[Genome] Human Promoters

[Mike Mitchell]

On 8/11/06 15:02, "Liron Levkovitz" <lironle4 at post.tau.ac.il> wrote:

> Thanks for your answer. I just want to make sure I understand: In case the
> promoters have different RefSeq IDs but the same locations-  they are
> promoters of splice variants (as a results from alternative splicing), and
> in the case they have the same RefSeq IDs but different locations- they are
> alternative promoters of the same gene (see example below).
> 
>> NM_000039_up_1000_chr11_116213549_r
>> NM_000039_up_1000_chr22_random_12498_f

Each RefSeq ID refers to one unique transcript, thus a gene will multiple
associated RefSeq IDs if there are multiple known transcripts. So if you get
several RefSeq IDs at the same locations *and strand orientation* then those
should be different transcripts of the same gene.

Each gene should also uniquely localise to the genome, in your example above
you have APO1 localised to chromosome 11 (as it should do) and to
chr22_random. This second localisation is worrying. The "random" chromosome
assignments indicate that the assembly is believed to be part of a specific
chromosome but has yet to be accurately mapped. Perhaps there is something
wrong with the chr22_random assembly - which you will need to clarify with
the originators of the data and assembly, the Sanger Centre and the NCBI
respectively.

In summary:

different RefSeq IDs, same location and strand = different transcripts of a
gene

same RefSeq ID, different location = trouble

-- 
Mike Mitchell
Bioinformatics & Biostatistics Service
Cancer Research UK +44 (0) 207 269 3115