Re: [Genome] ensemble version

[Hiram Clawson]

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: I downloaded ENSEMBL transcripts from UCSC website using “tablesâ€� 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

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 The human MT genome has been replaced by the revised reference sequence 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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