mat_peptide

[IGAQ]

Could someone answer a question for me please.

If you have a retrovirus that has a gag-pro-pol CDS and gene in the NCBI Genbank, but the env is a mat_peptide, where could the nucleotide sequence for that mat_peptide have come from?

[mchlbrmn]

mat_peptide means "mature peptide". At the NCBI website the genbank entry for the gene (or viral genome), or at least for the reference sequence entry for that gene, may (should?) be annotated to show which part is the mature protein. This may exclude amino acid residues that are removed during post translational modifications of the gene. For example here is the entry for mouse Ccl12:
http://www.ncbi.nlm.nih.gov/nuccore/NM_011331.2
The mat_peptide annotated excludes the signal peptide at the beginning of the coding sequence (CDS) that is removed, and the stop signal at the end.

[IGAQ]

Thanks

The sequence I am looking at has no gene, only the mat peptide.

This is the one. Can you explain why that would be this way?

http://www.ncbi.nlm.nih.gov/nuccore/FN692043.2

mat_peptide 5754..7691
/product="putative envelope polyprotein"

It is also here
http://www.ebi.ac.uk/ena/data/view/FN692043

[mchlbrmn]

[quote="I
http://www.ncbi.nlm.nih.gov/nuccore/FN692043.2

mat_peptide 5754..7691
/product="putative envelope polyprotein"
[/quote]
Well, I'm not a virologist, but it looks like the envelope protein is encoded by the inicated nucleotides. I don't know how you define "gene", but viruses (sp?) are tight for space, so it's not uncommon for a nucleotide to code for m ore than one product, by alternate splices for example. Perhaps, in this case, the transcript is translated, then the protein is lysed into multiple separate peptides.