How to find a promoter and TSS? - (Nov/14/2012 )
My gene of interest coded by 2 exons (1 untranslated exon + 1 coding exon)
I have the partial sequence (~350 bp) of untranslated exon (codes 5’ UTR) and complete sequence of coding exon.
(Note: the untranslated exon size is ~ <700bps in all organisms)
Complete genome sequence was not yet identified for this organism (Reptile).
I did Genome walking and got 1000 bps upstream sequence for 5’ exon.
Now, I want to find the transcription start site and promoter region for the exon.
To determine the exact TSS, you need to do primer extension assay, or do a 5' RACE to determine the 5' far end of the exon which can then be regarded as the TSS.
To predict whether the 1000 bp sequence derived from genome walking, you can use programs to predict promoters. There are many such programs, the one I use most is the Neural Network Promoter Prediction at http://www.fruitfly.org/seq_tools/promoter.html.