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