Can anyone explain the how to use the mutation site coordinates for alleles from the NBRP (Japan mutants)? I’m looking at a new one that is not in wormbase yet on the NBRP. I can’t figure out the numbers listed for location and gene structure. They don’t seem to line-up with gene structure I get from Wormbase.
Thanks
Where the National BioResourse Project site lists the “Mutation site”, those numbers are coordinates in the sequenced clone, the canonical cosmid or YAC containing the gene. Taking as an example the allele currently listed first on their “List of all mutants” page, unc-86(tm232), its mutation site is given as being:
12494/12495-AATAA-12872/12873This means that if you look up the cosmid containing [i]unc-86[/i], which is C30A5 (which you can tell from WormBase, or by looking at the National BioResource Page for [i]tm232[/i], where it says the gene is [i]C30A5.7[/i]), you can get its sequence (at [url=http://www.wormbase.org/db/seq/sequence?name=C30A5;class=Sequence]this WormBase page[/url] or at [url=http://www.ncbi.nlm.nih.gov/nuccore/156211]this NCBI page[/url]), and (if I'm reading the National BioResource Project's page correctly), nucleotides 12495 through 12872 of that sequence have been deleted and replaced with AATAA in [i]tm232[/i].
As for the gene structure models, if you look at the “Sequence Summary” page for a given gene (such as this one for unc-86), at the very bottom of the page is a table in which the positions of the exons are given relative to the start of the transcript (or perhaps relative to the start of the coding region) and relative to the sequenced clone.