This directory contains a dump of the UCSC genome annotation database for
the June 2008 assembly of the S. cerevisiae genome (sacCer2, SGD June 2008).
The annotations were generated by UCSC and collaborators worldwide.
The data is based on sequence dated June 2008 in the Saccharomyces Genome
Database (http://www.yeastgenome.org/) and was obtained from the site
http://downloads.yeastgenome.org/sequence/genomic_sequence/chromosomes/fasta/
The S288C strain was used in this sequencing project.
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=sacCer2
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/sacCer2/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/sacCer2/database/ .
For a single file, e.g. gc5BaseBw.txt.gz
rsync -avzP
rsync://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/database/gc5BaseBw.txt.gz .
Or with wget, all files:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/database/*'
With wget, a single file:
wget --timestamping
'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/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 sacCer2 < chromInfo.sql
## load data from the txt.gz file
$ zcat chromInfo.txt.gz | hgsql sacCer2 --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 -
yeastP2P.txt.gz 2009-08-09 10:20 27M
yeastP2P.sql 2009-08-09 10:20 1.3K
xenoRefSeqAli.txt.gz 2020-09-01 14:19 1.0M
xenoRefSeqAli.sql 2020-09-01 14:19 2.1K
xenoRefGene.txt.gz 2020-09-01 14:19 689K
xenoRefGene.sql 2020-09-01 14:19 2.0K
xenoRefFlat.txt.gz 2020-09-01 14:19 629K
xenoRefFlat.sql 2020-09-01 14:19 1.7K
uwFootprintsTagCounts.txt.gz 2009-08-16 10:16 35M
uwFootprintsTagCounts.sql 2009-08-16 10:16 1.9K
uwFootprintsPrints.txt.gz 2009-08-06 15:37 52K
uwFootprintsPrints.sql 2009-08-06 15:37 1.5K
uwFootprintsMappability.txt.gz 2009-08-06 15:37 100K
uwFootprintsMappability.sql 2009-08-06 15:37 1.4K
transRegCodeProbe.txt.gz 2009-08-09 10:20 143K
transRegCodeProbe.sql 2009-08-09 10:20 1.6K
transRegCodeMotif.txt.gz 2009-08-09 10:21 6.5K
transRegCodeMotif.sql 2009-08-09 10:21 1.4K
transRegCodeCondition.txt.gz 2013-11-10 22:14 1.2K
transRegCodeCondition.sql 2013-11-10 22:14 1.5K
transRegCode.txt.gz 2009-08-09 10:21 1.4M
transRegCode.sql 2009-08-09 10:21 1.6K
trackDb.txt.gz 2023-03-28 13:53 37K
trackDb.sql 2023-03-28 13:53 2.1K
tableList.txt.gz 2024-12-08 03:12 7.9K
tableList.sql 2024-12-08 03:12 1.6K
tableDescriptions.txt.gz 2024-12-07 02:03 8.3K
tableDescriptions.sql 2024-12-07 02:03 1.5K
simpleRepeat.txt.gz 2009-08-09 10:20 54K
simpleRepeat.sql 2009-08-09 10:20 2.0K
sgdToSwissProt.txt.gz 2009-08-09 10:20 32K
sgdToSwissProt.sql 2009-08-09 10:20 1.3K
sgdToPfam.txt.gz 2009-08-09 10:20 22K
sgdToPfam.sql 2009-08-09 10:20 1.3K
sgdToName.txt.gz 2009-08-06 15:37 38K
sgdToName.sql 2009-08-06 15:37 1.3K
sgdPep.txt.gz 2009-08-09 10:21 1.6M
sgdPep.sql 2009-08-09 10:21 1.3K
sgdOtherDescription.txt.gz 2009-08-09 10:20 15K
sgdOtherDescription.sql 2009-08-09 10:20 1.3K
sgdOther.txt.gz 2009-08-06 15:37 33K
sgdOther.sql 2009-08-06 15:37 1.6K
sgdLocalization.txt.gz 2009-08-06 15:37 19K
sgdLocalization.sql 2009-08-06 15:37 1.3K
sgdIsoforms.txt.gz 2009-08-06 15:37 30K
sgdIsoforms.sql 2009-08-06 15:37 1.4K
sgdGene.txt.gz 2009-08-09 10:21 131K
sgdGene.sql 2009-08-09 10:21 1.8K
sgdDescription.txt.gz 2009-08-06 15:37 317K
sgdDescription.sql 2009-08-06 15:37 1.3K
sgdClone.txt.gz 2009-08-09 10:20 16K
sgdClone.sql 2009-08-09 10:20 1.5K
sgdCanonical.txt.gz 2009-08-09 10:20 102K
sgdCanonical.sql 2009-08-09 10:20 1.6K
sgdBlastTab.txt.gz 2010-08-29 10:59 821K
sgdBlastTab.sql 2010-08-29 10:59 1.6K
sgdAbundance.txt.gz 2009-08-09 10:21 19K
sgdAbundance.sql 2009-08-09 10:21 1.3K
rnBlastTab.txt.gz 2010-08-29 10:59 31K
rnBlastTab.sql 2010-08-29 10:59 1.6K
pubsBlatPsl.txt.gz 2012-05-09 09:26 657K
pubsBlatPsl.sql 2012-05-09 09:26 2.1K
pubsBlat.txt.gz 2012-05-09 09:26 384K
pubsBlat.sql 2012-05-09 09:26 1.9K
pubsBingBlatPsl.txt.gz 2014-01-26 18:33 1.1M
pubsBingBlatPsl.sql 2014-01-26 18:33 2.2K
pubsBingBlat.txt.gz 2014-01-26 18:33 1.3M
pubsBingBlat.sql 2014-01-26 18:33 2.4K
phastConsElements7way.txt.gz 2009-08-09 10:21 382K
phastConsElements7way.sql 2009-08-09 10:21 1.6K
phastCons7way.txt.gz 2009-08-09 10:20 301K
phastCons7way.sql 2009-08-09 10:20 1.9K
oregannoLink.txt.gz 2016-05-15 11:29 83K
oregannoLink.sql 2016-05-15 11:29 1.4K
oregannoAttr.txt.gz 2016-05-15 11:29 118K
oregannoAttr.sql 2016-05-15 11:29 1.4K
oreganno.txt.gz 2016-05-15 11:29 85K
oreganno.sql 2016-05-15 11:29 1.5K
multiz7waySummary.txt.gz 2009-08-09 10:20 33K
multiz7waySummary.sql 2009-08-09 10:20 1.6K
multiz7wayFrames.txt.gz 2009-08-06 15:37 79K
multiz7wayFrames.sql 2009-08-06 15:37 1.8K
multiz7way.txt.gz 2009-08-09 10:20 537K
multiz7way.sql 2009-08-09 10:20 1.5K
mrnaOrientInfo.txt.gz 2020-09-01 14:05 18K
mrnaOrientInfo.sql 2020-09-01 14:05 1.8K
mmBlastTab.txt.gz 2011-05-30 01:51 55K
mmBlastTab.sql 2011-05-30 01:51 1.6K
microsat.txt.gz 2015-08-24 01:24 341
microsat.sql 2015-08-24 01:24 1.5K
history.txt.gz 2009-08-09 10:21 1.2K
history.sql 2009-08-09 10:21 1.6K
hgFindSpec.txt.gz 2023-03-28 13:53 944
hgFindSpec.sql 2023-03-28 13:53 1.8K
hgBlastTab.txt.gz 2010-08-29 10:59 56K
hgBlastTab.sql 2010-08-29 10:59 1.6K
grp.txt.gz 2014-03-02 04:14 199
grp.sql 2014-03-02 04:14 1.4K
growthCondition.txt.gz 2011-09-12 00:03 685
growthCondition.sql 2011-09-12 00:03 1.3K
gc5Base.txt.gz 2009-08-09 10:21 43K
gc5Base.sql 2009-08-09 10:21 1.9K
gbLoaded.txt.gz 2020-09-01 14:39 1.4K
gbLoaded.sql 2020-09-01 14:39 1.6K
extFile.txt.gz 2009-08-06 15:37 289
extFile.sql 2009-08-06 15:37 1.4K
estOrientInfo.txt.gz 2020-09-01 14:39 304K
estOrientInfo.sql 2020-09-01 14:39 1.8K
esRegUpstreamRegion.txt.gz 2009-08-09 10:20 19K
esRegUpstreamRegion.sql 2009-08-09 10:20 1.6K
esRegMotif.txt.gz 2009-08-06 15:37 17K
esRegMotif.sql 2009-08-06 15:37 1.4K
esRegGeneToMotif.txt.gz 2009-08-06 15:37 39K
esRegGeneToMotif.sql 2009-08-06 15:37 1.6K
esRegGeneToModule.txt.gz 2009-08-06 15:37 9.1K
esRegGeneToModule.sql 2009-08-06 15:37 1.3K
ensPep.txt.gz 2011-03-15 11:37 1.7M
ensPep.sql 2011-03-15 11:37 1.3K
ensGtp.txt.gz 2011-03-15 11:37 30K
ensGtp.sql 2011-03-15 11:37 1.4K
ensGene.txt.gz 2011-03-15 11:37 149K
ensGene.sql 2011-03-15 11:37 1.9K
drBlastTab.txt.gz 2013-10-27 21:15 55K
drBlastTab.sql 2013-10-27 21:15 1.7K
dmBlastTab.txt.gz 2010-08-29 10:59 49K
dmBlastTab.sql 2010-08-29 10:59 1.6K
chromInfo.txt.gz 2009-08-09 10:20 203
chromInfo.sql 2009-08-09 10:20 1.3K
chrX_mrna.txt.gz 2020-09-01 14:05 3.4K
chrX_mrna.sql 2020-09-01 14:05 2.1K
chrX_intronEst.txt.gz 2020-09-01 14:39 3.3K
chrX_intronEst.sql 2020-09-01 14:39 2.1K
chrX_gold.txt.gz 2009-08-09 10:20 68
chrX_gold.sql 2009-08-09 10:20 1.7K
chrX_gap.txt.gz 2009-08-09 10:21 33
chrX_gap.sql 2009-08-09 10:21 1.6K
chrX_est.txt.gz 2020-09-01 14:39 49K
chrX_est.sql 2020-09-01 14:39 2.1K
chrXV_mrna.txt.gz 2020-09-01 14:05 3.2K
chrXV_mrna.sql 2020-09-01 14:05 2.1K
chrXV_intronEst.txt.gz 2020-09-01 14:39 5.3K
chrXV_intronEst.sql 2020-09-01 14:39 2.1K
chrXV_gold.txt.gz 2009-08-09 10:21 71
chrXV_gold.sql 2009-08-09 10:21 1.7K
chrXV_gap.txt.gz 2009-08-09 10:20 34
chrXV_gap.sql 2009-08-09 10:20 1.6K
chrXV_est.txt.gz 2020-09-01 14:39 100K
chrXV_est.sql 2020-09-01 14:39 2.1K
chrXVI_mrna.txt.gz 2020-09-01 14:05 3.1K
chrXVI_mrna.sql 2020-09-01 14:05 2.1K
chrXVI_intronEst.txt.gz 2020-09-01 14:39 6.6K
chrXVI_intronEst.sql 2020-09-01 14:39 2.1K
chrXVI_gold.txt.gz 2009-08-09 10:21 73
chrXVI_gold.sql 2009-08-09 10:21 1.7K
chrXVI_gap.txt.gz 2009-08-09 10:20 35
chrXVI_gap.sql 2009-08-09 10:20 1.6K
chrXVI_est.txt.gz 2020-09-01 14:39 84K
chrXVI_est.sql 2020-09-01 14:39 2.1K
chrXI_mrna.txt.gz 2020-09-01 14:05 2.4K
chrXI_mrna.sql 2020-09-01 14:05 2.1K
chrXI_intronEst.txt.gz 2020-09-01 14:39 3.3K
chrXI_intronEst.sql 2020-09-01 14:39 2.1K
chrXI_gold.txt.gz 2009-08-09 10:21 71
chrXI_gold.sql 2009-08-09 10:21 1.7K
chrXI_gap.txt.gz 2009-08-09 10:21 34
chrXI_gap.sql 2009-08-09 10:21 1.6K
chrXI_est.txt.gz 2020-09-01 14:39 49K
chrXI_est.sql 2020-09-01 14:39 2.1K
chrXIV_mrna.txt.gz 2020-09-01 14:05 2.8K
chrXIV_mrna.sql 2020-09-01 14:05 2.1K
chrXIV_intronEst.txt.gz 2020-09-01 14:39 2.5K
chrXIV_intronEst.sql 2020-09-01 14:39 2.1K
chrXIV_gold.txt.gz 2009-08-06 15:37 73
chrXIV_gold.sql 2009-08-06 15:37 1.7K
chrXIV_gap.txt.gz 2009-08-09 10:21 35
chrXIV_gap.sql 2009-08-09 10:21 1.6K
chrXIV_est.txt.gz 2020-09-01 14:39 47K
chrXIV_est.sql 2020-09-01 14:39 2.1K
chrXII_mrna.txt.gz 2020-09-01 14:05 4.6K
chrXII_mrna.sql 2020-09-01 14:05 2.1K
chrXII_intronEst.txt.gz 2020-09-01 14:39 5.7K
chrXII_intronEst.sql 2020-09-01 14:39 2.1K
chrXII_gold.txt.gz 2009-08-09 10:20 73
chrXII_gold.sql 2009-08-09 10:20 1.7K
chrXII_gap.txt.gz 2009-08-06 15:37 35
chrXII_gap.sql 2009-08-06 15:37 1.6K
chrXII_est.txt.gz 2020-09-01 14:39 81K
chrXII_est.sql 2020-09-01 14:39 2.1K
chrXIII_mrna.txt.gz 2020-09-01 14:05 3.4K
chrXIII_mrna.sql 2020-09-01 14:05 2.1K
chrXIII_intronEst.txt.gz 2020-09-01 14:39 5.7K
chrXIII_intronEst.sql 2020-09-01 14:39 2.1K
chrXIII_gold.txt.gz 2009-08-06 15:37 75
chrXIII_gold.sql 2009-08-06 15:37 1.7K
chrXIII_gap.txt.gz 2009-08-09 10:21 36
chrXIII_gap.sql 2009-08-09 10:21 1.6K
chrXIII_est.txt.gz 2020-09-01 14:39 70K
chrXIII_est.sql 2020-09-01 14:39 2.1K
chrV_mrna.txt.gz 2020-09-01 14:05 2.6K
chrV_mrna.sql 2020-09-01 14:05 2.1K
chrV_intronEst.txt.gz 2020-09-01 14:39 3.5K
chrV_intronEst.sql 2020-09-01 14:39 2.1K
chrV_gold.txt.gz 2009-08-09 10:20 68
chrV_gold.sql 2009-08-09 10:20 1.7K
chrV_gap.txt.gz 2009-08-09 10:20 33
chrV_gap.sql 2009-08-09 10:20 1.6K
chrV_est.txt.gz 2020-09-01 14:39 52K
chrV_est.sql 2020-09-01 14:39 2.1K
chrVI_mrna.txt.gz 2020-09-01 14:05 1.1K
chrVI_mrna.sql 2020-09-01 14:05 2.1K
chrVI_intronEst.txt.gz 2020-09-01 14:39 2.9K
chrVI_intronEst.sql 2020-09-01 14:39 2.1K
chrVI_gold.txt.gz 2009-08-09 10:21 70
chrVI_gold.sql 2009-08-09 10:21 1.7K
chrVI_gap.txt.gz 2009-08-06 15:37 34
chrVI_gap.sql 2009-08-06 15:37 1.6K
chrVI_est.txt.gz 2020-09-01 14:39 30K
chrVI_est.sql 2020-09-01 14:39 2.1K
chrVII_mrna.txt.gz 2020-09-01 14:05 4.4K
chrVII_mrna.sql 2020-09-01 14:05 2.1K
chrVII_intronEst.txt.gz 2020-09-01 14:39 8.4K
chrVII_intronEst.sql 2020-09-01 14:39 2.1K
chrVII_gold.txt.gz 2009-08-06 15:37 72
chrVII_gold.sql 2009-08-06 15:37 1.7K
chrVII_gap.txt.gz 2009-08-09 10:20 35
chrVII_gap.sql 2009-08-09 10:20 1.6K
chrVII_est.txt.gz 2020-09-01 14:39 84K
chrVII_est.sql 2020-09-01 14:39 2.1K
chrVIII_mrna.txt.gz 2020-09-01 14:05 1.9K
chrVIII_mrna.sql 2020-09-01 14:05 2.1K
chrVIII_intronEst.txt.gz 2020-09-01 14:39 3.7K
chrVIII_intronEst.sql 2020-09-01 14:39 2.1K
chrVIII_gold.txt.gz 2009-08-09 10:21 74
chrVIII_gold.sql 2009-08-09 10:21 1.7K
chrVIII_gap.txt.gz 2009-08-09 10:21 36
chrVIII_gap.sql 2009-08-09 10:21 1.6K
chrVIII_est.txt.gz 2020-09-01 14:39 32K
chrVIII_est.sql 2020-09-01 14:39 2.1K
chrM_mrna.txt.gz 2020-09-01 14:05 854
chrM_mrna.sql 2020-09-01 14:05 2.1K
chrM_intronEst.txt.gz 2020-09-01 14:08 39
chrM_intronEst.sql 2020-09-01 14:08 2.1K
chrM_gold.txt.gz 2009-08-06 15:37 68
chrM_gold.sql 2009-08-06 15:37 1.7K
chrM_gap.txt.gz 2009-08-09 10:20 33
chrM_gap.sql 2009-08-09 10:20 1.6K
chrM_est.txt.gz 2020-09-01 14:06 33
chrM_est.sql 2020-09-01 14:06 2.1K
chrI_mrna.txt.gz 2020-09-01 14:05 941
chrI_mrna.sql 2020-09-01 14:05 2.1K
chrI_intronEst.txt.gz 2020-09-01 14:08 1.1K
chrI_intronEst.sql 2020-09-01 14:08 2.1K
chrI_gold.txt.gz 2009-08-09 10:20 68
chrI_gold.sql 2009-08-09 10:20 1.7K
chrI_gap.txt.gz 2009-08-09 10:20 33
chrI_gap.sql 2009-08-09 10:20 1.6K
chrI_est.txt.gz 2020-09-01 14:39 11K
chrI_est.sql 2020-09-01 14:39 2.1K
chrIX_mrna.txt.gz 2020-09-01 14:05 1.6K
chrIX_mrna.sql 2020-09-01 14:05 2.1K
chrIX_intronEst.txt.gz 2020-09-01 14:39 2.6K
chrIX_intronEst.sql 2020-09-01 14:39 2.1K
chrIX_gold.txt.gz 2009-08-06 15:37 70
chrIX_gold.sql 2009-08-06 15:37 1.7K
chrIX_gap.txt.gz 2009-08-09 10:21 34
chrIX_gap.sql 2009-08-09 10:21 1.6K
chrIX_est.txt.gz 2020-09-01 14:39 24K
chrIX_est.sql 2020-09-01 14:39 2.1K
chrIV_mrna.txt.gz 2020-09-01 14:05 5.6K
chrIV_mrna.sql 2020-09-01 14:05 2.1K
chrIV_intronEst.txt.gz 2020-09-01 14:39 12K
chrIV_intronEst.sql 2020-09-01 14:39 2.1K
chrIV_gold.txt.gz 2009-08-09 10:20 70
chrIV_gold.sql 2009-08-09 10:20 1.7K
chrIV_gap.txt.gz 2009-08-09 10:20 34
chrIV_gap.sql 2009-08-09 10:20 1.6K
chrIV_est.txt.gz 2020-09-01 14:39 148K
chrIV_est.sql 2020-09-01 14:39 2.1K
chrII_mrna.txt.gz 2020-09-01 14:05 3.2K
chrII_mrna.sql 2020-09-01 14:05 2.1K
chrII_intronEst.txt.gz 2020-09-01 14:39 9.0K
chrII_intronEst.sql 2020-09-01 14:39 2.1K
chrII_gold.txt.gz 2009-08-06 15:37 70
chrII_gold.sql 2009-08-06 15:37 1.7K
chrII_gap.txt.gz 2009-08-09 10:21 34
chrII_gap.sql 2009-08-09 10:21 1.6K
chrII_est.txt.gz 2020-09-01 14:39 71K
chrII_est.sql 2020-09-01 14:39 2.1K
chrIII_mrna.txt.gz 2020-09-01 14:05 1.2K
chrIII_mrna.sql 2020-09-01 14:05 2.1K
chrIII_intronEst.txt.gz 2020-09-01 14:39 1.5K
chrIII_intronEst.sql 2020-09-01 14:39 2.1K
chrIII_gold.txt.gz 2009-08-09 10:20 72
chrIII_gold.sql 2009-08-09 10:20 1.7K
chrIII_gap.txt.gz 2009-08-09 10:21 35
chrIII_gap.sql 2009-08-09 10:21 1.6K
chrIII_est.txt.gz 2020-09-01 14:39 32K
chrIII_est.sql 2020-09-01 14:39 2.1K
choExpDistance.txt.gz 2009-08-09 10:21 34M
choExpDistance.sql 2009-08-09 10:21 1.3K
ceBlastTab.txt.gz 2010-08-29 10:59 48K
ceBlastTab.sql 2010-08-29 10:59 1.6K
blastHg18KG.txt.gz 2009-08-09 10:21 293K
blastHg18KG.sql 2009-08-09 10:21 2.3K
bigFiles.txt.gz 2024-12-08 03:12 33
bigFiles.sql 2024-12-08 03:12 1.4K
augustusGene.txt.gz 2015-07-26 17:28 109K
augustusGene.sql 2015-07-26 17:28 1.9K
all_mrna.txt.gz 2020-09-01 14:05 44K
all_mrna.sql 2020-09-01 14:05 2.1K
all_est.txt.gz 2020-09-01 14:39 960K
all_est.sql 2020-09-01 14:39 2.1K
2micron_mrna.txt.gz 2009-08-09 10:21 37
2micron_mrna.sql 2009-08-09 10:21 2.3K
2micron_intronEst.txt.gz 2009-08-06 15:37 42
2micron_intronEst.sql 2009-08-06 15:37 2.3K
2micron_gold.txt.gz 2009-08-09 10:21 74
2micron_gold.sql 2009-08-09 10:21 1.7K
2micron_gap.txt.gz 2009-08-09 10:21 36
2micron_gap.sql 2009-08-09 10:21 1.6K
2micron_est.txt.gz 2012-05-28 14:19 607
2micron_est.sql 2012-05-28 14:19 2.3K