Dcode.org: Tools Developed by the Research Group of Ivan Ovcharenko at the National Library of Medicine

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Transcription factor binding sites (TFBS) in promoters.
TFBS length data [matrix_length.txt]


Promoters
Base genomeGene annotationTRANSFACDateNumber of TFBSFile sizeFile
Human (hg18)
UCSC known genesv10203-26-20085.5M19.5Mbtfbs_promoters.hg18.knownGene.v102.txt.gz
RefSeqv10203-26-20085.1M18.1Mbtfbs_promoters.hg18.refGene.v102.txt.gz
Other species RefSeqv10203-26-20084.8M17.4Mbtfbs_promoters.hg18.xenoRefFlat.v102.txt.gz
Macaque (rheMac2)
Other species RefSeqv10203-26-20082.7M10.1Mbtfbs_promoters.rheMac2.xenoRefFlat.v102.txt.gz
RefSeqv10203-26-2008109.0k411.9kbtfbs_promoters.rheMac2.refGene.v102.txt.gz
Chimp (panTro2)
RefSeqv10203-26-20084.5M16.4Mbtfbs_promoters.panTro2.refGene.v102.txt.gz
Other species RefSeqv10203-26-2008064tfbs_promoters.panTro2.xenoRefFlat.v102.txt.gz
Mouse (mm9)
Other species RefSeqv10203-26-20084.6M17.0Mbtfbs_promoters.mm9.xenoRefFlat.v102.txt.gz
UCSC known genesv10203-26-20085.8M21.5Mbtfbs_promoters.mm9.knownGene.v102.txt.gz
RefSeqv10203-26-20085.4M19.6Mbtfbs_promoters.mm9.refGene.v102.txt.gz
Rat (rn4)
Other species RefSeqv10203-26-20084.2M16.0Mbtfbs_promoters.rn4.xenoRefFlat.v102.txt.gz
RefSeqv10203-26-20084.0M14.6Mbtfbs_promoters.rn4.refGene.v102.txt.gz
UCSC known genesv10203-26-20082.1M7.9Mbtfbs_promoters.rn4.knownGene.v102.txt.gz
Cow (bosTau3)
RefSeqv10203-26-20083.0M10.7Mbtfbs_promoters.bosTau3.refGene.v102.txt.gz
Dog (canFam2)
Other species RefSeqv10203-26-20084.3M15.4Mbtfbs_promoters.canFam2.xenoRefFlat.v102.txt.gz
RefSeqv10203-26-2008275.7k994.3kbtfbs_promoters.canFam2.refGene.v102.txt.gz
Opossum (monDom4)
Other species RefSeqv10203-26-20083.9M14.6Mbtfbs_promoters.monDom4.xenoRefFlat.v102.txt.gz
RefSeqv10203-26-200835.4k139.8kbtfbs_promoters.monDom4.refGene.v102.txt.gz
Chicken (galGal3)
Other species RefSeqv10203-26-20082.6M9.5Mbtfbs_promoters.galGal3.xenoRefFlat.v102.txt.gz
RefSeqv10203-26-20081.4M4.9Mbtfbs_promoters.galGal3.refGene.v102.txt.gz
Frog (xenTro2)
RefSeqv10203-26-20082.0M7.3Mbtfbs_promoters.xenTro2.refGene.v102.txt.gz
Zebrafish (danRer5)
RefSeqv10203-26-20082.6M10.1Mbtfbs_promoters.danRer5.refGene.v102.txt.gz


File format:
> element1Location
  tfbsName1 strand_position1 strand_position2 ... strand_positionN
   ...
  tfbsNameK strand_position1 strand_position2 ... strand_positionN
> element2Location
...

For example, the record "SMAD3_Q6 +82 -101" describes two instances of the SMAD3_Q6 transcription factor binding site, one on a positive strand at the position 82, another one on a negative strand at the position 101. All positions are relative to the ECR/promoter starting position.


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