Promoter locations in human genome

4 posts / 0 new
Last post
Arniker
Arniker's picture
Promoter locations in human genome

Hi, there
I wish to know the step by step method to find the promoter locations in bp in the human sequences whose gene bank accession numbers are :

1)  L44140
2)  D87675
3)  AF017257
4) AC002368

I did try to extract from cold spring harbor lab, but not sucessful...

could some one pl. guide me..

Thanks,
Arniker

Jason King
Jason King's picture
I would start by loking on

I would start by loking on Ensembl.org

Select Human and Glucose 6 phosphate dehydrogenase (in the case of the L44140) to get:

http://www.ensembl.org/Homo_sapiens/Search/Summary?species=Homo_sapiens;idx=;q=glucose%206%20phosphate%20dehydrogenase

The first returned item is:

http://www.ensembl.org/Homo_sapiens/Transcript/Domains/Genes?domain=IPR001282;t=ENST00000377403

Which seems to suggest that there are copies on Chromosome 1 and X. If you select the X Chromosome copy you get:

http://www.ensembl.org/Homo_sapiens/Location/View?g=ENSG00000160211

...which gives you the region in detail. From here you should be able to "zoom in" to the region you are interested in. Im guessing it is the G6PDH promoter. It should eventually tell you the exact location details.

Good Luck.

Arniker
Arniker's picture
Hi PM,

Hi PM,

Thanks for ur reply.

i have query:

I down loaded the sequence from NCBI for gene FMR2, human chr X , whose accession num. is AC002368, with sequence length is 324816. i am want to know the location index of the promoter in this gene.

i go to cold spring harbor laboratory to extract promoters for gene FMR2, it says:

1st exon start : 147287789
1st exon end  : 147288209

how to correlate the sequence index info. of NCBI for gene FMR2 with that of cold spring harbor lab. promo. extractor co-ordinates,
its not clear for me.....
could u enlighten me...

Reg,
Arni

Arniker
Arniker's picture
Hi there,

Hi there,

 How to find the DNA sequence [-2000, +2000] relative to TSS and
   [+2001, end of gene] for
  1) L44140 COMT gene in human chromosome 22
  2) X52828  BCR gene in human chromosome 22
   

Thanks,
Arniker