obatining full nucelotide sequences for genes - where can i find them (May/14/2009 )
I have a quick question which some of you may be able to help me with.
I want to compare the homology of the oestrogen receptor alpha (abbrieviated ER α or ER1) between mouse and humans.
I dont want to find out how to do it only what the results are, for a paper i'm writing.
All i really need to know , is there a gene database that i could access this information as i know they have both been fully sequenced (although i dont have the full sequence myself) and compare the homolgy between them?
Thanks for any advice,
One way to get there:
Go here and enter "oestrogen receptor alpha" in the search box. This will give you all DB entries of genes with this name.
Click on one of the entries (say ESR1 from Homo sapiens), and scroll down to the NCBI Reference Sequences (RefSeq) section. In the genomic section, click on the appropriate download link (GenBank or FASTA) to get the full sequence of the genomic region, or choose the isoform you're interested in from the mRNA and Protein(s) section, and click on the NP_xxxxxxxxx number to get the protein sequence or the NM_xxxxxxxx for the mRNA sequence.
Do the same for the Mus musculus entry and you'll have your two sequences to compare.
Thanks for the detiled reply homebrew but as i have nbever used any of these programs before will i be able to compare the homology using software on the programs or do i have to do it manually by comparing sequences amino acid by amino acid?
If you just want to compare the human sequence to the mouse sequence you can go here. Paste one sequence in the top box, and one in the lower box.
Along the top tabs, select the appropriate program (blastn for nucleotide vs nucleotide, or blastp for amio acids vs amino acids), then click the Blast button in the lower left.
If you're comparing more than two sequences, use ClustaW2. Paste all the sequences in as one big FASTA file, and click Run.
BTW, these programs give you the degree of similarity or identity; there's no such thing as degree of homology -- two genes are either homologous, or they aren't. You can sometimes make inferences about whether they're homologous by the degree of similarity or identity.
Thanks very much homebrew as i said i havent done this before so homology was something i haver seeen mentioned on a paper when both the human oestrogen recepetor beta and the mouse oestrogen recepetor beta have been compared so i used this term
thanks again for your advice