Ucsc Knowngene List With Duplicate Entries [Promoter List Query]

Question

[Sukhi Singh]

Hi guys, I exported out a promoter list (+/- 2 KB of TSS of all genes) from the UCSC table browser, using knownGene from mm9 (July 2007) which is around 28,330. The unique entries correspond to around 24,257 so the rest 4073 entries are kinda duplicates in terms of locations (start, end, strand , chromosome, gene description) but just their promoter ID differs. For eg:

chr11 69485925 69485930 uc007jra.2_up_5_chr11_69485926_r 0 -0
chr11 69485925 69485930 uc007jqz.2_up_5_chr11_69485926_r 0 -0

What is the explanation for these. What I can think of is, 2 promoters sharing same TSS which might not make sense bilogically. Now, I know there is another table called knownCanonical [longest isoform of a gene kept which I think has something to do with the alternative splicing] which also returns a list of somewhat around 28,416 and is said not to have duplicate entries.

What I want is a list of all promoters including a gene having multiple promoters but in the above case, the location is same just the id is different which doesn't seems to be the case, as same gene having multiple promoters will have different TSS.

If you say that this is already the complete list, so should I remove this non-unique promoter id's as shown above or not. My aim is to do intersection analysis as if how many significant bindings fall into the promoter region.

Thanks for your input

Answer 1

[Pierre Lindenbaum]

uc007jra.2 and uc007jqz.2 : these are not the same transcripts

http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=uc007jqz.2

Description: eukaryotic initiation factor 4A-I isoform 2

http://genome.ucsc.edu/cgi-bin/hgTracks?db=mm9&position=uc007jra.2

Description: eukaryotic initiation factor 4A-I isoform 1

[Sukhi Singh]

Thanks Pierre, but this is still confusing. Why they are different transcripts, either it has to do with alternative splicing and the gene is regulated by same promoter else there is some internal promoter in which the location should be different according to TSS. So, if you just want a list of unique promoters, then I think these should be removed considering them as duplicates. What you say!!

Thanks