Hi Hiram,
Thank you very much for your answer. I would like to clarify one more thing:
I just looked at the ENSEMBL website for the specific transcript you gave as an
example below. When I did a search on UCSC genome browser for
" ENST00000361789" , the coordinate 14746 becomes 14747 which is +1.
1. Is this because the coordinate 14746 is in BED format start coordinate which
is 0 based whereas 14747 is in genomic coordinate format which is 1-based?
2. Please see attached figure. The protein sequence shown for this transcript
seems to be wrong. It is not the same as the sequence given below:
http://www.uniprot.org/uniprot/P00156
Could you please clarify if the protein sequence displayed
for ENST00000361789 is wrong on the UCSC browser website?
thank you,
Laura
________________________________
From: Hiram Clawson <[email protected]>
To: Laura Smith <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Thursday, March 22, 2012 3:10 PM
Subject: Re: [Genome] ensemble version
This also means that if you obtained DNA sequence, then what you have
matches nothing at all since the coordinates are chrM_rCRS but the DNA
is UCSC chrM.
--Hiram
Hiram Clawson wrote:
> Good Afternoon Laura:
>
> I have confirmed that the tables we have hosted on hg19 since at least
> November 2010 (ens v60) have been
> identical for the chrM predictions. They do appear to be predictions for
> chrM_rCRS instead
> of the UCSC chrM. We have mistakenly shown them in their chrM_rCRS locations
> on the UCSC
> chrM sequence. When you say "transcripts" are you talking about the gene
> prediction locations,
> for example:
> ENST00000361789 chrM + 14746 15887 14746 15887 1 14746, 15887, 0
> ENSG00000198727 cmpl incmpl 0,
> Or are you referring to the protein sequence:
> ENST00000361789
> MTPMRKTNPLMKLINHSFIDLPTPSNISAWWNFGSLLGACLILQITTGLFLAMHYSPDASTAFSSIAHITRDVNYGWIIRYLH
>
> ANGASMFFICLFLHIGRGLYYGSFLYSETWNIGIILLLATMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTDLVQWIWGGYSVDSPTLTRFFTFH
>
> FILPFIIAALATLHLLFLHETGSNNPLGITSHSDKITFHPYYTIKDALGLLLFLLSLMTLTLFSPDLLGDPDNYTLANPLNTPPHIKPEWYFLFAYTIL
>
> RSVPNKLGGVLALLLSILILAMIPILHMSKQQSMMFRPLSQSLYWLLAADLLILTWIGGQPVSYPFTIIGQVASVLYFTTILILMPTISLIENKMLKWA
>
>
> Both of these have been chrM_rCRS since 2010.
>
> --Hiram
>
> Laura Smith wrote:
>> Hi Vanessa,
>>
>> Thank you for your reply. However, this is not the answer to what I was
>> asking for.Â
>> Let me make the question short and more clear:
>>
>> Question:Â
>> I downloaded ENSEMBL transcripts from UCSC website using “tables� tab
>> on 06/2011 (version 62 of ENSEMBL at that time). Would these transcripts I
>> downloaded form UCSC already contain the correct coordinates for the rCRS
>> chr M?" Â Â
>>
>> I just need a "yes" or "no" answer.Â
>>
>>
>>
>> Let me give you some information that may be useful for you to be able to
>> answer this question more clearly:
>>
>> Facts:Â
>>
>> 1. The human MT genome has been replaced by the revised reference sequence
>> (rCRS) NC_012920 (AC_000021) in Ensembl 57
> (March 2010). See the news at the bottom of
> the page in the link below:Â
> http://mar2010.archive.ensembl.org/Homo_sapiens/Info/WhatsNew
>>
>>
>>
>> 2. So, any version of Ensembl after Ensembl version 57 would include the new
>> rCRS chrM trancript coordinates.
>>
>> 2. UCSC genome browser has NOT converted to rCRS chrM sequence and is still
>> using the old sequence for chrM.
>>
>>
>> 3. UCSC genome browser currently provides "tables" tab for users to download
>> ENSEMBL sequences.
>>
>>
>> 4. It is not clear that if the users download the ENSEMBL transcripts from
>> UCSC genome browser, will they get the new rCRS chrM coordinates or the old
>> chrM coordinates for these ENSEMBL transcripts?? Â
>> This is the issue.
>>
>>
>> thanks,
>> Laura
>
> ------------------------------------------------------------------------
>
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> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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