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;'
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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 -
genscanSubopt.sql 2012-06-11 07:53 1.5K
genscanSubopt.txt.gz 2012-06-11 07:54 6.6M
windowmaskerSdust.txt.gz 2012-06-17 20:43 127M
windowmaskerSdust.sql 2012-06-17 20:45 1.4K
netMm10.sql 2012-06-17 20:47 2.0K
netMm10.txt.gz 2012-06-17 20:48 56M
chainMm10Link.sql 2012-06-17 20:52 1.5K
chainMm10Link.txt.gz 2012-06-17 20:59 1.0G
gc5BaseBw.sql 2012-06-17 21:28 1.2K
gc5BaseBw.txt.gz 2012-06-17 21:28 59
chainMm10.sql 2012-06-17 21:29 1.6K
genscan.sql 2012-06-17 21:29 1.6K
genscan.txt.gz 2012-06-17 21:29 3.1M
history.sql 2012-06-17 21:29 1.5K
history.txt.gz 2012-06-17 21:29 391
rmsk.sql 2012-06-17 21:29 1.8K
rmsk.txt.gz 2012-06-17 21:30 123M
chainMm10.txt.gz 2012-06-17 21:30 179M
gap.sql 2012-06-17 21:32 1.5K
gap.txt.gz 2012-06-17 21:32 2.9M
gold.sql 2012-06-17 21:33 1.6K
gold.txt.gz 2012-06-17 21:33 2.0M
nestedRepeats.sql 2012-06-17 21:33 1.9K
nestedRepeats.txt.gz 2012-06-17 21:33 11M
cpgIslandExt.sql 2012-06-17 21:34 1.6K
cpgIslandExt.txt.gz 2012-06-17 21:34 378K
chromInfo.sql 2012-06-17 21:36 1.3K
chromInfo.txt.gz 2012-06-17 21:36 16K
simpleRepeat.sql 2012-06-17 21:37 1.9K
simpleRepeat.txt.gz 2012-06-17 21:37 36M
chainRheMac3Link.sql 2012-12-02 21:07 1.5K
chainRheMac3Link.txt.gz 2012-12-02 21:07 444M
chainRheMac3.sql 2012-12-02 21:09 1.7K
chainRheMac3.txt.gz 2012-12-02 21:09 51M
netRheMac3.sql 2012-12-02 21:09 2.1K
netRheMac3.txt.gz 2012-12-02 21:09 51M
cytoBand.sql 2013-07-28 06:10 1.5K
cytoBand.txt.gz 2013-07-28 06:10 2.3K
cytoBandIdeo.sql 2013-07-28 06:10 1.5K
cytoBandIdeo.txt.gz 2013-07-28 06:10 17K
ucscToINSDC.sql 2013-09-15 19:12 1.4K
ucscToINSDC.txt.gz 2013-09-15 19:12 22K
chainPanTro4.sql 2014-01-26 18:29 1.7K
chainPanTro4.txt.gz 2014-01-26 18:29 56M
chainPanTro4Link.sql 2014-01-26 18:29 1.5K
chainPanTro4Link.txt.gz 2014-01-26 18:30 485M
netPanTro4.sql 2014-01-26 18:32 2.1K
netPanTro4.txt.gz 2014-01-26 18:32 51M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
cpgIslandExtUnmasked.sql 2014-06-01 19:35 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:35 447K
extFile.sql 2014-06-22 17:01 1.4K
extFile.txt.gz 2014-06-22 17:01 77
multiz13way.sql 2014-06-22 17:01 1.5K
multiz13way.txt.gz 2014-06-22 17:01 207M
multiz13wayFrames.sql 2014-06-22 17:02 1.7K
multiz13wayFrames.txt.gz 2014-06-22 17:02 23M
multiz13waySummary.sql 2014-06-22 17:02 1.6K
multiz13waySummary.txt.gz 2014-06-22 17:02 30M
phastCons13way.sql 2014-06-22 17:02 1.8K
phastCons13way.txt.gz 2014-06-22 17:02 65M
phastConsElements13way.sql 2014-06-22 17:02 1.6K
phastConsElements13way.txt.gz 2014-06-22 17:02 16M
phyloP13way.sql 2014-06-22 17:03 1.8K
phyloP13way.txt.gz 2014-06-22 17:03 72M
ensPep.sql 2015-02-09 04:16 1.3K
ensPep.txt.gz 2015-02-09 04:16 7.5M
ensGtp.sql 2015-02-09 04:17 1.4K
ensGtp.txt.gz 2015-02-09 04:17 308K
ensemblSource.sql 2015-02-09 04:17 1.3K
ensemblSource.txt.gz 2015-02-09 04:17 89K
ensemblToGeneName.sql 2015-02-09 04:17 1.4K
ensemblToGeneName.txt.gz 2015-02-09 04:17 230K
ensGene.sql 2015-02-09 04:18 1.9K
ensGene.txt.gz 2015-02-09 04:18 2.4M
augustusGene.sql 2015-07-26 17:21 1.9K
augustusGene.txt.gz 2015-07-26 17:21 2.4M
microsat.sql 2015-08-24 01:15 1.5K
microsat.txt.gz 2015-08-24 01:15 2.2M
all_est.sql 2016-05-15 11:25 2.1K
all_est.txt.gz 2016-05-15 11:25 46M
estOrientInfo.sql 2016-05-15 11:26 1.8K
estOrientInfo.txt.gz 2016-05-15 11:26 13M
intronEst.sql 2016-05-15 11:27 2.1K
intronEst.txt.gz 2016-05-15 11:27 24M
chromAlias.sql 2016-09-15 18:03 1.4K
chromAlias.txt.gz 2016-09-15 18:03 1.1K
crisprRanges.sql 2016-11-06 09:26 1.4K
crisprRanges.txt.gz 2016-11-06 09:26 1.3M
crisprTargets.sql 2016-11-06 09:26 1.3K
crisprTargets.txt.gz 2016-11-06 09:26 59
locusName.sql 2016-11-06 09:26 1.5K
locusName.txt.gz 2016-11-06 09:26 3.4M
mgcFullMrna.sql 2020-03-01 08:51 2.1K
mgcFullMrna.txt.gz 2020-03-01 08:51 666K
mgcGenes.sql 2020-03-01 08:52 1.9K
mgcGenes.txt.gz 2020-03-01 08:52 614K
all_mrna.sql 2020-08-20 08:23 2.1K
all_mrna.txt.gz 2020-08-20 08:23 4.1M
xenoMrna.sql 2020-08-20 08:23 2.1K
xenoMrna.txt.gz 2020-08-20 08:23 236M
refGene.sql 2020-08-20 08:47 1.9K
refGene.txt.gz 2020-08-20 08:47 1.9M
refFlat.sql 2020-08-20 08:47 1.7K
refFlat.txt.gz 2020-08-20 08:47 1.7M
xenoRefGene.sql 2020-08-20 08:47 1.9K
xenoRefGene.txt.gz 2020-08-20 08:47 24M
xenoRefFlat.sql 2020-08-20 08:47 1.7K
xenoRefFlat.txt.gz 2020-08-20 08:47 22M
mrnaOrientInfo.sql 2020-08-20 08:47 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 08:47 1.7M
refSeqAli.sql 2020-08-20 08:47 2.1K
refSeqAli.txt.gz 2020-08-20 08:47 1.8M
xenoRefSeqAli.sql 2020-08-20 08:47 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 08:47 24M
gbLoaded.sql 2020-08-20 08:47 1.6K
gbLoaded.txt.gz 2020-08-20 08:47 44K
trackDb_pushedout.sql 2023-09-18 17:06 2.1K
trackDb_pushedout.txt.gz 2023-09-18 17:06 49K
hgFindSpec_pushedout.sql 2023-09-18 17:06 1.8K
hgFindSpec_pushedout.txt.gz 2023-09-18 17:06 1.0K
trackDb.sql 2023-09-19 16:08 2.1K
trackDb.txt.gz 2023-09-19 16:08 49K
hgFindSpec.sql 2023-09-19 16:08 1.8K
hgFindSpec.txt.gz 2023-09-19 16:08 1.0K
tableDescriptions.sql 2024-04-13 02:04 1.5K
tableDescriptions.txt.gz 2024-04-13 02:04 6.7K
tableList.sql 2024-04-14 03:35 1.6K
tableList.txt.gz 2024-04-14 03:35 3.8K
bigFiles.sql 2024-04-14 03:35 1.4K
bigFiles.txt.gz 2024-04-14 03:35 86