Y41E3.10 is a puzzle

We would value any lab work done to clarify the structure of Y41E3.10.

There is a large ORF in the middle of this gene.

There are four ESTs, some WABA coding regions and C. briggsae protein homology which support the creation of an isoform which includes this region.

The possible 5’ splice sites out of this ORF are very poor and one of the ESTs run past the last usable splice site out of this region suggesting that the possible isoform terminates at the end of this ORF and does not include the down-stream exon.

The down-stream exon contains the Pfam domain (PF00736 EF-1 guanine nucleotide exchange domain) without which the protein would lose its presumed function.

It is possible that the ORF is a fragment of another gene - partially supported by BLAST evidence which has it aligned at the first half of several Phenylalanyl-tRNA synthetase genes from a wide range of other species.

Any isoform including this ORF would be the longest isoform.

I just had to check it out for myself. Here’s the genomic region:


I would see what the ortholog looks like in some of the new nematodes with genome sequence: Haemonchus. Pristionchus, Trichinella. Do any of these species have the conserved ORF in the middle of the gene?


If its any help or interest I’ve put the 3-way MLAGAN alignment of C.elegans, C.briggsae and C.remanei up on the Sanger C.elegans pages


This is from something that Michael (mh6) has been working on where you can get the alignment for any gene. Works internally - just need to sort out getting it on the external site now !


Looks nice! Are the these precomputed?

Yes they’re precomputed as part of the COMPARA pipeline. The alignments are stored in the COMPARA database and Michael has written that page to pull out regions of alignment for whatever WBGene id you enter. We hope to roll it out either here (Sanger) and / or eventually integrate it more with the website. Its still embryonic but works quite nicely.