NCBI gene sequence SOURCE? - (Mar/21/2008 )
How can I determine where a gene sequence is coming from when using NCBI? I search for my gene, HCN1 (in rat), and after jumping through some hoops I can see the sequence on the gene (where the exons and introns are as well). But what is the source of this info?
Some stretches of NNNNNNN are present. Some NNNN are in the alternate assembly but not the reference sequence. I want to sequence the area myself to fill in the gaps and get a sequence I can trust, but it's hard to do. I wanted to see how these sequences were obtained in the first place?
i hate to go back and confirm this, but heck..
ncbi nucleotide report for any gene sequence has extensive details about the source.. tissue, organism, group, institute, country etc. Why don't you spend some time on it, it's all there.
ncbi nucleotide report for any gene sequence has extensive details about the source.. tissue, organism, group, institute, country etc. Why don't you spend some time on it, it's all there.
... Thanks, I have been looking and haven't been able to figure it out.. soooo I thought would ask rather than spend days trying to figure it out. Anyone have a quick example of where I can find this info - the NCBI has a labrynth of links (many circle back around or just give you letters and numbers click on the accession number of your gene. you'll get a new page, there's all the info. many of the sequence are unpublished results.
Thanks, but I still am having trouble.
I can easily find the sources listed for the mRNA transcripts. But what I am looking at is the DNA, the gene, the intron. Where is the DNA sequence coming from? Not the transcript mRNA sequence. The genes/dna seem to not have accession numbers.
then your problem relies on the sequence database that you're using, if you want to find DNA use a genomic database, if you want to find mRNA transcripts or cDNA sequences use an EST database. every sequence has a different accession number. even sequences that are repeated in the same database have different accessions. hope this makes it clearer.
when you click on the accession number there are different details (as shown in the drawing i put in previous post). one of it says AUTHORS or TITLE or JOURNAL. if it is still not clear by that information how they got it (in the example i put it says: "Maize Mapping Project/dupong concensus sequences for design of orvergo probes" then contact the authors directly. you say you want to fill in the gaps, then why don't you sequence all that region again and then do alignments to fill in the gap and submit that sequence as yours?
when you click on the accession number there are different details (as shown in the drawing i put in previous post). one of it says AUTHORS or TITLE or JOURNAL. if it is still not clear by that information how they got it (in the example i put it says: "Maize Mapping Project/dupong concensus sequences for design of orvergo probes" then contact the authors directly. you say you want to fill in the gaps, then why don't you sequence all that region again and then do alignments to fill in the gap and submit that sequence as yours?
We're trying to sequence the region, which is proving difficult. This is why we want to see who/how it was sequenced before.
Again, I am clear on clicking the accession number and finding the source, but this only works for cdna, mrna. I am looking at the gene sequence (includes introns, pre exon regions). That's what I want to know the source of, and they don't seem to have an accession number associated?