[Genome] SOD1 gene and its 5' upstream sequence

[Sue Copland]

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