ENSEMBL splice form prediction

[jbshin]

Hello,
I am analyzing alternative splice forms of a gene of interest in ENSEMBL and noticed that some of the splice forms do not contain a Start or Stop codon. Does anyone know what to think of these? For example, see this link:

http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000196872;r=2:99410309-99552722

There are several splice forms that do not contain a start or stop.
I would appreciate any input!
Thanks
jbshin

[dpryan]

Do you mean the "processed transcripts"?

[jbshin]

I found this with splice variants annotated as "processed transcripts" as well as "protein coding". Most of them have a start codon, but seem to terminate at the end of an exon, without an actual Stop codon.

[zhourui519]

some question about splice variant

Hi jbshin,

My name is Rui, from UCLA.
I plan to perform RNA-seq recently, I want to detect splice variants as well as gene expression, but I am a newer to RNA-seq and I found it was very hard to determine the read length and sequencing depth.(The core recommend me run 1 lane per sample, but the price is really too high to acceptable)
Looks like you also interested in splice variant, so may I know how many samples per lane you use, and read length?Is the results good?
I use human cell lines and I will isolated mRNA using a ployA tail capture, I will perform RNA seq using illumina 2000/2500.
Thanks!