[Genome] SOD1 gene and its 5' upstream sequence

[Archana Thakkapallayil]

Hello Sue,

The papers that you have attached are very old. We update the sequence 
on our Browser whenever NCBI provides a new release  (approximately once 
a year). The sequence that you have obtained from our Browser is from 
the recent Human assembly, hg18 (March 2006), which corresponds to the 
latest NCBI Build 36.1. I have checked the upstream sequence for this 
gene on NCBI and our Browser and it is the same. As far as I can tell, 
everything is correct on our Browser.

If you are interested in older Human assemblies, they are available on 
our archives server here:
http://genome-archive.cse.ucsc.edu/

I hope that this helps you. Please let us know if you have further 
questions.

Regards,

Archana
UCSC Genome Bioinformatics Group


Sue Copland wrote:
> Hi
>
>  
>
> I've got a concern about sequence information acquired through the UCSC
> genome browser (March 2006 assembly, clade vertebrate, genome human).
>
>  
>
> The problem is the sequence upstream of the SOD 1 gene in the genome
> browser sequence (chr21:31953106-31954728) does not match published
> genomic sequence for that region.
>
>  
>
> Please refer to papers 
>
>  
>
> The Human Copper-Zinc Superoxide Dismutase Gene (SOD1) Proximal Promoter
> Is Regulated by Sp1, Egr-1, and WT1 via Non-canonical Binding Sites.
> Journal of Biological Chemistry vol. 274. No. 1, issue of January 1, pp.
> 503-509, 1999
>
>  
>
> Study of 5'-Flanking Region of Human Cu/Zn Superoxide Dismutase.
> Biochemical and biophysical Research Communications, June 30, pp.
> 1526-1533, 1994.
>
>  
>
> I searched UCSC genome browser for CpG islands upstream of superoxide
> dismutase 1 (SOD 1) and focused on CpG 91. I downloaded sequence
> chr21:31953106-31954728 which includes 500 bases flanking the 5' region
> and 200 bases flanking the 3' region of CpG 91. 
>
>  
>
> This sequence runs in the same direction as the SOD 1 gene (+ strand)
> and overlaps the 5' region of SOD 1. I confirmed this by locating the 5'
> region of the SOD 1 gene (exon1 and part of intron1) within
> chr21:31953106-31954728. 
>
>  
>
> Sequence upstream of the human SOD 1 gene has been extensively studied
> and found to contain promoter elements such as the TATA box and well
> known transcription factor binding sites and it's this sequence that I
> want. Am I able to get the real sequence upstream of SOD 1 from the
> genome browser?
>
>  
>
>  
>
> Kind regards
>
>  
>
>  
>
> Sue Copland
>
> Research Technician
>
> Liggins Institute
>
> The University of Auckland
>
> 2-6 Park Ave, Grafton 1023
>
> Auckland, New Zealand
>
> Ph +649 373 7599 ext 83439
>
> fax +649 373 8763
>
> sue.copland at auckland.ac.nz
>
>  
>
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>