This directory contains a dump of the UCSC genome annotation database for the
Aug. 2011 (CHO K1 cell line/criGriChoV1) assembly of the chinese hamster genome
(criGriChoV1, Beijing Genomics Institute) .
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/2791
http://www.ncbi.nlm.nih.gov/genome/assembly/309608
http://www.ncbi.nlm.nih.gov/bioproject/69991
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=criGriChoV1
and click the "describe table schema" button. There is also a "view
table schema" link on the configuration page for each track.
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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.soe.ucsc.edu, then go to
the directory goldenPath/criGriChoV1/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.soe.ucsc.edu/goldenPath/criGriChoV1/database/ .
For a single file, e.g. gc5Base.txt.gz
rsync -avzP
rsync://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV1/database/gc5Base.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV1/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.soe.ucsc.edu/goldenPath/criGriChoV1/database/gc5Base.txt.gz'
-O gc5Base.txt.gz
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 criGriChoV1 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql criGriChoV1 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
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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 2020-08-21 07:48 36M
xenoRefSeqAli.sql 2020-08-21 07:48 2.2K
xenoRefGene.txt.gz 2020-08-21 07:48 37M
xenoRefGene.sql 2020-08-21 07:48 2.0K
xenoRefFlat.txt.gz 2020-08-21 07:48 34M
xenoRefFlat.sql 2020-08-21 07:48 1.8K
windowmaskerSdust.txt.gz 2017-11-06 19:33 125M
windowmaskerSdust.sql 2017-11-06 19:33 1.5K
ucscToRefSeq.txt.gz 2017-11-06 19:33 539K
ucscToRefSeq.sql 2017-11-06 19:33 1.4K
ucscToINSDC.txt.gz 2017-11-06 19:33 532K
ucscToINSDC.sql 2017-11-06 19:33 1.4K
trackDb.txt.gz 2023-12-05 13:52 41K
trackDb.sql 2023-12-05 13:52 2.1K
tandemDups.txt.gz 2017-11-06 19:33 8.8M
tandemDups.sql 2017-11-06 19:33 1.8K
tableList.txt.gz 2024-11-17 03:15 3.5K
tableList.sql 2024-11-17 03:15 1.6K
tableDescriptions.txt.gz 2024-11-16 02:03 6.7K
tableDescriptions.sql 2024-11-16 02:03 1.4K
simpleRepeat.txt.gz 2017-11-06 19:33 25M
simpleRepeat.sql 2017-11-06 19:33 1.9K
seqNcbiRefSeq.txt.gz 2021-02-10 16:42 696K
seqNcbiRefSeq.sql 2021-02-10 16:42 1.6K
rmsk.txt.gz 2017-11-06 19:33 106M
rmsk.sql 2017-11-06 19:33 1.9K
refSeqAli.txt.gz 2020-05-07 18:31 42K
refSeqAli.sql 2020-05-07 18:31 2.1K
refGene.txt.gz 2020-08-21 07:31 39K
refGene.sql 2020-08-21 07:31 1.9K
refFlat.txt.gz 2020-08-21 07:31 35K
refFlat.sql 2020-08-21 07:31 1.7K
netMm10.txt.gz 2017-11-06 19:32 73M
netMm10.sql 2017-11-06 19:32 2.1K
netHg38.txt.gz 2017-11-06 19:32 51M
netHg38.sql 2017-11-06 19:32 2.1K
netCriGri1.txt.gz 2017-11-06 19:27 16M
netCriGri1.sql 2017-11-06 19:27 2.1K
nestedRepeats.txt.gz 2017-11-06 19:23 8.8M
nestedRepeats.sql 2017-11-06 19:23 1.9K
ncbiRefSeqPsl.txt.gz 2021-02-10 16:03 3.3M
ncbiRefSeqPsl.sql 2021-02-10 16:03 2.1K
ncbiRefSeqPredicted.txt.gz 2021-02-10 16:03 2.6M
ncbiRefSeqPredicted.sql 2021-02-10 16:03 2.0K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:42 9.2M
ncbiRefSeqPepTable.sql 2021-02-10 16:42 1.4K
ncbiRefSeqOther.txt.gz 2021-02-10 16:42 79
ncbiRefSeqOther.sql 2021-02-10 16:42 1.3K
ncbiRefSeqLink.txt.gz 2021-02-10 16:03 1.4M
ncbiRefSeqLink.sql 2021-02-10 16:03 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 16:03 40K
ncbiRefSeqCurated.sql 2021-02-10 16:03 2.0K
ncbiRefSeqCds.txt.gz 2021-02-10 16:42 256K
ncbiRefSeqCds.sql 2021-02-10 16:42 1.4K
ncbiRefSeq.txt.gz 2021-02-10 16:03 2.7M
ncbiRefSeq.sql 2021-02-10 16:03 2.0K
mrnaOrientInfo.txt.gz 2020-05-07 18:31 796K
mrnaOrientInfo.sql 2020-05-07 18:31 1.8K
microsat.txt.gz 2017-11-06 19:01 2.0M
microsat.sql 2017-11-06 19:01 1.5K
locusName.txt.gz 2017-11-06 19:33 3.4M
locusName.sql 2017-11-06 19:33 1.5K
intronEst.txt.gz 2017-11-06 19:33 557
intronEst.sql 2017-11-06 19:33 2.1K
history.txt.gz 2017-11-06 19:33 848
history.sql 2017-11-06 19:33 1.6K
hgFindSpec.txt.gz 2023-12-05 13:52 1.2K
hgFindSpec.sql 2023-12-05 13:52 1.8K
grp.txt.gz 2017-11-06 19:32 213
grp.sql 2017-11-06 19:32 1.4K
gold.txt.gz 2017-11-06 19:32 3.3M
gold.sql 2017-11-06 19:32 1.7K
genscan.txt.gz 2017-11-06 19:32 1.8M
genscan.sql 2017-11-06 19:32 1.7K
gc5BaseBw.txt.gz 2017-11-06 19:32 70
gc5BaseBw.sql 2017-11-06 19:32 1.3K
gbLoaded.txt.gz 2020-08-21 07:48 32K
gbLoaded.sql 2020-08-21 07:48 1.6K
gapOverlap.txt.gz 2017-11-06 19:23 6.5K
gapOverlap.sql 2017-11-06 19:23 1.8K
gap.txt.gz 2017-11-06 19:04 1.9M
gap.sql 2017-11-06 19:04 1.6K
extNcbiRefSeq.txt.gz 2021-02-10 16:42 95
extNcbiRefSeq.sql 2021-02-10 16:42 1.5K
estOrientInfo.txt.gz 2017-11-06 19:33 269
estOrientInfo.sql 2017-11-06 19:33 1.8K
ensemblToGeneName.txt.gz 2021-05-25 14:26 14K
ensemblToGeneName.sql 2021-05-25 14:26 1.4K
ensemblSource.txt.gz 2021-05-25 14:27 86K
ensemblSource.sql 2021-05-25 14:27 1.4K
ensPep.txt.gz 2021-05-25 14:27 6.0M
ensPep.sql 2021-05-25 14:27 1.3K
ensGtp.txt.gz 2021-05-25 14:26 345K
ensGtp.sql 2021-05-25 14:26 1.4K
ensGene.txt.gz 2021-05-25 14:26 2.3M
ensGene.sql 2021-05-25 14:26 1.9K
cytoBandIdeo.txt.gz 2017-11-06 19:32 283K
cytoBandIdeo.sql 2017-11-06 19:32 1.5K
crisprTargets.txt.gz 2017-11-06 19:32 65
crisprTargets.sql 2017-11-06 19:32 1.3K
crisprRanges.txt.gz 2017-11-06 19:32 2.0M
crisprRanges.sql 2017-11-06 19:32 1.5K
cpgIslandExtUnmasked.txt.gz 2017-11-06 19:32 269K
cpgIslandExtUnmasked.sql 2017-11-06 19:32 1.7K
cpgIslandExt.txt.gz 2017-11-06 19:32 226K
cpgIslandExt.sql 2017-11-06 19:32 1.7K
chromInfo.txt.gz 2017-11-06 19:32 308K
chromInfo.sql 2017-11-06 19:32 1.4K
chromAlias.txt.gz 2017-11-06 19:32 1.0M
chromAlias.sql 2017-11-06 19:32 1.4K
chainMm10Link.txt.gz 2017-11-06 19:28 1.0G
chainMm10Link.sql 2017-11-06 19:27 1.5K
chainMm10.txt.gz 2017-11-06 19:26 146M
chainMm10.sql 2017-11-06 19:26 1.7K
chainHg38Link.txt.gz 2017-11-06 19:24 616M
chainHg38Link.sql 2017-11-06 19:23 1.5K
chainHg38.txt.gz 2017-11-06 19:23 117M
chainHg38.sql 2017-11-06 19:22 1.7K
chainCriGri1Link.txt.gz 2017-11-06 19:09 3.6G
chainCriGri1Link.sql 2017-11-06 19:04 1.6K
chainCriGri1.txt.gz 2017-11-06 19:01 776M
chainCriGri1.sql 2017-11-06 19:01 1.7K
bigFiles.txt.gz 2024-11-17 03:15 120
bigFiles.sql 2024-11-17 03:15 1.4K
augustusGene.txt.gz 2017-11-06 19:01 1.6M
augustusGene.sql 2017-11-06 19:01 1.9K
all_mrna.txt.gz 2018-11-04 06:14 2.8M
all_mrna.sql 2018-11-04 06:14 2.1K
all_est.txt.gz 2017-11-06 19:01 783
all_est.sql 2017-11-06 19:01 2.1K