Annotation

The zebrafish Zv9 assembly was annotated using a modified Ensembl pipeline. Predictions from zebrafish proteins have been given priority over predictions from other non-mammalian vertebrate species. All Uniprot proteins were filtered to remove predictions ( PE levels 3 and above ). Aligned zebrafish cDNAs have been used to add UTR regions.8,374 RNASeq models made from a range of zebrafish developmental stages and tissues were added into the gene build where they added a novel model or splice variant.Genes are named based on the alignment of their coding regions to known entries in public databases; ZFIN genes have priority in this process.

The Ensembl annotations were then merged with Vega annotations at the transcript level. Transcripts were merged if they shared the same internal exon-intron boundaries (i.e. had identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Vega source transcripts (regardless of merge status) were included in the final merged gene set.

Vega logo Additional manual annotation of this genome can be found in Vega