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 -
xenoRefSeqAli.txt.gz 09-Jul-2017 12:51 19M
xenoRefSeqAli.sql 09-Jul-2017 12:51 2.1K
xenoRefGene.txt.gz 09-Jul-2017 12:52 20M
xenoRefGene.sql 09-Jul-2017 12:52 1.9K
xenoRefFlat.txt.gz 09-Jul-2017 12:52 18M
xenoRefFlat.sql 09-Jul-2017 12:52 1.7K
xenoMrna.txt.gz 09-Jul-2017 12:50 202M
xenoMrna.sql 09-Jul-2017 12:50 2.1K
windowmaskerSdust.txt.gz 17-Jun-2012 20:43 127M
windowmaskerSdust.sql 17-Jun-2012 20:45 1.4K
ucscToINSDC.txt.gz 15-Sep-2013 19:12 22K
ucscToINSDC.sql 15-Sep-2013 19:12 1.4K
trackDb.txt.gz 16-Jul-2017 06:16 42K
trackDb.sql 16-Jul-2017 06:16 2.0K
tableList.txt.gz 16-Jul-2017 06:16 3.5K
tableList.sql 16-Jul-2017 06:16 1.5K
tableDescriptions.txt.gz 16-Jul-2017 06:16 5.6K
tableDescriptions.sql 16-Jul-2017 06:16 1.4K
simpleRepeat.txt.gz 17-Jun-2012 21:37 36M
simpleRepeat.sql 17-Jun-2012 21:37 1.9K
rmsk.txt.gz 17-Jun-2012 21:30 123M
rmsk.sql 17-Jun-2012 21:29 1.8K
refSeqAli.txt.gz 09-Jul-2017 12:51 1.8M
refSeqAli.sql 09-Jul-2017 12:51 2.1K
refGene.txt.gz 09-Jul-2017 12:52 1.9M
refGene.sql 09-Jul-2017 12:52 1.9K
refFlat.txt.gz 09-Jul-2017 12:52 1.7M
refFlat.sql 09-Jul-2017 12:52 1.7K
phyloP13way.txt.gz 22-Jun-2014 17:03 72M
phyloP13way.sql 22-Jun-2014 17:03 1.8K
phastConsElements13way.txt.gz 22-Jun-2014 17:02 16M
phastConsElements13way.sql 22-Jun-2014 17:02 1.6K
phastCons13way.txt.gz 22-Jun-2014 17:02 65M
phastCons13way.sql 22-Jun-2014 17:02 1.8K
netRheMac3.txt.gz 02-Dec-2012 21:09 51M
netRheMac3.sql 02-Dec-2012 21:09 2.1K
netPanTro4.txt.gz 26-Jan-2014 18:32 51M
netPanTro4.sql 26-Jan-2014 18:32 2.1K
netMm10.txt.gz 17-Jun-2012 20:48 56M
netMm10.sql 17-Jun-2012 20:47 2.0K
nestedRepeats.txt.gz 17-Jun-2012 21:33 11M
nestedRepeats.sql 17-Jun-2012 21:33 1.9K
multiz13waySummary.txt.gz 22-Jun-2014 17:02 30M
multiz13waySummary.sql 22-Jun-2014 17:02 1.6K
multiz13wayFrames.txt.gz 22-Jun-2014 17:02 23M
multiz13wayFrames.sql 22-Jun-2014 17:02 1.7K
multiz13way.txt.gz 22-Jun-2014 17:01 207M
multiz13way.sql 22-Jun-2014 17:01 1.5K
mrnaOrientInfo.txt.gz 09-Jul-2017 12:51 1.6M
mrnaOrientInfo.sql 09-Jul-2017 12:51 1.8K
microsat.txt.gz 24-Aug-2015 01:15 2.2M
microsat.sql 24-Aug-2015 01:15 1.5K
mgcGenes.txt.gz 15-May-2016 11:26 654K
mgcGenes.sql 15-May-2016 11:26 1.9K
mgcFullMrna.txt.gz 15-May-2016 11:26 666K
mgcFullMrna.sql 15-May-2016 11:26 2.1K
locusName.txt.gz 06-Nov-2016 09:26 3.4M
locusName.sql 06-Nov-2016 09:26 1.5K
intronEst.txt.gz 15-May-2016 11:27 24M
intronEst.sql 15-May-2016 11:27 2.1K
history.txt.gz 17-Jun-2012 21:29 391
history.sql 17-Jun-2012 21:29 1.5K
hgFindSpec.txt.gz 16-Jul-2017 06:16 863
hgFindSpec.sql 16-Jul-2017 06:16 1.7K
grp.txt.gz 02-Mar-2014 04:14 208
grp.sql 02-Mar-2014 04:14 1.3K
gold.txt.gz 17-Jun-2012 21:33 2.0M
gold.sql 17-Jun-2012 21:33 1.6K
genscanSubopt.txt.gz 11-Jun-2012 07:54 6.6M
genscanSubopt.sql 11-Jun-2012 07:53 1.5K
genscan.txt.gz 17-Jun-2012 21:29 3.1M
genscan.sql 17-Jun-2012 21:29 1.6K
gc5BaseBw.txt.gz 17-Jun-2012 21:28 59
gc5BaseBw.sql 17-Jun-2012 21:28 1.2K
gbLoaded.txt.gz 09-Jul-2017 12:52 17K
gbLoaded.sql 09-Jul-2017 12:52 1.6K
gap.txt.gz 17-Jun-2012 21:32 2.9M
gap.sql 17-Jun-2012 21:32 1.5K
extFile.txt.gz 22-Jun-2014 17:01 77
extFile.sql 22-Jun-2014 17:01 1.4K
estOrientInfo.txt.gz 15-May-2016 11:26 13M
estOrientInfo.sql 15-May-2016 11:26 1.8K
ensemblToGeneName.txt.gz 09-Feb-2015 04:17 230K
ensemblToGeneName.sql 09-Feb-2015 04:17 1.4K
ensemblSource.txt.gz 09-Feb-2015 04:17 89K
ensemblSource.sql 09-Feb-2015 04:17 1.3K
ensPep.txt.gz 09-Feb-2015 04:16 7.5M
ensPep.sql 09-Feb-2015 04:16 1.3K
ensGtp.txt.gz 09-Feb-2015 04:17 308K
ensGtp.sql 09-Feb-2015 04:17 1.4K
ensGene.txt.gz 09-Feb-2015 04:18 2.4M
ensGene.sql 09-Feb-2015 04:18 1.9K
cytoBandIdeo.txt.gz 28-Jul-2013 06:10 17K
cytoBandIdeo.sql 28-Jul-2013 06:10 1.5K
cytoBand.txt.gz 28-Jul-2013 06:10 2.3K
cytoBand.sql 28-Jul-2013 06:10 1.5K
crisprTargets.txt.gz 06-Nov-2016 09:26 59
crisprTargets.sql 06-Nov-2016 09:26 1.3K
crisprRanges.txt.gz 06-Nov-2016 09:26 1.3M
crisprRanges.sql 06-Nov-2016 09:26 1.4K
cpgIslandExtUnmasked.txt.gz 01-Jun-2014 19:35 447K
cpgIslandExtUnmasked.sql 01-Jun-2014 19:35 1.7K
cpgIslandExt.txt.gz 17-Jun-2012 21:34 378K
cpgIslandExt.sql 17-Jun-2012 21:34 1.6K
chromInfo.txt.gz 17-Jun-2012 21:36 16K
chromInfo.sql 17-Jun-2012 21:36 1.3K
chainRheMac3Link.txt.gz 02-Dec-2012 21:07 444M
chainRheMac3Link.sql 02-Dec-2012 21:07 1.5K
chainRheMac3.txt.gz 02-Dec-2012 21:09 51M
chainRheMac3.sql 02-Dec-2012 21:09 1.7K
chainPanTro4Link.txt.gz 26-Jan-2014 18:30 485M
chainPanTro4Link.sql 26-Jan-2014 18:29 1.5K
chainPanTro4.txt.gz 26-Jan-2014 18:29 56M
chainPanTro4.sql 26-Jan-2014 18:29 1.7K
chainMm10Link.txt.gz 17-Jun-2012 20:59 1.0G
chainMm10Link.sql 17-Jun-2012 20:52 1.5K
chainMm10.txt.gz 17-Jun-2012 21:30 179M
chainMm10.sql 17-Jun-2012 21:29 1.6K
bigFiles.txt.gz 16-Jul-2017 06:16 86
bigFiles.sql 16-Jul-2017 06:16 1.3K
augustusGene.txt.gz 26-Jul-2015 17:21 2.4M
augustusGene.sql 26-Jul-2015 17:21 1.9K
all_mrna.txt.gz 09-Jul-2017 12:52 4.0M
all_mrna.sql 09-Jul-2017 12:52 2.1K
all_est.txt.gz 15-May-2016 11:25 46M
all_est.sql 15-May-2016 11:25 2.1K