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 -
uwFootprintsTagCounts.txt.gz 2009-08-16 10:16 35M
choExpDistance.txt.gz 2009-08-09 10:21 34M
yeastP2P.txt.gz 2009-08-09 10:20 27M
ensPep.txt.gz 2011-03-15 11:37 1.7M
sgdPep.txt.gz 2009-08-09 10:21 1.6M
transRegCode.txt.gz 2009-08-09 10:21 1.4M
pubsBingBlat.txt.gz 2014-01-26 18:33 1.3M
pubsBingBlatPsl.txt.gz 2014-01-26 18:33 1.1M
xenoRefSeqAli.txt.gz 2020-09-01 14:19 1.0M
all_est.txt.gz 2020-09-01 14:39 960K
sgdBlastTab.txt.gz 2010-08-29 10:59 821K
xenoRefGene.txt.gz 2020-09-01 14:19 689K
pubsBlatPsl.txt.gz 2012-05-09 09:26 657K
xenoRefFlat.txt.gz 2020-09-01 14:19 629K
multiz7way.txt.gz 2009-08-09 10:20 537K
pubsBlat.txt.gz 2012-05-09 09:26 384K
phastConsElements7way.txt.gz 2009-08-09 10:21 382K
sgdDescription.txt.gz 2009-08-06 15:37 317K
estOrientInfo.txt.gz 2020-09-01 14:39 304K
phastCons7way.txt.gz 2009-08-09 10:20 301K
blastHg18KG.txt.gz 2009-08-09 10:21 293K
ensGene.txt.gz 2011-03-15 11:37 149K
chrIV_est.txt.gz 2020-09-01 14:39 148K
transRegCodeProbe.txt.gz 2009-08-09 10:20 143K
sgdGene.txt.gz 2009-08-09 10:21 131K
oregannoAttr.txt.gz 2016-05-15 11:29 118K
augustusGene.txt.gz 2015-07-26 17:28 109K
sgdCanonical.txt.gz 2009-08-09 10:20 102K
uwFootprintsMappability.txt.gz 2009-08-06 15:37 100K
chrXV_est.txt.gz 2020-09-01 14:39 100K
oreganno.txt.gz 2016-05-15 11:29 85K
chrXVI_est.txt.gz 2020-09-01 14:39 84K
chrVII_est.txt.gz 2020-09-01 14:39 84K
oregannoLink.txt.gz 2016-05-15 11:29 83K
chrXII_est.txt.gz 2020-09-01 14:39 81K
multiz7wayFrames.txt.gz 2009-08-06 15:37 79K
chrII_est.txt.gz 2020-09-01 14:39 71K
chrXIII_est.txt.gz 2020-09-01 14:39 70K
hgBlastTab.txt.gz 2010-08-29 10:59 56K
mmBlastTab.txt.gz 2011-05-30 01:51 55K
drBlastTab.txt.gz 2013-10-27 21:15 55K
simpleRepeat.txt.gz 2009-08-09 10:20 54K
chrV_est.txt.gz 2020-09-01 14:39 52K
uwFootprintsPrints.txt.gz 2009-08-06 15:37 52K
chrXI_est.txt.gz 2020-09-01 14:39 49K
dmBlastTab.txt.gz 2010-08-29 10:59 49K
chrX_est.txt.gz 2020-09-01 14:39 49K
ceBlastTab.txt.gz 2010-08-29 10:59 48K
chrXIV_est.txt.gz 2020-09-01 14:39 47K
all_mrna.txt.gz 2020-09-01 14:05 44K
gc5Base.txt.gz 2009-08-09 10:21 43K
esRegGeneToMotif.txt.gz 2009-08-06 15:37 39K
sgdToName.txt.gz 2009-08-06 15:37 38K
trackDb.txt.gz 2023-03-28 13:53 37K
trackDb_pushedout.txt.gz 2021-12-27 12:23 35K
sgdOther.txt.gz 2009-08-06 15:37 33K
multiz7waySummary.txt.gz 2009-08-09 10:20 33K
chrVIII_est.txt.gz 2020-09-01 14:39 32K
sgdToSwissProt.txt.gz 2009-08-09 10:20 32K
chrIII_est.txt.gz 2020-09-01 14:39 32K
rnBlastTab.txt.gz 2010-08-29 10:59 31K
sgdIsoforms.txt.gz 2009-08-06 15:37 30K
chrVI_est.txt.gz 2020-09-01 14:39 30K
ensGtp.txt.gz 2011-03-15 11:37 30K
chrIX_est.txt.gz 2020-09-01 14:39 24K
sgdToPfam.txt.gz 2009-08-09 10:20 22K
sgdLocalization.txt.gz 2009-08-06 15:37 19K
esRegUpstreamRegion.txt.gz 2009-08-09 10:20 19K
sgdAbundance.txt.gz 2009-08-09 10:21 19K
mrnaOrientInfo.txt.gz 2020-09-01 14:05 18K
esRegMotif.txt.gz 2009-08-06 15:37 17K
sgdClone.txt.gz 2009-08-09 10:20 16K
sgdOtherDescription.txt.gz 2009-08-09 10:20 15K
chrIV_intronEst.txt.gz 2020-09-01 14:39 12K
chrI_est.txt.gz 2020-09-01 14:39 11K
esRegGeneToModule.txt.gz 2009-08-06 15:37 9.1K
chrII_intronEst.txt.gz 2020-09-01 14:39 9.0K
chrVII_intronEst.txt.gz 2020-09-01 14:39 8.4K
tableDescriptions.txt.gz 2024-05-04 02:04 8.3K
tableList.txt.gz 2024-05-05 03:12 8.0K
chrXVI_intronEst.txt.gz 2020-09-01 14:39 6.6K
transRegCodeMotif.txt.gz 2009-08-09 10:21 6.5K
chrXII_intronEst.txt.gz 2020-09-01 14:39 5.7K
chrXIII_intronEst.txt.gz 2020-09-01 14:39 5.7K
chrIV_mrna.txt.gz 2020-09-01 14:05 5.6K
chrXV_intronEst.txt.gz 2020-09-01 14:39 5.3K
chrXII_mrna.txt.gz 2020-09-01 14:05 4.6K
chrVII_mrna.txt.gz 2020-09-01 14:05 4.4K
chrVIII_intronEst.txt.gz 2020-09-01 14:39 3.7K
chrV_intronEst.txt.gz 2020-09-01 14:39 3.5K
chrXIII_mrna.txt.gz 2020-09-01 14:05 3.4K
chrX_mrna.txt.gz 2020-09-01 14:05 3.4K
chrX_intronEst.txt.gz 2020-09-01 14:39 3.3K
chrXI_intronEst.txt.gz 2020-09-01 14:39 3.3K
chrII_mrna.txt.gz 2020-09-01 14:05 3.2K
chrXV_mrna.txt.gz 2020-09-01 14:05 3.2K
chrXVI_mrna.txt.gz 2020-09-01 14:05 3.1K
chrVI_intronEst.txt.gz 2020-09-01 14:39 2.9K
chrXIV_mrna.txt.gz 2020-09-01 14:05 2.8K
chrV_mrna.txt.gz 2020-09-01 14:05 2.6K
chrIX_intronEst.txt.gz 2020-09-01 14:39 2.6K
chrXIV_intronEst.txt.gz 2020-09-01 14:39 2.5K
chrXI_mrna.txt.gz 2020-09-01 14:05 2.4K
pubsBingBlat.sql 2014-01-26 18:33 2.4K
2micron_intronEst.sql 2009-08-06 15:37 2.3K
blastHg18KG.sql 2009-08-09 10:21 2.3K
2micron_mrna.sql 2009-08-09 10:21 2.3K
2micron_est.sql 2012-05-28 14:19 2.3K
pubsBingBlatPsl.sql 2014-01-26 18:33 2.2K
xenoRefSeqAli.sql 2020-09-01 14:19 2.1K
chrXIII_intronEst.sql 2020-09-01 14:39 2.1K
chrVIII_intronEst.sql 2020-09-01 14:39 2.1K
chrXVI_intronEst.sql 2020-09-01 14:39 2.1K
chrXIV_intronEst.sql 2020-09-01 14:39 2.1K
chrXII_intronEst.sql 2020-09-01 14:39 2.1K
chrVII_intronEst.sql 2020-09-01 14:39 2.1K
chrIII_intronEst.sql 2020-09-01 14:39 2.1K
chrXV_intronEst.sql 2020-09-01 14:39 2.1K
chrXI_intronEst.sql 2020-09-01 14:39 2.1K
chrVI_intronEst.sql 2020-09-01 14:39 2.1K
chrIX_intronEst.sql 2020-09-01 14:39 2.1K
chrIV_intronEst.sql 2020-09-01 14:39 2.1K
chrII_intronEst.sql 2020-09-01 14:39 2.1K
chrX_intronEst.sql 2020-09-01 14:39 2.1K
chrV_intronEst.sql 2020-09-01 14:39 2.1K
chrM_intronEst.sql 2020-09-01 14:08 2.1K
chrI_intronEst.sql 2020-09-01 14:08 2.1K
all_mrna.sql 2020-09-01 14:05 2.1K
chrXIII_mrna.sql 2020-09-01 14:05 2.1K
chrVIII_mrna.sql 2020-09-01 14:05 2.1K
all_est.sql 2020-09-01 14:39 2.1K
chrXVI_mrna.sql 2020-09-01 14:05 2.1K
chrXIV_mrna.sql 2020-09-01 14:05 2.1K
chrXII_mrna.sql 2020-09-01 14:05 2.1K
chrXIII_est.sql 2020-09-01 14:39 2.1K
chrVII_mrna.sql 2020-09-01 14:05 2.1K
chrVIII_est.sql 2020-09-01 14:39 2.1K
chrIII_mrna.sql 2020-09-01 14:05 2.1K
chrXV_mrna.sql 2020-09-01 14:05 2.1K
chrXVI_est.sql 2020-09-01 14:39 2.1K
chrXI_mrna.sql 2020-09-01 14:05 2.1K
chrXIV_est.sql 2020-09-01 14:39 2.1K
chrXII_est.sql 2020-09-01 14:39 2.1K
chrVI_mrna.sql 2020-09-01 14:05 2.1K
chrVII_est.sql 2020-09-01 14:39 2.1K
chrIX_mrna.sql 2020-09-01 14:05 2.1K
chrIV_mrna.sql 2020-09-01 14:05 2.1K
chrII_mrna.sql 2020-09-01 14:05 2.1K
chrIII_est.sql 2020-09-01 14:39 2.1K
chrX_mrna.sql 2020-09-01 14:05 2.1K
chrXV_est.sql 2020-09-01 14:39 2.1K
chrXI_est.sql 2020-09-01 14:39 2.1K
chrV_mrna.sql 2020-09-01 14:05 2.1K
chrVI_est.sql 2020-09-01 14:39 2.1K
chrM_mrna.sql 2020-09-01 14:05 2.1K
chrI_mrna.sql 2020-09-01 14:05 2.1K
chrIX_est.sql 2020-09-01 14:39 2.1K
chrIV_est.sql 2020-09-01 14:39 2.1K
chrII_est.sql 2020-09-01 14:39 2.1K
chrX_est.sql 2020-09-01 14:39 2.1K
chrV_est.sql 2020-09-01 14:39 2.1K
chrM_est.sql 2020-09-01 14:06 2.1K
chrI_est.sql 2020-09-01 14:39 2.1K
pubsBlatPsl.sql 2012-05-09 09:26 2.1K
trackDb_pushedout.sql 2021-12-27 12:23 2.1K
trackDb.sql 2023-03-28 13:53 2.1K
simpleRepeat.sql 2009-08-09 10:20 2.0K
xenoRefGene.sql 2020-09-01 14:19 2.0K
augustusGene.sql 2015-07-26 17:28 1.9K
uwFootprintsTagCounts.sql 2009-08-16 10:16 1.9K
pubsBlat.sql 2012-05-09 09:26 1.9K
phastCons7way.sql 2009-08-09 10:20 1.9K
chrVIII_mrna.txt.gz 2020-09-01 14:05 1.9K
gc5Base.sql 2009-08-09 10:21 1.9K
ensGene.sql 2011-03-15 11:37 1.9K
multiz7wayFrames.sql 2009-08-06 15:37 1.8K
mrnaOrientInfo.sql 2020-09-01 14:05 1.8K
sgdGene.sql 2009-08-09 10:21 1.8K
estOrientInfo.sql 2020-09-01 14:39 1.8K
hgFindSpec_pushedout.sql 2021-12-27 12:23 1.8K
hgFindSpec.sql 2023-03-28 13:53 1.8K
xenoRefFlat.sql 2020-09-01 14:19 1.7K
chrXIII_gold.sql 2009-08-06 15:37 1.7K
chrVIII_gold.sql 2009-08-09 10:21 1.7K
2micron_gold.sql 2009-08-09 10:21 1.7K
chrXVI_gold.sql 2009-08-09 10:21 1.7K
chrXIV_gold.sql 2009-08-06 15:37 1.7K
chrXII_gold.sql 2009-08-09 10:20 1.7K
chrVII_gold.sql 2009-08-06 15:37 1.7K
chrIII_gold.sql 2009-08-09 10:20 1.7K
chrXV_gold.sql 2009-08-09 10:21 1.7K
chrXI_gold.sql 2009-08-09 10:21 1.7K
chrVI_gold.sql 2009-08-09 10:21 1.7K
chrIX_gold.sql 2009-08-06 15:37 1.7K
chrIV_gold.sql 2009-08-09 10:20 1.7K
chrII_gold.sql 2009-08-06 15:37 1.7K
chrX_gold.sql 2009-08-09 10:20 1.7K
chrV_gold.sql 2009-08-09 10:20 1.7K
chrI_gold.sql 2009-08-09 10:20 1.7K
chrM_gold.sql 2009-08-06 15:37 1.7K
drBlastTab.sql 2013-10-27 21:15 1.7K
chrXIII_gap.sql 2009-08-09 10:21 1.6K
chrVIII_gap.sql 2009-08-09 10:21 1.6K
2micron_gap.sql 2009-08-09 10:21 1.6K
chrXVI_gap.sql 2009-08-09 10:20 1.6K
chrXIV_gap.sql 2009-08-09 10:21 1.6K
chrXII_gap.sql 2009-08-06 15:37 1.6K
chrVII_gap.sql 2009-08-09 10:20 1.6K
chrIII_gap.sql 2009-08-09 10:21 1.6K
chrXV_gap.sql 2009-08-09 10:20 1.6K
chrXI_gap.sql 2009-08-09 10:21 1.6K
chrVI_gap.sql 2009-08-06 15:37 1.6K
chrIX_gap.sql 2009-08-09 10:21 1.6K
chrIV_gap.sql 2009-08-09 10:20 1.6K
chrII_gap.sql 2009-08-09 10:21 1.6K
chrX_gap.sql 2009-08-09 10:21 1.6K
chrV_gap.sql 2009-08-09 10:20 1.6K
chrI_gap.sql 2009-08-09 10:20 1.6K
esRegGeneToMotif.sql 2009-08-06 15:37 1.6K
transRegCode.sql 2009-08-09 10:21 1.6K
sgdBlastTab.sql 2010-08-29 10:59 1.6K
rnBlastTab.sql 2010-08-29 10:59 1.6K
mmBlastTab.sql 2011-05-30 01:51 1.6K
hgBlastTab.sql 2010-08-29 10:59 1.6K
dmBlastTab.sql 2010-08-29 10:59 1.6K
ceBlastTab.sql 2010-08-29 10:59 1.6K
chrM_gap.sql 2009-08-09 10:20 1.6K
gbLoaded.sql 2020-09-01 14:39 1.6K
transRegCodeProbe.sql 2009-08-09 10:20 1.6K
tableList.sql 2024-05-05 03:12 1.6K
multiz7waySummary.sql 2009-08-09 10:20 1.6K
chrIX_mrna.txt.gz 2020-09-01 14:05 1.6K
sgdCanonical.sql 2009-08-09 10:20 1.6K
sgdOther.sql 2009-08-06 15:37 1.6K
esRegUpstreamRegion.sql 2009-08-09 10:20 1.6K
phastConsElements7way.sql 2009-08-09 10:21 1.6K
history.sql 2009-08-09 10:21 1.6K
multiz7way.sql 2009-08-09 10:20 1.5K
oreganno.sql 2016-05-15 11:29 1.5K
sgdClone.sql 2009-08-09 10:20 1.5K
uwFootprintsPrints.sql 2009-08-06 15:37 1.5K
chrIII_intronEst.txt.gz 2020-09-01 14:39 1.5K
microsat.sql 2015-08-24 01:24 1.5K
tableDescriptions.sql 2024-05-04 02:04 1.5K
transRegCodeCondition.sql 2013-11-10 22:14 1.5K
uwFootprintsMappability.sql 2009-08-06 15:37 1.4K
gbLoaded.txt.gz 2020-09-01 14:39 1.4K
transRegCodeMotif.sql 2009-08-09 10:21 1.4K
oregannoLink.sql 2016-05-15 11:29 1.4K
esRegMotif.sql 2009-08-06 15:37 1.4K
bigFiles.sql 2024-05-05 03:12 1.4K
extFile.sql 2009-08-06 15:37 1.4K
grp.sql 2014-03-02 04:14 1.4K
oregannoAttr.sql 2016-05-15 11:29 1.4K
ensGtp.sql 2011-03-15 11:37 1.4K
sgdIsoforms.sql 2009-08-06 15:37 1.4K
sgdOtherDescription.sql 2009-08-09 10:20 1.3K
choExpDistance.sql 2009-08-09 10:21 1.3K
esRegGeneToModule.sql 2009-08-06 15:37 1.3K
chromInfo.sql 2009-08-09 10:20 1.3K
sgdLocalization.sql 2009-08-06 15:37 1.3K
sgdAbundance.sql 2009-08-09 10:21 1.3K
sgdDescription.sql 2009-08-06 15:37 1.3K
sgdToSwissProt.sql 2009-08-09 10:20 1.3K
sgdToPfam.sql 2009-08-09 10:20 1.3K
sgdToName.sql 2009-08-06 15:37 1.3K
yeastP2P.sql 2009-08-09 10:20 1.3K
growthCondition.sql 2011-09-12 00:03 1.3K
sgdPep.sql 2009-08-09 10:21 1.3K
ensPep.sql 2011-03-15 11:37 1.3K
transRegCodeCondition.txt.gz 2013-11-10 22:14 1.2K
history.txt.gz 2009-08-09 10:21 1.2K
chrIII_mrna.txt.gz 2020-09-01 14:05 1.2K
chrI_intronEst.txt.gz 2020-09-01 14:08 1.1K
chrVI_mrna.txt.gz 2020-09-01 14:05 1.1K
hgFindSpec.txt.gz 2023-03-28 13:53 944
chrI_mrna.txt.gz 2020-09-01 14:05 941
hgFindSpec_pushedout.txt.gz 2021-12-27 12:23 904
chrM_mrna.txt.gz 2020-09-01 14:05 854
growthCondition.txt.gz 2011-09-12 00:03 685
2micron_est.txt.gz 2012-05-28 14:19 607
microsat.txt.gz 2015-08-24 01:24 341
extFile.txt.gz 2009-08-06 15:37 289
chromInfo.txt.gz 2009-08-09 10:20 203
grp.txt.gz 2014-03-02 04:14 199
chrXIII_gold.txt.gz 2009-08-06 15:37 75
chrVIII_gold.txt.gz 2009-08-09 10:21 74
2micron_gold.txt.gz 2009-08-09 10:21 74
chrXVI_gold.txt.gz 2009-08-09 10:21 73
chrXIV_gold.txt.gz 2009-08-06 15:37 73
chrXII_gold.txt.gz 2009-08-09 10:20 73
chrVII_gold.txt.gz 2009-08-06 15:37 72
chrIII_gold.txt.gz 2009-08-09 10:20 72
chrXV_gold.txt.gz 2009-08-09 10:21 71
chrXI_gold.txt.gz 2009-08-09 10:21 71
chrVI_gold.txt.gz 2009-08-09 10:21 70
chrIX_gold.txt.gz 2009-08-06 15:37 70
chrIV_gold.txt.gz 2009-08-09 10:20 70
chrII_gold.txt.gz 2009-08-06 15:37 70
chrX_gold.txt.gz 2009-08-09 10:20 68
chrV_gold.txt.gz 2009-08-09 10:20 68
chrM_gold.txt.gz 2009-08-06 15:37 68
chrI_gold.txt.gz 2009-08-09 10:20 68
2micron_intronEst.txt.gz 2009-08-06 15:37 42
chrM_intronEst.txt.gz 2020-09-01 14:08 39
2micron_mrna.txt.gz 2009-08-09 10:21 37
chrXIII_gap.txt.gz 2009-08-09 10:21 36
chrVIII_gap.txt.gz 2009-08-09 10:21 36
2micron_gap.txt.gz 2009-08-09 10:21 36
chrXVI_gap.txt.gz 2009-08-09 10:20 35
chrXIV_gap.txt.gz 2009-08-09 10:21 35
chrXII_gap.txt.gz 2009-08-06 15:37 35
chrVII_gap.txt.gz 2009-08-09 10:20 35
chrIII_gap.txt.gz 2009-08-09 10:21 35
chrXV_gap.txt.gz 2009-08-09 10:20 34
chrXI_gap.txt.gz 2009-08-09 10:21 34
chrVI_gap.txt.gz 2009-08-06 15:37 34
chrIX_gap.txt.gz 2009-08-09 10:21 34
chrIV_gap.txt.gz 2009-08-09 10:20 34
chrII_gap.txt.gz 2009-08-09 10:21 34
chrX_gap.txt.gz 2009-08-09 10:21 33
chrV_gap.txt.gz 2009-08-09 10:20 33
chrM_gap.txt.gz 2009-08-09 10:20 33
chrM_est.txt.gz 2020-09-01 14:06 33
chrI_gap.txt.gz 2009-08-09 10:20 33
bigFiles.txt.gz 2024-05-05 03:12 33