 1.4K
ensemblToGeneName.sql 2015-02-09 04:17 1.4K
ensemblSource.sql 2015-02-09 04:17 1.3K
grp.sql 2014-03-02 04:14 1.3K
ensPep.sql 2015-02-09 04:16 1.3K
chromInfo.sql 2012-06-17 21:36 1.3K
crisprTargets.sql 2016-11-06 09:26 1.3K
gc5BaseBw.sql 2012-06-17 21:28 1.2K
chromAlias.txt.gz 2016-09-15 18:03 1.1K
hgFindSpec.txt.gz 2024-07-25 09:34 1.0K
history.txt.gz 2012-06-17 21:29 391
grp.txt.gz 2014-03-02 04:14 208
bigFiles.txt.gz 2024-12-08 03:34 86
extFile.txt.gz 2014-06-22 17:01 77
gc5BaseBw.txt.gz 2012-06-17 21:28 59
crisprTargets.txt.gz 2016-11-06 09:26 59