This directory contains a dump of the UCSC genome annotation database for
the Apr. 2011 (SacCer_Apr2011/sacCer3) assembly of the S. cerevisiae genome
(sacCer3, Saccharomyces cerevisiae S288c assembly from
Saccharomyces Genome Database (GCA_000146055.2)).
The annotations were generated by UCSC and collaborators worldwide.
This assembly is based on sequence dated April 2011 in the Saccharomyces Genome
Database (http://www.yeastgenome.org/) and was obtained from the site
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/fungi/Saccharomyces_cerevisiae/SacCer_Apr2011/
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=sacCer3
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/sacCer3/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/sacCer3/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer3/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 sacCer3 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql sacCer3 --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 2012-05-28 14:19 2.0K
all_est.txt.gz 2012-05-28 14:19 962K
all_mrna.sql 2020-05-07 04:28 2.1K
all_mrna.txt.gz 2020-05-07 04:28 43K
augustusGene.sql 2015-07-26 17:28 1.9K
augustusGene.txt.gz 2015-07-26 17:28 109K
bigFiles.sql 2024-11-17 03:36 1.4K
bigFiles.txt.gz 2024-11-17 03:36 114
blastHg18KG.sql 2011-10-06 16:15 2.1K
blastHg18KG.txt.gz 2011-10-06 16:15 350K
ceBlastTab.sql 2011-10-06 16:15 1.6K
ceBlastTab.txt.gz 2011-10-06 16:15 87K
choExpDistance.sql 2011-10-06 16:16 1.3K
choExpDistance.txt.gz 2011-10-06 16:16 34M
chrIII_est.sql 2012-05-28 14:19 2.0K
chrIII_est.txt.gz 2012-05-28 14:19 32K
chrIII_intronEst.sql 2011-10-06 16:18 2.1K
chrIII_intronEst.txt.gz 2011-10-06 16:18 1.5K
chrIII_mrna.sql 2020-05-07 04:20 2.1K
chrIII_mrna.txt.gz 2020-05-07 04:20 1.1K
chrII_est.sql 2012-05-28 14:19 2.0K
chrII_est.txt.gz 2012-05-28 14:19 71K
chrII_intronEst.sql 2011-10-06 16:17 2.1K
chrII_intronEst.txt.gz 2011-10-06 16:17 9.4K
chrII_mrna.sql 2020-05-07 04:20 2.1K
chrII_mrna.txt.gz 2020-05-07 04:20 3.0K
chrIV_est.sql 2012-05-28 14:19 2.0K
chrIV_est.txt.gz 2012-05-28 14:19 150K
chrIV_intronEst.sql 2012-05-28 14:19 2.1K
chrIV_intronEst.txt.gz 2012-05-28 14:19 12K
chrIV_mrna.sql 2020-05-07 04:20 2.1K
chrIV_mrna.txt.gz 2020-05-07 04:20 5.5K
chrIX_est.sql 2012-05-28 14:19 2.0K
chrIX_est.txt.gz 2012-05-28 14:19 24K
chrIX_intronEst.sql 2011-10-06 16:15 2.1K
chrIX_intronEst.txt.gz 2011-10-06 16:15 2.6K
chrIX_mrna.sql 2020-05-07 04:20 2.1K
chrIX_mrna.txt.gz 2020-05-07 04:20 1.5K
chrI_est.sql 2012-05-28 14:19 2.0K
chrI_est.txt.gz 2012-05-28 14:19 11K
chrI_intronEst.sql 2011-10-06 16:18 2.0K
chrI_intronEst.txt.gz 2011-10-06 16:18 1.1K
chrI_mrna.sql 2020-05-07 04:20 2.1K
chrI_mrna.txt.gz 2020-05-07 04:20 845
chrM_est.sql 2011-10-06 16:16 2.0K
chrM_est.txt.gz 2011-10-06 16:16 33
chrM_intronEst.sql 2011-10-06 16:17 2.0K
chrM_intronEst.txt.gz 2011-10-06 16:17 39
chrM_mrna.sql 2020-05-07 04:20 2.1K
chrM_mrna.txt.gz 2020-05-07 04:20 863
chrVIII_est.sql 2012-05-28 14:19 2.0K
chrVIII_est.txt.gz 2012-05-28 14:19 32K
chrVIII_intronEst.sql 2011-10-06 16:17 2.1K
chrVIII_intronEst.txt.gz 2011-10-06 16:17 3.7K
chrVIII_mrna.sql 2020-05-07 04:20 2.1K
chrVIII_mrna.txt.gz 2020-05-07 04:20 1.8K
chrVII_est.sql 2012-05-28 14:19 2.0K
chrVII_est.txt.gz 2012-05-28 14:19 84K
chrVII_intronEst.sql 2011-10-06 16:18 2.1K
chrVII_intronEst.txt.gz 2011-10-06 16:18 8.4K
chrVII_mrna.sql 2020-05-07 04:25 2.1K
chrVII_mrna.txt.gz 2020-05-07 04:25 4.4K
chrVI_est.sql 2012-05-28 14:19 2.0K
chrVI_est.txt.gz 2012-05-28 14:19 30K
chrVI_intronEst.sql 2012-05-28 14:19 2.1K
chrVI_intronEst.txt.gz 2012-05-28 14:19 3.0K
chrVI_mrna.sql 2020-05-07 04:20 2.1K
chrVI_mrna.txt.gz 2020-05-07 04:20 1.1K
chrV_est.sql 2012-05-28 14:19 2.0K
chrV_est.txt.gz 2012-05-28 14:19 52K
chrV_intronEst.sql 2011-10-06 16:15 2.0K
chrV_intronEst.txt.gz 2011-10-06 16:15 3.4K
chrV_mrna.sql 2020-05-07 04:21 2.1K
chrV_mrna.txt.gz 2020-05-07 04:21 2.6K
chrXIII_est.sql 2012-05-28 14:19 2.0K
chrXIII_est.txt.gz 2012-05-28 14:19 70K
chrXIII_intronEst.sql 2011-10-06 16:18 2.1K
chrXIII_intronEst.txt.gz 2011-10-06 16:18 5.6K
chrXIII_mrna.sql 2020-05-07 04:20 2.1K
chrXIII_mrna.txt.gz 2020-05-07 04:20 3.3K
chrXII_est.sql 2012-05-28 14:19 2.0K
chrXII_est.txt.gz 2012-05-28 14:19 81K
chrXII_intronEst.sql 2012-05-28 14:19 2.1K
chrXII_intronEst.txt.gz 2012-05-28 14:19 5.7K
chrXII_mrna.sql 2020-05-07 04:20 2.1K
chrXII_mrna.txt.gz 2020-05-07 04:20 4.7K
chrXIV_est.sql 2012-05-28 14:19 2.0K
chrXIV_est.txt.gz 2012-05-28 14:19 46K
chrXIV_intronEst.sql 2011-10-06 16:17 2.1K
chrXIV_intronEst.txt.gz 2011-10-06 16:17 2.5K
chrXIV_mrna.sql 2020-05-07 04:20 2.1K
chrXIV_mrna.txt.gz 2020-05-07 04:20 2.8K
chrXI_est.sql 2012-05-28 14:19 2.0K
chrXI_est.txt.gz 2012-05-28 14:19 49K
chrXI_intronEst.sql 2011-10-06 16:18 2.1K
chrXI_intronEst.txt.gz 2011-10-06 16:18 3.2K
chrXI_mrna.sql 2020-05-07 04:20 2.1K
chrXI_mrna.txt.gz 2020-05-07 04:20 2.3K
chrXVI_est.sql 2012-05-28 14:19 2.0K
chrXVI_est.txt.gz 2012-05-28 14:19 85K
chrXVI_intronEst.sql 2012-05-28 14:19 2.1K
chrXVI_intronEst.txt.gz 2012-05-28 14:19 6.6K
chrXVI_mrna.sql 2020-05-07 04:20 2.1K
chrXVI_mrna.txt.gz 2020-05-07 04:20 3.1K
chrXV_est.sql 2012-05-28 14:19 2.0K
chrXV_est.txt.gz 2012-05-28 14:19 100K
chrXV_intronEst.sql 2011-10-06 16:15 2.1K
chrXV_intronEst.txt.gz 2011-10-06 16:15 5.3K
chrXV_mrna.sql 2020-05-07 04:20 2.1K
chrXV_mrna.txt.gz 2020-05-07 04:20 3.2K
chrX_est.sql 2012-05-28 14:19 2.0K
chrX_est.txt.gz 2012-05-28 14:19 49K
chrX_intronEst.sql 2012-05-28 14:19 2.0K
chrX_intronEst.txt.gz 2012-05-28 14:19 3.3K
chrX_mrna.sql 2020-05-07 04:25 2.1K
chrX_mrna.txt.gz 2020-05-07 04:25 3.4K
chromAlias.sql 2018-08-05 09:15 1.4K
chromAlias.txt.gz 2018-08-05 09:15 338
chromInfo.sql 2011-10-06 16:17 1.3K
chromInfo.txt.gz 2011-10-06 16:17 193
crisprRanges.sql 2016-11-06 09:28 1.4K
crisprRanges.txt.gz 2016-11-06 09:28 22K
crisprTargets.sql 2016-11-06 09:28 1.3K
crisprTargets.txt.gz 2016-11-06 09:28 63
dmBlastTab.sql 2011-10-06 16:17 1.6K
dmBlastTab.txt.gz 2011-10-06 16:17 85K
drBlastTab.sql 2017-09-11 02:52 1.7K
drBlastTab.txt.gz 2017-09-11 02:52 61K
ensGene.sql 2021-05-25 14:46 1.9K
ensGene.txt.gz 2021-05-25 14:46 150K
ensGtp.sql 2021-05-25 14:46 1.4K
ensGtp.txt.gz 2021-05-25 14:46 59K
ensPep.sql 2021-05-25 14:46 1.3K
ensPep.txt.gz 2021-05-25 14:46 1.7M
ensemblSource.sql 2021-05-25 14:46 1.4K
ensemblSource.txt.gz 2021-05-25 14:46 22K
ensemblToGeneName.sql 2021-05-25 14:46 1.4K
ensemblToGeneName.txt.gz 2021-05-25 14:46 31K
esRegGeneToModule.sql 2011-10-06 16:18 1.3K
esRegGeneToModule.txt.gz 2011-10-06 16:18 9.1K
esRegGeneToMotif.sql 2011-10-06 16:18 1.6K
esRegGeneToMotif.txt.gz 2011-10-06 16:18 38K
esRegMotif.sql 2011-10-06 16:15 1.4K
esRegMotif.txt.gz 2011-10-06 16:15 17K
esRegUpstreamRegion.sql 2011-10-06 16:18 1.6K
esRegUpstreamRegion.txt.gz 2011-10-06 16:18 19K
estOrientInfo.sql 2012-05-28 14:19 1.7K
estOrientInfo.txt.gz 2012-05-28 14:19 306K
extFile.sql 2011-10-06 16:17 1.4K
extFile.txt.gz 2011-10-06 16:17 265
extNcbiRefSeq.sql 2021-02-10 16:08 1.5K
extNcbiRefSeq.txt.gz 2021-02-10 16:08 89
gap.sql 2011-10-06 16:17 1.5K
gap.txt.gz 2011-10-06 16:17 28
gbLoaded.sql 2020-08-20 09:58 1.6K
gbLoaded.txt.gz 2020-08-20 09:58 90K
gc5BaseBw.sql 2011-10-06 16:17 1.2K
gc5BaseBw.txt.gz 2011-10-06 16:17 63
gold.sql 2011-10-06 16:17 1.6K
gold.txt.gz 2011-10-06 16:17 287
growthCondition.sql 2014-10-19 15:03 1.4K
growthCondition.txt.gz 2014-10-19 15:03 685
grp.sql 2014-03-02 04:14 1.3K
grp.txt.gz 2014-03-02 04:14 199
hgBlastTab.sql 2022-07-12 17:02 1.7K
hgBlastTab.txt.gz 2022-07-12 17:02 60K
hgFindSpec.sql 2024-07-25 09:34 1.8K
hgFindSpec.txt.gz 2024-07-25 09:34 1.2K
history.sql 2014-10-19 15:03 1.6K
history.txt.gz 2014-10-19 15:03 1.9K
locusName.sql 2016-11-06 09:28 1.5K
locusName.txt.gz 2016-11-06 09:28 141K
microsat.sql 2015-08-24 01:24 1.5K
microsat.txt.gz 2015-08-24 01:24 345
mmBlastTab.sql 2022-07-12 17:09 1.7K
mmBlastTab.txt.gz 2022-07-12 17:09 61K
mrnaOrientInfo.sql 2020-05-07 04:28 1.8K
mrnaOrientInfo.txt.gz 2020-05-07 04:28 19K
multiz7way.sql 2011-10-06 16:15 1.5K
multiz7way.txt.gz 2011-10-06 16:15 669K
multiz7wayFrames.sql 2011-10-06 16:18 1.7K
multiz7wayFrames.txt.gz 2011-10-06 16:18 83K
multiz7waySummary.sql 2011-10-06 16:15 1.5K
multiz7waySummary.txt.gz 2011-10-06 16:15 33K
ncbiRefSeq.sql 2021-02-10 15:45 2.0K
ncbiRefSeq.txt.gz 2021-02-10 15:45 140K
ncbiRefSeqCds.sql 2021-02-10 16:08 1.4K
ncbiRefSeqCds.txt.gz 2021-02-10 16:08 30K
ncbiRefSeqCurated.sql 2021-02-10 15:45 2.0K
ncbiRefSeqCurated.txt.gz 2021-02-10 15:45 140K
ncbiRefSeqLink.sql 2021-02-10 15:45 2.0K
ncbiRefSeqLink.txt.gz 2021-02-10 15:45 661K
ncbiRefSeqOther.sql 2021-02-10 16:07 1.3K
ncbiRefSeqOther.txt.gz 2021-02-10 16:07 75
ncbiRefSeqPepTable.sql 2021-02-10 16:08 1.4K
ncbiRefSeqPepTable.txt.gz 2021-02-10 16:08 1.6M
ncbiRefSeqPsl.sql 2021-02-10 15:45 2.1K
ncbiRefSeqPsl.txt.gz 2021-02-10 15:45 158K
oreganno.sql 2016-05-15 11:29 1.5K
oreganno.txt.gz 2016-05-15 11:29 85K
oregannoAttr.sql 2016-05-15 11:29 1.4K
oregannoAttr.txt.gz 2016-05-15 11:29 118K
oregannoLink.sql 2016-05-15 11:29 1.4K
oregannoLink.txt.gz 2016-05-15 11:29 83K
phastCons7way.sql 2011-10-06 16:15 1.7K
phastCons7way.txt.gz 2011-10-06 16:15 305K
phastConsElements7way.sql 2011-10-06 16:15 1.5K
phastConsElements7way.txt.gz 2011-10-06 16:15 503K
pslChainAWRI1631.sql 2011-10-06 16:15 2.1K
pslChainAWRI1631.txt.gz 2011-10-06 16:15 3.3M
rnBlastTab.sql 2012-02-26 05:30 1.6K
rnBlastTab.txt.gz 2012-02-26 05:30 42K
seqNcbiRefSeq.sql 2021-02-10 16:08 1.6K
seqNcbiRefSeq.txt.gz 2021-02-10 16:08 88K
sgdBlastTab.sql 2011-10-06 16:15 1.6K
sgdBlastTab.txt.gz 2011-10-06 16:15 943K
sgdCanonical.sql 2011-10-06 16:18 1.5K
sgdCanonical.txt.gz 2011-10-06 16:18 102K
sgdClone.sql 2011-10-06 16:18 1.5K
sgdClone.txt.gz 2011-10-06 16:18 16K
sgdDescription.sql 2011-10-06 16:17 1.3K
sgdDescription.txt.gz 2011-10-06 16:17 337K
sgdGene.sql 2011-10-06 16:18 1.7K
sgdGene.txt.gz 2011-10-06 16:18 131K
sgdIsoforms.sql 2011-10-06 16:18 1.3K
sgdIsoforms.txt.gz 2011-10-06 16:18 31K
sgdOther.sql 2011-10-06 16:15 1.5K
sgdOther.txt.gz 2011-10-06 16:15 41K
sgdOtherDescription.sql 2011-10-06 16:17 1.3K
sgdOtherDescription.txt.gz 2011-10-06 16:17 12K
sgdPep.sql 2011-10-06 16:15 1.3K
sgdPep.txt.gz 2011-10-06 16:15 1.7M
sgdToName.sql 2011-10-06 16:18 1.3K
sgdToName.txt.gz 2011-10-06 16:18 36K
sgdToSwissProt.sql 2011-10-06 16:18 1.3K
sgdToSwissProt.txt.gz 2011-10-06 16:18 31K
simpleRepeat.sql 2011-10-06 16:18 1.9K
simpleRepeat.txt.gz 2011-10-06 16:18 54K
tableDescriptions.sql 2024-11-16 02:03 1.4K
tableDescriptions.txt.gz 2024-11-16 02:03 7.6K
tableList.sql 2024-11-17 03:36 1.6K
tableList.txt.gz 2024-11-17 03:36 6.9K
trackDb.sql 2024-07-25 09:34 2.1K
trackDb.txt.gz 2024-07-25 09:34 49K
transRegCode.sql 2011-10-06 16:15 1.5K
transRegCode.txt.gz 2011-10-06 16:15 1.4M
transRegCodeCondition.sql 2011-10-06 16:18 1.4K
transRegCodeCondition.txt.gz 2011-10-06 16:18 1.2K
transRegCodeMotif.sql 2011-10-06 16:18 1.4K
transRegCodeMotif.txt.gz 2011-10-06 16:18 6.5K
transRegCodeProbe.sql 2011-10-06 16:15 1.5K
transRegCodeProbe.txt.gz 2011-10-06 16:15 143K
xenoRefFlat.sql 2020-08-20 09:46 1.7K
xenoRefFlat.txt.gz 2020-08-20 09:46 1.0M
xenoRefGene.sql 2020-08-20 09:46 2.0K
xenoRefGene.txt.gz 2020-08-20 09:46 1.1M
xenoRefSeqAli.sql 2020-08-20 09:46 2.1K
xenoRefSeqAli.txt.gz 2020-08-20 09:46 1.2M