isoforms showing on Wormbase

Are the protein peptide isoforms showing on Wormbase all just in silico prediction from alternative splicing, but not from experimental data (i.e. RNA-seq)?
We had a discussion in our group, and I want to confirm with a broader community.
Thank you very much!

I think it is (certainly, I think it used to be?) a mixture of gene-prediction models and RNA cloning and sequencing results, with some hand-curation correcting some gene-prediction models.

If there is a particular gene you’re interested in, it’s very useful to go to the genome browser and look at the data underlying the gene models, especially the ESTs and any RNAseq data.

Thanks Dr. Schwartz!
The gene we were discussing was daf-16, while my questions was more for the future If I look for isoforms for other genes, how should I interpret what I see on the page…
In last week’s journal club we discussed a paper, about a certain phenotype is daf-16 dependent, but did not specify which one (isoform) of daf-16. And so we came to the point of discussing how many different daf-16 isoforms there are; are they different between tissues, or develop/aging dependent. According to Wormbase, they are labeled from a to k, so 10+ isoforms; while someone in the lab had experience working with daf-16 says there were only 4 isoforms that are real. I saw papers analyzing thousands of C. elegans RNA-seq data sets for all the detected isoforms, just did not know if that has been incorporated to Wormbase yet.

Just to add: you can see the comments for the isoforms in the sequence widget under “curator comments”, plus there is a “confirmation status” (which is bases on transcript coverage) in the details bit.
In the daf-16 case, every isoform looks like it came from a cDNA clone … for better and worse.

Generally most of the newer curation is including lots of RNA-seq data for information on possible isoforms, but the older ones were mostly dependent on cDNAs/ESTs/SAGE, etc. But we also use mass-spec data, homologies and various gene prediction tools.

But as always: if you see something that might look potentially dodgy, give a shout on and we will see what we can do.