How Alternative Splice Variants Are Annotated In A Sequenced Genomes?

Question

[GR]

Hello everyone,

I was looking for alternative splice variants in some sequenced genomes. The most common representation for these are geneA.1, geneA.2, geneA.3 but recently I have seen few genomes where I can't see gene names with .1, .2.,.3 it is just geneA, geneB, geneC.

This way I thought to conclude that there is no alternative splice variants predicted for these genomes. But when I looked in the paper, it is given that alternative splice variants are predicted while annotating these genomes. Is there any alternative representation for alternative splice variants? What should I conclude? Can some one please help.

Thanks, R.

[Alex Paciorkowski]

"But when I looked in the paper..." Which paper?

[Arun]

This figure might help? AT1G01020 is a gene with 2 different transcripts AT1G01020.1 and AT1G01020.2. You can see that AT1G01020.2 is shorter than AT1G01020.1 from the respective mRNA columns start and end positions.

[Alex Paciorkowski]

Nice figure. From which paper is it?

[Arun]

Oh I just took a screenshot of the GFF file of Arabidopsis thaliana

Answer 1

[Michael]

Genes and transcripts are not the same concept. Splice variants could be annotated as different transcripts or coding sequences of the same gene, e.g. when representing an annotation in a GFF file. Using the descriptive features of GFF3 format it is possible to reconstruct which exons constitute the splice variants. Which identifiers are assigned to these splice variants is rather irrelevant as long as they are unique and will depend of the naming scheme of the genome annotation.

If you are referring to representation of alternative splicing events in ensembl, this page might be a good starting point.