CBS protein annotations for ENCODE peptides.

This page shows a summary of the results of CBS's prediction servers run on the 1097 transcripts in the CDS AA file. The data contain 1097 proteins from 434 loci. Of these, variable transcripts occur in 258 loci, accounting for 921 of the proteins. The prediction servers have been run on all the peptides, but this page only shows results for those loci that have different transcripts and variation in CBS predictions within these transcripts. The annotations are produced for the protein sequence "as-is" and no sort of CDS validation has been performed.

If you click on the name of a gene you will arrive at a page with a figure of every transcript, showing the CBS predicted annotations along with the exons, mapped onto protein coordinates. As the same exons have different names, depending on the transcript they are projected from, we display the exons in terms of absolute chromosome coordinates, so the exon structure between peptides can be compared. An easier way would be to name the exons by the locus, and not the transcript, which should be fairly easy to do.

An example of the figures:




These figures show 2 different transcripts from the AC006985.9 (UGT1A6) gene. They both share the 3 exons in the middle, but it is the first exon in the first transcript that is interesting, as it seems to code for a propeptide and a signal peptide, missing from the second transcript.

Some annotation types, such as a negative SignalP prediction "NOSIGNAL", TargetP predictions and SecretomeP predictions are not bound to specific coordinates on the protein, and therefore stretch over the entire length of the figure, which is ugly, but it can still be useful info.

Looking specifically at signal peptides and propeptides, a total of 112 of all the 434 genes have predicted signal peptides. 31 of the 258 variably transcribed genes have transcripts both with, and without a signal peptide. The same is true for 47 genes, when looking at propeptides. Transcripts with and without BOTH a signal- and a propeptide are found on 6 occasions.

Below are all the predictions in figure form, grouped by loci, and with a short description of which CBS annotations we see variations in within transcripts from that gene. The whole set of CBS prediction results is available here. The file is in a simple GFF-like, tab-separated format with fields: "Transcript-ID Annotation-method Annotation-type Start End Score Note".