Spliced and Unspliced Sequences

Model Organism: Worms WormBase
1

In the past, under “Sequences” for a given C. elegans transcript page, spliced and unspliced DNA sequences were displayed with exons highlighted in orange and yellow.

It appears now that genes are only displayed as an unspliced sequence with UTR.

Are the old annotated/spliced sequences still available somewhere? (I can find them on the old legacy site of Wormbase, but they seem to be lost on WormBase2).

Thanks,

2

To do:

  1. Implement WormBase2 update that eliminates distracting intron/exon information.
  2. Take much needed vacation.
  3. TBA.
3

I’ve never run into this. Every transcript I looked up has a conceptual translation, spliced+UTR, and unspliced+UTR. You’re searching by transcript, not CDS, yes?

4

This issue seemed to last for a week or so, and then the predicted spliced/unspliced sequences returned. I don’t know why.

We use the predicted sequences a lot for primer design, so having annotated introns and exons is pretty important.

It’s functional now, so that’s good.

5

Just a heads-up: the genbank format of the cosmid sequences at the NCBI always has the coordinates of the coding exons (albeit, the latest information when the cosmid sequence was uploaded); you can look at those directly, or some DNA sequence viewing software (MacVector, for instance) can interpret the genbank format to annotate the DNA for you. This came in handy a couple of weeks ago when WormBase was down for a day or two …