[Genome] mRNA Track

[Galt Barber]

It is odd that the 5' UTR of AF361221 (chr17) does align nearly perfectly,
but on an entirely different chromosome (chr20).

I can think of a few possibilities:
1. It is new science of importance.
2. It is some laboratory artifact.
3. It is some data processing error.
4. The breast carcinoma tissue from which the mRNA was harvested
differs from the reference genome.

Oddly enough, if you blat the 5'UTR of AF361221 on chr20
and go to the location in the browser, you end up at the
5'UTR position of AF361220.

AF361221
AF361220

-Galt


On Wed, 21 May 2008, Pauline Fujita wrote:

> Dear Prof. Kim,
>
> The BLAT results are displayed according to the identity as you
> described, but they are also subject to a length criteria. For the Human
> assembly, a search result must be at least 25% of the query in length to
> be retained and in this case the the 283bp piece found by BLAT on
> chromosome 20 is only 21.4 % (283/1321 bp) of the query in length:
>
> BLAT Search Results
> ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
> ---------------------------------------------------------------------------------------------------
> browser details YourSeq 1022 279 1303 1321 100.0% 17 + 56800468 56824974
> 24507
> browser details YourSeq 281 1 283 1321 99.7% 20 + 48844838 48845120 283
>
> For assemblies of lower quality this length requirement may be different
> (i.e. it is not 25% for all assemblies). Hopefully this information was
> helpful and answers your question. If you have further questions or
> require clarification feel free to contact the mailing list at
> genome at soe.ucsc.edu.
>
> Regards,
>
> Pauline Fujita
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
> Prof. Sangsoo Kim wrote:
>> Dear sir,
>>
>> The GenBank mRNA track shows AF361221.1 on the human chromosome 17,
>> missing the 5' 278 bp.
>> It does not show the missing part in any other part of the human genome.
>>
>> If I 'blat' the mRNA sequence against human genome, I can see that the
>> missing part can be aligned with 99.7% identity.
>> According to the Methods describing how the alignment was made, the
>> alignments having identify within 0.5% of the best match and higer than
>> 96% are to be kept.
>>
>> I wonder why the 5' part the sequence was not captured in the track.
>>
>> Sincerely,
>>
>> Sangsoo
>>
>> ------------------------------------------------------------------------
>>
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>
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