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 The human MT genome has been replaced by the revised reference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
------------------------------------------------------------------------
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
