[Genome] Human Promoters

[Brooke Rhead]

Hello Liron,

I would like to add to Mike's excellent answer.  It is not unheard of 
for mRNAs to align to multiple places in the genome.  From the RefSeq 
gene details page:

"RefSeq mRNAs were aligned against the human genome using blat; those 
with an alignment of less than 15% were discarded. When a single mRNA 
aligned in multiple places, the alignment having the highest base 
identity was identified. Only alignments having a base identity level 
within 0.1% of the best and at least 96% base identity with the genomic 
sequence were kept."

There is also an answer to a very similar, previously-asked question 
located here:

http://www.cse.ucsc.edu/pipermail/genome/2005-September/008553.html

This FAQ (also referenced in the above link) contains some tips about 
determining whether an mRNA that aligns to multiple locations is an 
artifact of the assembly build process or is an actual gene duplication:

http://genome.ucsc.edu/FAQ/FAQtracks#tracks9

Also, thank you, Mike, for your answers.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group


Mike Mitchell wrote:
> 
> 
> 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
>