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.
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All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
chainCriGri1Link.txt.gz 2017-11-06 19:09 3.6G
chainMm10Link.txt.gz 2017-11-06 19:28 1.0G
chainCriGri1.txt.gz 2017-11-06 19:01 776M
chainHg38Link.txt.gz 2017-11-06 19:24 616M
chainMm10.txt.gz 2017-11-06 19:26 146M
windowmaskerSdust.txt.gz 2017-11-06 19:33 125M
chainHg38.txt.gz 2017-11-06 19:23 117M
rmsk.txt.gz 2017-11-06 19:33 106M
netMm10.txt.gz 2017-11-06 19:32 73M
netHg38.txt.gz 2017-11-06 19:32 51M
xenoRefGene.txt.gz 2020-08-21 07:48 37M
xenoRefSeqAli.txt.gz 2020-08-21 07:48 36M
xenoRefFlat.txt.gz 2020-08-21 07:48 34M
simpleRepeat.txt.gz 2017-11-06 19:33 25M
netCriGri1.txt.gz 2017-11-06 19:27 16M
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:42 9.2M
tandemDups.txt.gz 2017-11-06 19:33 8.8M
nestedRepeats.txt.gz 2017-11-06 19:23 8.8M
ensPep.txt.gz 2021-05-25 14:27 6.0M
locusName.txt.gz 2017-11-06 19:33 3.4M
ncbiRefSeqPsl.txt.gz 2021-02-10 16:03 3.3M
gold.txt.gz 2017-11-06 19:32 3.3M
all_mrna.txt.gz 2018-11-04 06:14 2.8M
ncbiRefSeq.txt.gz 2021-02-10 16:03 2.7M
ncbiRefSeqPredicted.txt.gz 2021-02-10 16:03 2.6M
ensGene.txt.gz 2021-05-25 14:26 2.3M
microsat.txt.gz 2017-11-06 19:01 2.0M
crisprRanges.txt.gz 2017-11-06 19:32 2.0M
gap.txt.gz 2017-11-06 19:04 1.9M
genscan.txt.gz 2017-11-06 19:32 1.8M
augustusGene.txt.gz 2017-11-06 19:01 1.6M
ncbiRefSeqLink.txt.gz 2021-02-10 16:03 1.4M
chromAlias.txt.gz 2017-11-06 19:32 1.0M
mrnaOrientInfo.txt.gz 2020-05-07 18:31 796K
seqNcbiRefSeq.txt.gz 2021-02-10 16:42 696K
ucscToRefSeq.txt.gz 2017-11-06 19:33 539K
ucscToINSDC.txt.gz 2017-11-06 19:33 532K
ensGtp.txt.gz 2021-05-25 14:26 345K
chromInfo.txt.gz 2017-11-06 19:32 308K
cytoBandIdeo.txt.gz 2017-11-06 19:32 283K
cpgIslandExtUnmasked.txt.gz 2017-11-06 19:32 269K
ncbiRefSeqCds.txt.gz 2021-02-10 16:42 256K
cpgIslandExt.txt.gz 2017-11-06 19:32 226K
ensemblSource.txt.gz 2021-05-25 14:27 86K
refSeqAli.txt.gz 2020-05-07 18:31 42K
trackDb.txt.gz 2023-12-05 13:52 41K
ncbiRefSeqCurated.txt.gz 2021-02-10 16:03 40K
refGene.txt.gz 2020-08-21 07:31 39K
refFlat.txt.gz 2020-08-21 07:31 35K
gbLoaded.txt.gz 2020-08-21 07:48 32K
ensemblToGeneName.txt.gz 2021-05-25 14:26 14K
tableDescriptions.txt.gz 2024-11-23 02:03 6.7K
gapOverlap.txt.gz 2017-11-06 19:23 6.5K
tableList.txt.gz 2024-11-24 03:06 3.5K
xenoRefSeqAli.sql 2020-08-21 07:48 2.2K
ncbiRefSeqPsl.sql 2021-02-10 16:03 2.1K
refSeqAli.sql 2020-05-07 18:31 2.1K
intronEst.sql 2017-11-06 19:33 2.1K
all_mrna.sql 2018-11-04 06:14 2.1K
all_est.sql 2017-11-06 19:01 2.1K
netCriGri1.sql 2017-11-06 19:27 2.1K
netMm10.sql 2017-11-06 19:32 2.1K
netHg38.sql 2017-11-06 19:32 2.1K
trackDb.sql 2023-12-05 13:52 2.1K
ncbiRefSeqLink.sql 2021-02-10 16:03 2.0K
ncbiRefSeqPredicted.sql 2021-02-10 16:03 2.0K
ncbiRefSeqCurated.sql 2021-02-10 16:03 2.0K
xenoRefGene.sql 2020-08-21 07:48 2.0K
ncbiRefSeq.sql 2021-02-10 16:03 2.0K
refGene.sql 2020-08-21 07:31 1.9K
ensGene.sql 2021-05-25 14:26 1.9K
augustusGene.sql 2017-11-06 19:01 1.9K
nestedRepeats.sql 2017-11-06 19:23 1.9K
simpleRepeat.sql 2017-11-06 19:33 1.9K
rmsk.sql 2017-11-06 19:33 1.9K
mrnaOrientInfo.sql 2020-05-07 18:31 1.8K
tandemDups.sql 2017-11-06 19:33 1.8K
gapOverlap.sql 2017-11-06 19:23 1.8K
estOrientInfo.sql 2017-11-06 19:33 1.8K
hgFindSpec.sql 2023-12-05 13:52 1.8K
xenoRefFlat.sql 2020-08-21 07:48 1.8K
refFlat.sql 2020-08-21 07:31 1.7K
cpgIslandExtUnmasked.sql 2017-11-06 19:32 1.7K
chainCriGri1.sql 2017-11-06 19:01 1.7K
chainMm10.sql 2017-11-06 19:26 1.7K
chainHg38.sql 2017-11-06 19:22 1.7K
cpgIslandExt.sql 2017-11-06 19:32 1.7K
genscan.sql 2017-11-06 19:32 1.7K
gold.sql 2017-11-06 19:32 1.7K
gbLoaded.sql 2020-08-21 07:48 1.6K
gap.sql 2017-11-06 19:04 1.6K
history.sql 2017-11-06 19:33 1.6K
seqNcbiRefSeq.sql 2021-02-10 16:42 1.6K
tableList.sql 2024-11-24 03:06 1.6K
chainCriGri1Link.sql 2017-11-06 19:04 1.6K
chainMm10Link.sql 2017-11-06 19:27 1.5K
chainHg38Link.sql 2017-11-06 19:23 1.5K
cytoBandIdeo.sql 2017-11-06 19:32 1.5K
windowmaskerSdust.sql 2017-11-06 19:33 1.5K
crisprRanges.sql 2017-11-06 19:32 1.5K
locusName.sql 2017-11-06 19:33 1.5K
microsat.sql 2017-11-06 19:01 1.5K
extNcbiRefSeq.sql 2021-02-10 16:42 1.5K
ensGtp.sql 2021-05-25 14:26 1.4K
ucscToRefSeq.sql 2017-11-06 19:33 1.4K
tableDescriptions.sql 2024-11-23 02:03 1.4K
ucscToINSDC.sql 2017-11-06 19:33 1.4K
chromAlias.sql 2017-11-06 19:32 1.4K
ensemblToGeneName.sql 2021-05-25 14:26 1.4K
chromInfo.sql 2017-11-06 19:32 1.4K
ncbiRefSeqPepTable.sql 2021-02-10 16:42 1.4K
bigFiles.sql 2024-11-24 03:06 1.4K
ensemblSource.sql 2021-05-25 14:27 1.4K
ncbiRefSeqCds.sql 2021-02-10 16:42 1.4K
grp.sql 2017-11-06 19:32 1.4K
ensPep.sql 2021-05-25 14:27 1.3K
ncbiRefSeqOther.sql 2021-02-10 16:42 1.3K
crisprTargets.sql 2017-11-06 19:32 1.3K
gc5BaseBw.sql 2017-11-06 19:32 1.3K
hgFindSpec.txt.gz 2023-12-05 13:52 1.2K
history.txt.gz 2017-11-06 19:33 848
all_est.txt.gz 2017-11-06 19:01 783
intronEst.txt.gz 2017-11-06 19:33 557
estOrientInfo.txt.gz 2017-11-06 19:33 269
grp.txt.gz 2017-11-06 19:32 213
bigFiles.txt.gz 2024-11-24 03:06 120
extNcbiRefSeq.txt.gz 2021-02-10 16:42 95
ncbiRefSeqOther.txt.gz 2021-02-10 16:42 79
gc5BaseBw.txt.gz 2017-11-06 19:32 70
crisprTargets.txt.gz 2017-11-06 19:32 65