I would like to find the genomic sequence of a given gene. I have used the NCBI Blast for a sequence from the CDS of the gene and it gave hits corresponding to the location of this sequence on the chromosome yet I want to see the whole sequence on the chromosome where I will find out about the sequence of introns deduced from the exon sequence I have had. Moreover, I would like to view the sequence of the chromosome upstream and downstream of the Coding region as the 5' and 3' UTR. Therefore, I would like to ask if any body could help as how to do that.
You can find it in Entrez (http://www.ncbi.nlm.nih.gov/gene), UCSC genome browser (http://genome.ucsc.edu/cgi-bin/hgGateway), or Ensembl (htt://www.ensembl.org) . In UCSC genome browser, type the name of your gene---->submit-----you'll see a graphical window......click on the track....next page will open---->scroll down..click on genomic sequence from assembly-----choose what you want. promoter, 5',3'UTR, CDS, and them submit. you can also choose 'CDS in uppercase or UTRs in lower case. Good luck..
You can find it in Entrez (http://www.ncbi.nlm.nih.gov/gene), UCSC genome browser (http://genome.ucsc.edu/cgi-bin/hgGateway), or Ensembl (htt://www.ensembl.org) . In UCSC genome browser, type the name of your gene---->submit-----you'll see a graphical window......click on the track....next page will open---->scroll down..click on genomic sequence from assembly-----choose what you want. promoter, 5',3'UTR, CDS, and them submit. you can also choose 'CDS in uppercase or UTRs in lower case. Good luck..
Ruhul Amin is right. In order to make things easier for you, I have included here a pdf handout on how to do it using the UCSC genome browser.
Good luck!
great info!
Ruhul and Rolando, can you also suggest something similar that would work/suitable for plants?
Thanks!
Nurniwalis, you can use Ensembl Plants (http://plants.ensembl.org/index.html) genome browser . You can search the specific gene by name or Gene ID and then click export data. In that page you'll find your desired region.
Hi everyone, I would really appreciate it if you can help me with finding 5UTR on NCBI..
Thank you
Try to use Refseq sequence from NCBI ...Or just take a sequence/ accession number, then use the following databases given below..
http://itbtools.ba.itb.cnr.it/utrscan
http://utrdb.ba.itb.cnr.it/search
https://www.ba.itb.cnr.it/BIG/Blast/BlastUTR.html
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