How To Get Ucsc Locations For Mrna And Non-Coding

Question

[daniel.soronellas]

Hi everyone!

I have been trying all day long to download coordinates for several refseqs that are mRNA and non-coding RNAs and been failing getting few or none results. So How one could retrieve locations using UCSC table browser or MySQL query for example for the following RefSeqs?

NM_001080438
XM_001717469
XR_040005
XR_040875
XM_001134462 
NR_002823
XM_940966
XM_942664
XR_015764 
NM_024018
XR_017648
NM_017609
NM_182901
XR_041798

Sorry for this newbie question but I'm totally lost with this

Any kind of hel would be really appreciated!!

Answer 1

[Pierre Lindenbaum]

the ucsc doesn't use all the accession numbers:

http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg19&position=XR_041798

Sorry, couldn't locate XR_041798 in genome database

probably because this record has been listed as deprecated in genbank;

http://www.ncbi.nlm.nih.gov/nuccore/XR_041798

record removed. This record was removed as a result of standard genome annotation processing. See the genome build documentation at http://www.ncbi.nlm.nih.gov/genome/guide/build.html for further information, or contact [e-mail].

you can always blat your sequences on the human genome.

Answer 2

[daniel.soronellas]

Thanks for your answer!

I think I will have to use BLAT, do you know if requires the RefSeq or FASTA sequences? Because I've tried with all my RefSeqs and gives me an error

Just to know If I'm in the right way.

Many Thanks!

[Pierre Lindenbaum]

this should be a comment, not an answer. RefSeq is a database, fasta is a sequence format. blat uses FASTA.

[daniel.soronellas]

Thanks for your post and suggestion

Do you how I could get the FASTA seqs for a bunch of RefSeqs?

Thanks.

[Pierre Lindenbaum]

use the NCBI e-utilities , search biostar for many examples.

Answer 3

[biorepine]

If you good with command line download refseq gene list from UCSC and you can use join command to join the accession ids otherwise follow these steps ..

1. Go to table browser of UCSC
2. Select your genome assembly and select "Genes and Genes Prediction Tracks" under Group.
3. Select refseqGenes under track
4. Paste or upload you given identifiers (NR* XR* or NM*) under Identifiers.
5. Select output format as BED

and done!