Promoter prediction in eukaryotes. Grupo 5. Eukaryotic Gene Structure. branchpoint site. 5’site. 3’site. exon 1 intron 1 exon 2 intron 2. CAG/NT. AG/GT. Key Eukaryotic Gene Signals. Pol II RNA promoter elements Cap and CCAAT region GC and TATA region
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exon 1 intron 1 exon 2 intron 2
RNA Pol II
Exon Intron Exon
start site (TSS)
TATA box is found in ~70% of promoters
Computational Biology and Informatics Laboratory, School of Medicine, University of Pennsylvania, 1997
Eukaryotic Promoter Database Swiss Institute for Experimental Cancer Research
Prediction of transcription factor binding sites by
constructing matrices on the fly from TRANSFAC 4.0 sites.
Density of TF from EPD (PromoterScan)
Searches of weight matrices against a test sequence
Gene expression is also influenced by the region upstream of the core promoter and other enhancer sites.