3 replies to this topic

[andyg2886]

Hi

I have the gDNA of a gene. It's 32,518bp long.

The ATG start site begins at position 329bp.

Is it possible to find the sequence of the promoter?

Thanks

[pDNA]

yes it is!
eukaryotic or prokaryotic system?

Regards,
p

[andyg2886]

Eukaryotic... It's the human EWSR1 gene.

[pDNA]

i'm no specialist on eukaryotic genomics (i'm overwhelmed by the complexitiy of prokaryotes ...i do not need a nucleus to get messed up everyday!)
...but there are prediction algorithems available to predict eukaryotic promoters e.g.:
http://molbiol-tools.ca/Promoters.htm
or
http://rulai.cshl.ed...l?species=Human

the laterone lets you e.g. extract promoter sequences of genes based on the accession number.
This is what i found for EWSR1:
>NM_005243-Human-1 EP73961 chr22 + 27988154 27989154 hchr22_00279
aaagggcctgctccacctcgaccgttaccggggatagggtctcggggccaggcacggcgttcgaggcctcccacccagcc
gaccggccttggggacccttccccgctggcccgggccacgcgtcccgggtactcactgcagagcgcgcccggcaaccccg
aaaggccggtcggggaccccggctgggagtcaggactctagctcccgggcgcgacccgagaaccctgaatccattccgcg
cacacccggccgcgtgacccctgccgaccggctggcgcgccacccattccccgcggcccgcggattagtcagcagttgtt
ctagtccgggtcccttcccccagccctcccgccgatctccgtctccctgcagggccgactcttcagcgaccgtccctaga
gccagcggacggaaccattccaaacagcctagtctcgtgctgagagcctctccggtttcacgctgagacccgctcacccc
cgctctggccccttagatgctattttggcccgagtgtcacgtcgggcgctctttagagaggactgggacaagagttgcgg
acgcgaagaacgagtaagcggtggttcatccctcctgaccccacccccgtggcctggcccgatggtcgcgcccggggttg
cgagatttgcgcctgcgcagtgcggcgcctagagggaaagcgagagggagacggacgttgAGAGAACGAGGAGGAAGGAG
AGAAAATGGCGTCCACGGGTGAGTATGGTGGAACTGCGGTCGCGCCGGCGGTAGCCGGAACGCCCAAACTGGGGGTCGTT
CGTCTCTGGGCTTGGCTGGGAAGACTGAGTGGAGTTGCCGAGAGGGGGTTGAGGCACCCGCCGCGGCCCGACGAGCTCGG
GGATCCGCATTCCTCTCCCCTCCCCCAACCGGGCGGGCCGGTTCTGGAATCTTCCGGCGCCCGTGGCGCGCGGGGGGCTT
GCTGCGGCGGGGGCGCGCGGGGCCCGCCTTGGCCTCCATT

base pairs in the upstream region of transcript start site are in lower cases while those in the downstream are in capital cases.

Regards,
p