This directory contains a dump of the UCSC genome annotation database for
Nov. 2009 (SGSC Sscrofa9.2/susScr2) assembly of the pig
genome (susScr2, SGSC Sscrofa9.2 (NCBI project 10718, GCA_000003025.2)),
The annotations were generated by UCSC and collaborators worldwide.
This assembly was produced by the Swine Genome Sequencing Consortium
and Wellcome Trust Sange Institute.
For more information on the pig genome, see the project website:
http://piggenome.org/
http://www.sanger.ac.uk/resources/
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=susScr2
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/susScr2/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/susScr2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/susScr2/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 susScr2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql susScr2 --local-infile=1
-e 'LOAD DATA LOCAL INFILE "/dev/stdin" INTO TABLE chromInfo;'
All the files and tables in this directory are freely usable for any purpose.
Name Last modified Size Description
Parent Directory -
all_est.sql 2016-07-17 11:28 2.1K
all_est.txt.gz 2016-07-17 11:28 50M
all_mrna.sql 2020-09-02 07:33 2.1K
all_mrna.txt.gz 2020-09-02 07:33 2.3M
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 2.0M
bamAllNumtSSorted.sql 2013-07-28 06:10 1.3K
bamAllNumtSSorted.txt.gz 2013-07-28 06:10 84
bigFiles.sql 2024-12-01 03:06 1.4K
bigFiles.txt.gz 2024-12-01 03:06 87
blastHg18KG.sql 2010-05-11 17:01 2.1K
blastHg18KG.txt.gz 2010-05-11 17:01 3.7M
chainBosTau7.sql 2012-06-17 22:40 1.6K
chainBosTau7.txt.gz 2012-06-17 22:45 786M
chainBosTau7Link.sql 2012-06-17 22:58 1.5K
chainBosTau7Link.txt.gz 2012-06-17 23:20 3.1G
chainHg19.sql 2010-05-11 17:01 1.6K
chainHg19.txt.gz 2010-05-11 17:01 118M
chainHg19Link.sql 2010-05-11 16:47 1.5K
chainHg19Link.txt.gz 2010-05-11 16:48 654M
chainMm9.sql 2010-05-11 17:00 1.6K
chainMm9.txt.gz 2010-05-11 17:00 48M
chainMm9Link.sql 2010-05-11 16:52 1.5K
chainMm9Link.txt.gz 2010-05-11 16:52 419M
chainMonDom5.sql 2010-05-11 16:59 1.6K
chainMonDom5.txt.gz 2010-05-11 16:59 152M
chainMonDom5Link.sql 2010-05-11 16:55 1.5K
chainMonDom5Link.txt.gz 2010-05-11 16:56 510M
chr1_est.sql 2016-07-17 11:27 2.1K
chr1_est.txt.gz 2016-07-17 11:27 5.2M
chr1_intronEst.sql 2016-07-17 11:28 2.1K
chr1_intronEst.txt.gz 2016-07-17 11:28 2.7M
chr1_mrna.sql 2020-09-02 07:33 2.1K
chr1_mrna.txt.gz 2020-09-02 07:33 224K
chr2_est.sql 2016-07-17 11:28 2.1K
chr2_est.txt.gz 2016-07-17 11:28 4.1M
chr2_intronEst.sql 2016-07-17 11:27 2.1K
chr2_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr2_mrna.sql 2020-05-11 17:36 2.1K
chr2_mrna.txt.gz 2020-05-11 17:36 197K
chr3_est.sql 2016-07-17 11:27 2.1K
chr3_est.txt.gz 2016-07-17 11:27 3.2M
chr3_intronEst.sql 2016-07-17 11:27 2.1K
chr3_intronEst.txt.gz 2016-07-17 11:27 1.7M
chr3_mrna.sql 2020-05-11 17:36 2.1K
chr3_mrna.txt.gz 2020-05-11 17:36 141K
chr4_est.sql 2016-07-17 11:27 2.1K
chr4_est.txt.gz 2016-07-17 11:27 3.7M
chr4_intronEst.sql 2016-07-17 11:27 2.1K
chr4_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr4_mrna.sql 2020-09-02 07:33 2.1K
chr4_mrna.txt.gz 2020-09-02 07:33 149K
chr5_est.sql 2016-07-17 11:27 2.1K
chr5_est.txt.gz 2016-07-17 11:27 3.2M
chr5_intronEst.sql 2016-07-17 11:25 2.1K
chr5_intronEst.txt.gz 2016-07-17 11:25 1.7M
chr5_mrna.sql 2020-05-11 17:36 2.1K
chr5_mrna.txt.gz 2020-05-11 17:36 132K
chr6_est.sql 2016-07-17 11:27 2.1K
chr6_est.txt.gz 2016-07-17 11:27 3.5M
chr6_intronEst.sql 2016-07-17 11:27 2.1K
chr6_intronEst.txt.gz 2016-07-17 11:27 2.0M
chr6_mrna.sql 2020-05-11 17:36 2.1K
chr6_mrna.txt.gz 2020-05-11 17:36 168K
chr7_est.sql 2016-07-17 11:27 2.1K
chr7_est.txt.gz 2016-07-17 11:27 4.0M
chr7_intronEst.sql 2016-07-17 11:27 2.1K
chr7_intronEst.txt.gz 2016-07-17 11:27 2.3M
chr7_mrna.sql 2020-09-02 07:33 2.1K
chr7_mrna.txt.gz 2020-09-02 07:33 245K
chr8_est.sql 2016-07-17 11:27 2.1K
chr8_est.txt.gz 2016-07-17 11:27 2.0M
chr8_intronEst.sql 2016-07-17 11:28 2.1K
chr8_intronEst.txt.gz 2016-07-17 11:28 1.1M
chr8_mrna.sql 2020-05-11 17:36 2.1K
chr8_mrna.txt.gz 2020-05-11 17:36 85K
chr9_est.sql 2016-07-17 11:27 2.1K
chr9_est.txt.gz 2016-07-17 11:27 2.6M
chr9_intronEst.sql 2016-07-17 11:27 2.1K
chr9_intronEst.txt.gz 2016-07-17 11:27 1.4M
chr9_mrna.sql 2020-05-11 17:36 2.1K
chr9_mrna.txt.gz 2020-05-11 17:36 119K
chr10_est.sql 2016-07-17 11:27 2.1K
chr10_est.txt.gz 2016-07-17 11:27 1.1M
chr10_intronEst.sql 2016-07-17 11:28 2.1K
chr10_intronEst.txt.gz 2016-07-17 11:28 529K
chr10_mrna.sql 2020-05-11 17:13 2.1K
chr10_mrna.txt.gz 2020-05-11 17:13 60K
chr11_est.sql 2016-07-17 11:27 2.1K
chr11_est.txt.gz 2016-07-17 11:27 879K
chr11_intronEst.sql 2016-07-17 11:28 2.1K
chr11_intronEst.txt.gz 2016-07-17 11:28 379K
chr11_mrna.sql 2020-05-11 17:13 2.1K
chr11_mrna.txt.gz 2020-05-11 17:13 40K
chr12_est.sql 2016-07-17 11:28 2.1K
chr12_est.txt.gz 2016-07-17 11:28 2.3M
chr12_intronEst.sql 2016-07-17 11:28 2.1K
chr12_intronEst.txt.gz 2016-07-17 11:28 1.3M
chr12_mrna.sql 2020-05-11 17:36 2.1K
chr12_mrna.txt.gz 2020-05-11 17:36 118K
chr13_est.sql 2016-07-17 11:27 2.1K
chr13_est.txt.gz 2016-07-17 11:27 2.4M
chr13_intronEst.sql 2016-07-17 11:27 2.1K
chr13_intronEst.txt.gz 2016-07-17 11:27 1.2M
chr13_mrna.sql 2020-09-02 07:33 2.1K
chr13_mrna.txt.gz 2020-09-02 07:33 122K
chr14_est.sql 2016-07-17 11:27 2.1K
chr14_est.txt.gz 2016-07-17 11:27 3.5M
chr14_intronEst.sql 2016-07-17 11:28 2.1K
chr14_intronEst.txt.gz 2016-07-17 11:28 1.8M
chr14_mrna.sql 2020-05-11 17:36 2.1K
chr14_mrna.txt.gz 2020-05-11 17:36 158K
chr15_est.sql 2016-07-17 11:27 2.1K
chr15_est.txt.gz 2016-07-17 11:27 2.2M
chr15_intronEst.sql 2016-07-17 11:28 2.1K
chr15_intronEst.txt.gz 2016-07-17 11:28 1.0M
chr15_mrna.sql 2020-05-11 17:36 2.1K
chr15_mrna.txt.gz 2020-05-11 17:36 103K
chr16_est.sql 2016-07-17 11:27 2.1K
chr16_est.txt.gz 2016-07-17 11:27 936K
chr16_intronEst.sql 2016-07-17 11:28 2.1K
chr16_intronEst.txt.gz 2016-07-17 11:28 380K
chr16_mrna.sql 2020-05-11 17:36 2.1K
chr16_mrna.txt.gz 2020-05-11 17:36 50K
chr17_est.sql 2016-07-17 11:28 2.1K
chr17_est.txt.gz 2016-07-17 11:28 1.6M
chr17_intronEst.sql 2016-07-17 11:28 2.1K
chr17_intronEst.txt.gz 2016-07-17 11:28 950K
chr17_mrna.sql 2020-05-11 17:36 2.1K
chr17_mrna.txt.gz 2020-05-11 17:36 82K
chr18_est.sql 2016-07-17 11:25 2.1K
chr18_est.txt.gz 2016-07-17 11:25 1.0M
chr18_intronEst.sql 2016-07-17 11:27 2.1K
chr18_intronEst.txt.gz 2016-07-17 11:27 466K
chr18_mrna.sql 2020-05-11 17:36 2.1K
chr18_mrna.txt.gz 2020-05-11 17:36 62K
chrM_est.sql 2016-07-17 11:27 2.1K
chrM_est.txt.gz 2016-07-17 11:27 1.1M
chrM_intronEst.sql 2016-07-17 11:28 2.1K
chrM_intronEst.txt.gz 2016-07-17 11:28 495
chrM_mrna.sql 2016-07-17 11:27 2.1K
chrM_mrna.txt.gz 2016-07-17 11:27 2.9K
chrX_est.sql 2016-07-17 11:27 2.1K
chrX_est.txt.gz 2016-07-17 11:27 1.7M
chrX_intronEst.sql 2016-07-17 11:27 2.1K
chrX_intronEst.txt.gz 2016-07-17 11:27 855K
chrX_mrna.sql 2020-05-11 17:36 2.1K
chrX_mrna.txt.gz 2020-05-11 17:36 74K
chromInfo.sql 2010-05-11 16:22 1.3K
chromInfo.txt.gz 2010-05-11 16:22 219
cpgIslandExt.sql 2010-05-11 16:43 1.6K
cpgIslandExt.txt.gz 2010-05-11 16:43 805K
cpgIslandExtUnmasked.sql 2014-06-01 19:54 1.7K
cpgIslandExtUnmasked.txt.gz 2014-06-01 19:54 1.3M
ctgPos2.sql 2010-05-11 16:59 1.5K
ctgPos2.txt.gz 2010-05-11 16:59 53K
ensGene.sql 2011-10-04 16:28 1.9K
ensGene.txt.gz 2011-10-04 16:28 1.7M
ensGtp.sql 2011-10-04 16:28 1.4K
ensGtp.txt.gz 2011-10-04 16:28 167K
ensPep.sql 2011-10-04 16:28 1.3K
ensPep.txt.gz 2011-10-04 16:28 4.4M
ensemblSource.sql 2011-10-04 16:31 1.3K
ensemblSource.txt.gz 2011-10-04 16:31 62K
ensemblToGeneName.sql 2011-10-04 16:31 1.3K
ensemblToGeneName.txt.gz 2011-10-04 16:31 118K
estOrientInfo.sql 2016-07-17 11:27 1.8K
estOrientInfo.txt.gz 2016-07-17 11:27 16M
gap.sql 2010-05-11 16:55 1.5K
gap.txt.gz 2010-05-11 16:55 2.1M
gbLoaded.sql 2020-09-02 07:33 1.6K
gbLoaded.txt.gz 2020-09-02 07:33 41K
gc5Base.sql 2010-05-11 16:51 1.7K
gc5Base.txt.gz 2010-05-11 16:51 9.4M
gold.sql 2010-05-11 16:52 1.6K
gold.txt.gz 2010-05-11 16:52 2.1M
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 208
hgFindSpec.sql 2023-03-28 13:53 1.8K
hgFindSpec.txt.gz 2023-03-28 13:53 1.0K
history.sql 2010-05-11 16:45 1.5K
history.txt.gz 2010-05-11 16:45 567
microsat.sql 2015-08-24 02:07 1.5K
microsat.txt.gz 2015-08-24 02:07 375K
mrnaOrientInfo.sql 2020-09-02 07:33 1.8K
mrnaOrientInfo.txt.gz 2020-09-02 07:33 569K
nestedRepeats.sql 2010-05-11 16:59 1.9K
nestedRepeats.txt.gz 2010-05-11 16:59 11M
netBosTau7.sql 2012-06-18 00:03 2.0K
netBosTau7.txt.gz 2012-06-18 00:04 69M
netHg19.sql 2010-05-11 16:46 2.0K
netHg19.txt.gz 2010-05-11 16:46 59M
netMm9.sql 2010-05-11 16:46 2.0K
netMm9.txt.gz 2010-05-11 16:46 51M
netMonDom5.sql 2010-05-11 17:01 2.0K
netMonDom5.txt.gz 2010-05-11 17:01 16M
nscanGene.sql 2010-05-11 16:46 1.9K
nscanGene.txt.gz 2010-05-11 16:46 1.9M
numtS.sql 2013-07-28 06:10 1.7K
numtS.txt.gz 2013-07-28 06:10 8.7K
numtSAssembled.sql 2013-07-28 06:10 1.8K
numtSAssembled.txt.gz 2013-07-28 06:10 2.1K
numtSMitochondrion.sql 2013-07-28 06:10 1.6K
numtSMitochondrion.txt.gz 2013-07-28 06:10 2.8K
rmsk.sql 2010-05-11 16:44 1.8K
rmsk.txt.gz 2010-05-11 16:44 108M
simpleRepeat.sql 2010-05-11 16:44 1.9K
simpleRepeat.txt.gz 2010-05-11 16:44 14M
tRNAs.sql 2012-04-23 11:59 1.7K
tRNAs.txt.gz 2012-04-23 11:59 19K
tableDescriptions.sql 2024-11-30 02:04 1.5K
tableDescriptions.txt.gz 2024-11-30 02:04 5.9K
tableList.sql 2024-12-01 03:06 1.6K
tableList.txt.gz 2024-12-01 03:06 6.7K
trackDb.sql 2023-03-28 13:53 2.1K
trackDb.txt.gz 2023-03-28 13:53 36K
xenoMrna.sql 2020-09-02 07:33 2.1K
xenoMrna.txt.gz 2020-09-02 07:33 336M
xenoRefFlat.sql 2020-09-02 07:33 1.7K
xenoRefFlat.txt.gz 2020-09-02 07:33 33M
xenoRefGene.sql 2020-09-02 07:33 2.0K
xenoRefGene.txt.gz 2020-09-02 07:33 37M
xenoRefSeqAli.sql 2020-09-02 07:33 2.1K
xenoRefSeqAli.txt.gz 2020-09-02 07:33 36M