Determine Where Is My Oligo Probe In The Gene? In Exonic Region Or Interonic Region

Question

[Omid]

I have an oligo probe(A14P129484)and its position is chr13:24361317-24361376 I want to know where it is in the gene named(CENPJ)? Please consider the probe is on + strand and CENPJ gene is on the reverse strand. Is it located in exonic or intronic region?If it is in intron is it located in intron splice site or near to splice site ?

Thanks

[Bert Overduin]

It would help if you would mention what organism you are working on and on which genome assembly the genome coordinates are defined. By the way, that the probe is defined on the + strand and the gene is located on the - strand doesn't of course matter a bit ....

[Omid]

thanks Bert the subjet is human and I used hg18.Thanks again

Answer 1

[biobot 0.0.77.a.1099]

Go to Ensembl, select Human and type your probe name into the general search box. This will immediately locate your probe. Click on the link to open the viewer at the probe location. Use 'Configure this page' (on the left) to activate the Agilent probe tracks. Zoom out a little to see the probe in the context of the transcripts. You will see that the probe lies in the UTR of CENPJ-002.

[Omid]

thanks I really appreciate is it possible to explain more about Agilent probe track I couldnot find it

[Omid]

I really really appreciate Keith it helped me too much

[brentp]

Very useful. I didn't know about this.

Answer 2

[ALchEmiXt]

If the probe is of typical length 60-mer you could simply BLAST the probe sequence (limiting on taxid for instance) and figure out the position in the CENPJ gene and whether its in a coding region or not. This is useful to do if you have only a few now regular recurring queries though.

PS: if yu don't have the actual sequence. Get it from Entrez using the proper genome build that match to the coordinates given.

Answer 3

[Pierre Lindenbaum]

If you're working with the human genome, the knownGene table at the ucsc ( search Biostar for knownGene ) will give you the structure of the transcripts (CDS, transcription start/end, etc...). overlapping your position. The next part is a simple calculation (e.g.: Do Exons Ever Have Different Reading Frames In Spliced Variants? )