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Old 03-16-2011, 06:40 PM   #1
mathew
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Default getting genomic coordinates from gene accesion information

I have list of gene accession numbers (e.g AY.... - Chr no start --- and stop ---).
Is there any way that I can get genomic location of these regions in Hg18.
I have tried USCS geneom browser Table that will not work.
Thanks
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Old 03-17-2011, 07:43 AM   #2
Bert
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Hello Mathew,

From the title and content of your post it's not clear to me what you want to accomplish .... What data do you exactly have and what data do you want to retrieve?

Cheers,
Bert
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Old 03-17-2011, 07:59 AM   #3
mathew
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Default genomic coordinates

What I have is Genebank accession Id (like AY293855) - Chr no (6 ) and start (140600) and stop (1407890) so I want to find out corresponding genomic coordinates in Hg18.
Thanks Bert
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Old 03-17-2011, 08:35 AM   #4
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Mathew,

It's still not clear to me what your coordinates represent. Relative to which sequence are they?

And how many of these ID's do you have?

Cheers,
Bert
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Old 03-17-2011, 08:40 AM   #5
Pankaj kumar
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Hi,
check the ucsc genome browser.
http://genome.ucsc.edu/cgi-bin/hgLiftOver
You need to give input as chr# start_position end_position
select your assembly and you are done.
Pankaj
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Old 03-17-2011, 08:48 AM   #6
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What Matthew has are not genomic coordinates as far as I can see .... AY293855 is a sequence from the IGF2R gene, and that is located in GRCh37 (hg19) at position 160390131-160534539 (http://www.ensembl.org/Homo_sapiens/...0131-160534539).

Cheers,
Bert
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Old 03-17-2011, 08:51 AM   #7
Pankaj kumar
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Hi Bert,
He has genomic co-ordinate.
see "Chr no (6 ) and start (140600) and stop (1407890)"
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Old 03-17-2011, 09:01 AM   #8
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Pankaj,

Please read my reply carefully. Mathew has a GenBank / EMBL / DDBJ ID and some coordinates. If you would look up the ID (AY293855), you would see that this is the sequence for the human IGF2R gene (http://www.ebi.ac.uk/ena/data/view/AY293855). When you then would look up where this gene is located in GRCh37 (hg19) you would see that it is on chromosome 6 at position 160390131-160534539 (http://www.ensembl.org/Homo_sapiens/...0131-160534539). Now, that are quite different numbers from 140600-1407890, right? So, the coordinates Mathew has cannot be genomic coordinates. I suspect they are relative to e.g. a clone or so.

Cheers,
Bert
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Old 03-17-2011, 02:26 PM   #9
mathew
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Bert,
You are right I have locations which have been published in paper with the corresponding gene bank accession # (Ay...,AC.. etc) I only have handful of these. I have sent to you partial list via email. I was thinking perhaps I can blast theses positions (of gene bank accession #) but still the location which I get is not corresponding to the actual coordinates cooresponding to particular gene. Any help will be appreciated.
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Old 03-17-2011, 07:23 PM   #10
Pankaj kumar
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Yes bret was right.
I think you need to extract specific sequence from each clone. For example
PEG3 AC006115 19 163172 163493
PEG3 AC006115 19 161667 161938
Same AC number but two different probe. You need to extract the particular region from each clone and need to do the blast search with hg19.

thanks
Pankaj
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Old 03-18-2011, 04:14 AM   #11
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Hello Mathew,

Ok, so as far as I understand now you want to know where the region of GenBank / EMBL / DDBJ sequence AY293855 with coordinates start 140618 and stop 140769 is located on the NCBI36 (hg18) genome assembly.

I would suggest the following steps:

1 - Retrieve the sequence for AY293855
2 - Get from this sequence the sequence corresponding to bp 140618 - 140769
3 - BLAST this sequence against GRCh37 (hg19) at e.g. NCBI or Ensembl
4 - Lift the resulting coordinates over from GRCh37 (hg19) to NCBI36 (hg18)

It would of course be easier to directly BLAST to the NCBI36 (hg18) assembly, but I don't see this option in NCBI BLAST. In Ensembl it certainly isn't possible to BLAST to older assemblies.

As we have annotated several Illumina arrays in Ensembl, another option would be to do step 3 using Ensembl BLAST and then directly look in Ensembl if there are any probes mapped to your regions of interest, instead of having to use the NCBI36 (hg18) based Illumina files.

Hope this helps.
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Old 03-18-2011, 12:37 PM   #12
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You could get the hg18 (build 36) start and end co-ordinates of accessions like AY293855 from the relevant table at NCBI:

ftp://ftp.ncbi.nih.gov/genomes/MapView/Homo_sapiens/

e.g.:

ftp://ftp.ncbi.nih.gov/genomes/MapVi...eq_extra.md.gz

(other accessions may be in other tables). If you have internal co-ordinates relative to the AY293855 sequence, you can then get the equivalent hg18 co-ordinates by simple arithmetic. However, some of the numbers quoted above are too big for the 139947 bp AY293855 sequence, so perhaps they refer to something else, like a clone or contig.
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