This directory contains a dump of the UCSC genome annotation database for the
Jul. 2014 (RGSC 6.0/rn6) assembly of the rat genome
(rn6, RGSC Rnor_6.0)
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/assembly/GCA_000001895.4/
http://www.ncbi.nlm.nih.gov/bioproject/10629
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=rn6
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/rn6/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/rn6/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/rn6/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 rn6 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql rn6 --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 -
chromInfo.sql 2014-07-31 16:12 1.4K
chromInfo.txt.gz 2014-07-31 16:12 6.8K
cpgIslandExt.sql 2014-07-31 16:12 1.7K
cpgIslandExt.txt.gz 2014-07-31 16:12 411K
cpgIslandExtUnmasked.sql 2014-07-31 16:13 1.7K
cpgIslandExtUnmasked.txt.gz 2014-07-31 16:13 503K
genscanSubopt.sql 2014-07-31 16:13 1.6K
genscanSubopt.txt.gz 2014-07-31 16:13 6.9M
gold.sql 2014-07-31 16:13 1.7K
gold.txt.gz 2014-07-31 16:13 1.4M
gap.sql 2014-07-31 16:14 1.6K
gap.txt.gz 2014-07-31 16:14 1.7M
nestedRepeats.sql 2014-07-31 16:14 1.9K
nestedRepeats.txt.gz 2014-07-31 16:14 12M
history.sql 2014-07-31 16:14 1.6K
history.txt.gz 2014-07-31 16:14 413
gc5BaseBw.sql 2014-07-31 16:16 1.3K
gc5BaseBw.txt.gz 2014-07-31 16:16 62
genscan.sql 2014-07-31 16:16 1.7K
genscan.txt.gz 2014-07-31 16:16 3.2M
rmsk.sql 2014-07-31 16:16 1.9K
rmsk.txt.gz 2014-07-31 16:17 132M
simpleRepeat.sql 2014-07-31 16:17 1.9K
simpleRepeat.txt.gz 2014-07-31 16:17 40M
ucscToINSDC.sql 2014-07-31 16:17 1.4K
ucscToINSDC.txt.gz 2014-07-31 16:17 8.4K
windowmaskerSdust.sql 2014-07-31 16:17 1.5K
windowmaskerSdust.txt.gz 2014-07-31 16:17 133M
grp.sql 2014-08-03 13:05 1.3K
grp.txt.gz 2014-08-03 13:05 200
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.4M
microsat.sql 2015-08-24 01:23 1.5K
microsat.txt.gz 2015-08-24 01:23 2.3M
sgpGene.sql 2015-08-31 07:00 1.9K
sgpGene.txt.gz 2015-08-31 07:00 2.5M
geneid.sql 2015-11-22 21:02 1.9K
geneid.txt.gz 2015-11-22 21:02 2.5M
all_est.sql 2016-07-10 09:32 2.1K
all_est.txt.gz 2016-07-10 09:32 50M
estOrientInfo.sql 2016-07-10 09:33 1.8K
estOrientInfo.txt.gz 2016-07-10 09:33 15M
intronEst.sql 2016-07-10 09:33 2.1K
intronEst.txt.gz 2016-07-10 09:33 25M
cloneEndRNB1.sql 2016-07-10 09:33 1.8K
cloneEndRNB1.txt.gz 2016-07-10 09:33 3.1M
cloneEndCH230.sql 2016-07-10 09:33 1.8K
cloneEndCH230.txt.gz 2016-07-10 09:33 2.0M
cloneEndRNB2.sql 2016-07-10 09:33 1.8K
cloneEndRNB2.txt.gz 2016-07-10 09:33 2.3M
cloneEndmultipleMaps.sql 2016-07-10 09:33 1.8K
cloneEndmultipleMaps.txt.gz 2016-07-10 09:33 163K
cloneEndRP32.sql 2016-07-10 09:33 1.8K
cloneEndRP32.txt.gz 2016-07-10 09:33 2.9K
cloneEndbadEnds.sql 2016-07-10 09:33 1.8K
cloneEndbadEnds.txt.gz 2016-07-10 09:33 573K
cloneEndcoverageForward.sql 2016-07-10 09:33 1.3K
cloneEndcoverageForward.txt.gz 2016-07-10 09:33 90
cloneEndcoverageReverse.sql 2016-07-10 09:33 1.3K
cloneEndcoverageReverse.txt.gz 2016-07-10 09:33 89
ensToRgd.sql 2016-08-28 08:08 1.4K
ensToRgd.txt.gz 2016-08-28 08:08 205K
chainGalGal5.sql 2016-09-18 11:10 1.7K
chainGalGal5.txt.gz 2016-09-18 11:10 14M
chainGalGal5Link.sql 2016-09-18 11:10 1.5K
chainGalGal5Link.txt.gz 2016-09-18 11:10 95M
netGalGal5.sql 2016-09-18 11:10 2.1K
netGalGal5.txt.gz 2016-09-18 11:10 10M
cytoBandIdeo.sql 2017-03-20 14:10 1.4K
cytoBandIdeo.txt.gz 2017-03-20 14:10 8.4K
chainAilMel1.sql 2017-03-20 14:21 1.7K
chainAilMel1.txt.gz 2017-03-20 14:21 53M
chainAilMel1Link.sql 2017-03-20 14:22 1.5K
chainAilMel1Link.txt.gz 2017-03-20 14:24 462M
chainBosTau8.sql 2017-03-20 14:41 1.7K
chainBosTau8.txt.gz 2017-03-20 14:42 115M
chainBosTau8Link.sql 2017-03-20 14:43 1.5K
chainBosTau8Link.txt.gz 2017-03-20 14:47 656M
chainCalMil1.sql 2017-03-20 15:09 1.7K
chainCalMil1.txt.gz 2017-03-20 15:09 79M
chainCalMil1Link.sql 2017-03-20 15:11 1.5K
chainCalMil1Link.txt.gz 2017-03-20 15:13 309M
chainCanFam3.sql 2017-03-20 15:25 1.7K
chainCanFam3.txt.gz 2017-03-20 15:26 61M
chainCanFam3Link.sql 2017-03-20 15:27 1.5K
chainCanFam3Link.txt.gz 2017-03-20 15:30 487M
chainCavPor3.sql 2017-03-20 15:47 1.7K
chainCavPor3.txt.gz 2017-03-20 15:48 86M
chainCavPor3Link.sql 2017-03-20 15:50 1.5K
chainCavPor3Link.txt.gz 2017-03-20 15:54 611M
chainDanRer10.sql 2017-03-20 16:15 1.7K
chainDanRer10.txt.gz 2017-03-20 16:16 59M
chainDanRer10Link.sql 2017-03-20 16:16 1.5K
chainDanRer10Link.txt.gz 2017-03-20 16:20 287M
chainFelCat8.sql 2017-03-20 16:28 1.7K
chainFelCat8.txt.gz 2017-03-20 16:28 124M
chainFelCat8Link.sql 2017-03-20 16:30 1.5K
chainFelCat8Link.txt.gz 2017-03-20 16:36 626M
chainHg38.sql 2017-03-20 16:53 1.7K
chainHg38.txt.gz 2017-03-20 16:55 319M
chainHg38Link.sql 2017-03-20 16:59 1.5K
chainHg38Link.txt.gz 2017-03-20 17:06 1.1G
chainMelGal5.sql 2017-03-20 17:46 1.7K
chainMelGal5.txt.gz 2017-03-20 17:46 5.6M
chainMelGal5Link.sql 2017-03-20 17:46 1.5K
chainMelGal5Link.txt.gz 2017-03-20 17:46 26M
chainMm10.sql 2017-03-20 17:46 1.7K
chainMm10.txt.gz 2017-03-20 17:48 298M
chainMm10Link.sql 2017-03-20 17:57 1.5K
chainMm10Link.txt.gz 2017-03-20 18:10 2.3G
chainMonDom5.sql 2017-03-20 19:34 1.7K
chainMonDom5.txt.gz 2017-03-20 19:34 102M
chainMonDom5Link.sql 2017-03-20 19:38 1.5K
chainMonDom5Link.txt.gz 2017-03-20 19:41 743M
chainOrnAna2.sql 2017-03-20 20:10 1.7K
chainOrnAna2.txt.gz 2017-03-20 20:10 130M
chainOrnAna2Link.sql 2017-03-20 20:12 1.5K
chainOrnAna2Link.txt.gz 2017-03-20 20:18 619M
chainOryCun2.sql 2017-03-20 20:36 1.7K
chainOryCun2.txt.gz 2017-03-20 20:36 82M
chainOryCun2Link.sql 2017-03-20 20:38 1.5K
chainOryCun2Link.txt.gz 2017-03-20 20:41 505M
chainPanTro5.sql 2017-03-20 21:02 1.7K
chainPanTro5.txt.gz 2017-03-20 21:10 949M
chainPanTro5Link.sql 2017-03-20 21:35 1.5K
chainPanTro5Link.txt.gz 2017-03-20 21:51 2.9G
chainRheMac8.sql 2017-03-20 23:17 1.7K
chainRheMac8.txt.gz 2017-03-20 23:20 610M
chainRheMac8Link.sql 2017-03-20 23:31 1.5K
chainRheMac8Link.txt.gz 2017-03-20 23:59 2.2G
chainTarSyr2.sql 2017-03-21 01:38 1.7K
chainTarSyr2.txt.gz 2017-03-21 01:39 374M
chainTarSyr2Link.sql 2017-03-21 01:52 1.5K
chainTarSyr2Link.txt.gz 2017-03-21 02:01 1.7G
chainXenTro7.sql 2017-03-21 03:11 1.7K
chainXenTro7.txt.gz 2017-03-21 03:15 311M
chainXenTro7Link.sql 2017-03-21 03:19 1.5K
chainXenTro7Link.txt.gz 2017-03-21 03:35 1.4G
cytoBand.sql 2017-03-21 04:16 1.5K
cytoBand.txt.gz 2017-03-21 04:16 8.4K
extFile.sql 2017-03-21 04:16 1.4K
extFile.txt.gz 2017-03-21 04:16 77
multiz20way.sql 2017-03-21 04:16 1.5K
multiz20way.txt.gz 2017-03-21 04:18 339M
multiz20wayFrames.sql 2017-03-21 04:30 1.7K
multiz20wayFrames.txt.gz 2017-03-21 04:30 26M
multiz20waySummary.sql 2017-03-21 04:31 1.6K
multiz20waySummary.txt.gz 2017-03-21 04:31 48M
netAilMel1.sql 2017-03-21 04:32 2.1K
netAilMel1.txt.gz 2017-03-21 04:33 49M
netBosTau8.sql 2017-03-21 04:34 2.1K
netBosTau8.txt.gz 2017-03-21 04:35 44M
netCalMil1.sql 2017-03-21 04:35 2.1K
netCalMil1.txt.gz 2017-03-21 04:35 6.0M
netCanFam3.sql 2017-03-21 04:35 2.1K
netCanFam3.txt.gz 2017-03-21 04:36 46M
netCavPor3.sql 2017-03-21 04:37 2.1K
netCavPor3.txt.gz 2017-03-21 04:37 53M
netDanRer10.sql 2017-03-21 04:39 2.1K
netDanRer10.txt.gz 2017-03-21 04:39 10M
netFelCat8.sql 2017-03-21 04:39 2.1K
netFelCat8.txt.gz 2017-03-21 04:40 49M
netHg38.sql 2017-03-21 04:41 2.1K
netHg38.txt.gz 2017-03-21 04:41 53M
netMelGal5.sql 2017-03-21 04:42 2.1K
netMelGal5.txt.gz 2017-03-21 04:42 7.4M
netMm10.sql 2017-03-21 04:42 2.1K
netMm10.txt.gz 2017-03-21 04:43 64M
netMonDom5.sql 2017-03-21 04:45 2.1K
netMonDom5.txt.gz 2017-03-21 04:45 22M
netOrnAna2.sql 2017-03-21 04:46 2.1K
netOrnAna2.txt.gz 2017-03-21 04:46 18M
netOryCun2.sql 2017-03-21 04:46 2.1K
netOryCun2.txt.gz 2017-03-21 04:47 46M
netPanTro5.sql 2017-03-21 04:48 2.1K
netPanTro5.txt.gz 2017-03-21 04:50 59M
netRheMac8.sql 2017-03-21 04:51 2.1K
netRheMac8.txt.gz 2017-03-21 04:52 58M
netTarSyr2.sql 2017-03-21 04:54 2.1K
netTarSyr2.txt.gz 2017-03-21 04:54 60M
netXenTro7.sql 2017-03-21 04:55 2.1K
netXenTro7.txt.gz 2017-03-21 04:55 13M
phastCons20way.sql 2017-03-21 04:56 1.8K
phastCons20way.txt.gz 2017-03-21 04:56 65M
phastConsElements20way.sql 2017-03-21 04:58 1.6K
phastConsElements20way.txt.gz 2017-03-21 04:58 24M
phyloP20way.sql 2017-03-21 04:59 1.8K
phyloP20way.txt.gz 2017-03-21 05:00 74M
ucscToRefSeq.sql 2017-03-21 05:02 1.4K
ucscToRefSeq.txt.gz 2017-03-21 05:02 8.4K
chromAlias.sql 2018-08-05 09:15 1.4K
chromAlias.txt.gz 2018-08-05 09:15 11K
mgcGenes.sql 2020-03-01 08:53 1.9K
mgcGenes.txt.gz 2020-03-01 08:53 620K
mgcFullMrna.sql 2020-03-01 08:53 2.1K
mgcFullMrna.txt.gz 2020-03-01 08:53 672K
ncbiRefSeqPsl.sql 2020-05-10 03:29 2.1K
ncbiRefSeqPsl.txt.gz 2020-05-10 03:29 5.0M
extNcbiRefSeq.sql 2020-05-10 03:29 1.4K
extNcbiRefSeq.txt.gz 2020-05-10 03:29 87
seqNcbiRefSeq.sql 2020-05-10 03:29 1.5K
seqNcbiRefSeq.txt.gz 2020-05-10 03:29 1.0M
ncbiRefSeq.sql 2020-05-10 03:29 1.9K
ncbiRefSeq.txt.gz 2020-05-10 03:29 3.7M
ncbiRefSeqCds.sql 2020-05-10 03:29 1.3K
ncbiRefSeqCds.txt.gz 2020-05-10 03:29 390K
ncbiRefSeqCurated.sql 2020-05-10 03:29 1.9K
ncbiRefSeqCurated.txt.gz 2020-05-10 03:29 1.8M
ncbiRefSeqLink.sql 2020-05-10 03:29 2.0K
ncbiRefSeqLink.txt.gz 2020-05-10 03:29 2.7M
ncbiRefSeqOther.sql 2020-05-10 03:29 1.3K
ncbiRefSeqOther.txt.gz 2020-05-10 03:29 71
ncbiRefSeqPredicted.sql 2020-05-10 03:29 2.0K
ncbiRefSeqPredicted.txt.gz 2020-05-10 03:29 2.7M
ncbiRefSeqPepTable.sql 2020-05-10 03:29 1.4K
ncbiRefSeqPepTable.txt.gz 2020-05-10 03:29 13M
all_mrna.sql 2020-08-20 08:47 2.1K
all_mrna.txt.gz 2020-08-20 08:47 6.5M
xenoMrna.sql 2020-08-20 08:47 2.1K
xenoMrna.txt.gz 2020-08-20 08:47 243M
refGene.sql 2020-08-20 08:47 1.9K
refGene.txt.gz 2020-08-20 08:47 2.0M
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 25M
xenoRefFlat.sql 2020-08-20 08:59 1.7K
xenoRefFlat.txt.gz 2020-08-20 08:59 22M
mrnaOrientInfo.sql 2020-08-20 08:59 1.8K
mrnaOrientInfo.txt.gz 2020-08-20 08:59 3.0M
refSeqAli.sql 2020-08-20 08:59 2.1K
refSeqAli.txt.gz 2020-08-20 08:59 1.9M
xenoRefSeqAli.sql 2020-08-20 09:02 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 09:02 25M
gbLoaded.sql 2020-08-20 09:02 1.6K
gbLoaded.txt.gz 2020-08-20 09:02 41K
chainMm39.sql 2020-10-21 09:46 1.7K
chainMm39.txt.gz 2020-10-21 09:46 318M
chainMm39Link.sql 2020-10-21 10:09 1.6K
chainMm39Link.txt.gz 2020-10-21 10:09 2.3G
netMm39.sql 2020-10-21 10:12 2.1K
netMm39.txt.gz 2020-10-21 10:12 64M
ensGene.sql 2021-05-25 14:47 1.9K
ensGene.txt.gz 2021-05-25 14:47 2.9M
ensGtp.sql 2021-05-25 14:47 1.4K
ensGtp.txt.gz 2021-05-25 14:47 454K
ensemblToGeneName.sql 2021-05-25 14:47 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:47 324K
ensemblSource.sql 2021-05-25 14:49 1.4K
ensemblSource.txt.gz 2021-05-25 14:49 139K
ensPep.sql 2021-05-25 14:49 1.3K
ensPep.txt.gz 2021-05-25 14:49 8.6M
hgBlastTab.sql 2022-07-13 01:39 1.7K
hgBlastTab.txt.gz 2022-07-13 01:39 617K
mmBlastTab.sql 2022-07-13 01:39 1.7K
mmBlastTab.txt.gz 2022-07-13 01:39 628K
trackDb.sql 2024-08-29 15:19 2.1K
trackDb.txt.gz 2024-08-29 15:19 96K
hgFindSpec.sql 2024-08-29 15:19 1.8K
hgFindSpec.txt.gz 2024-08-29 15:19 1.7K
tableDescriptions.sql 2024-11-23 02:03 1.5K
tableDescriptions.txt.gz 2024-11-23 02:03 9.8K
tableList.sql 2024-11-24 03:33 1.6K
tableList.txt.gz 2024-11-24 03:33 7.1K
bigFiles.sql 2024-11-24 03:33 1.4K
bigFiles.txt.gz 2024-11-24 03:33 139