What’s new in e!77?
- Updated human gene set (GENCODE 21)
- Updated rat gene set including manual annotation from HAVANA
- New species: Vervet-African green monkey
- Imported Transcript Support Levels (TSLs) from UCSC for human and mouse
- Imported APPRIS flag for human and mouse
- Updated Amazon molly gene set
Imported Transcript Support Levels (TSLs) from UCSC
We have imported Transcript Support Levels (TSLs) from UCSC and we are displaying them as a new flag in the human and mouse Gene and Transcript tables. TSLs for human are based on the GENCODE 20 gene set and TSLs for mouse are based on the GENCODE M2 gene set. Transcript Support Level is a method to highlight the well-supported and poorly-supported transcript models for users.
New APPRIS flag for human and mouse
We’ve added a new flag for human and mouse in the Gene and Transcript tables to represent the principal isoform generated by APPRIS which is a system that deploys a range of computational methods to provide value to the annotations of the human genome. It aims to select a single CDS for each gene as the principal isoform by combining protein structural information, functionally important residues and evidence from cross-species alignments. APPRIS is a joint project between Centro Nacional de Investigaciones Oncologicas and Instituto Nacional de Bioinformatica.
Improved alignments export
- Location -> Alignments (image)
- Location -> Alignments (text)
- Gene -> Genomic alignments
- Variation -> Phylogenetic context
Select an alignment, click on the “Download sequence” button, select your favourite output format from CLUSTALW, FASTA, Mega, MSF, Nexus, Pfam, Phylip, PSI, RTF (text alignment views only) or Stockholm, preview the output file, and save it.
The Vervet-AGM (Chlorocebus sabaeus), also known as the Vervet Monkey or African Green Monkey, ChlSab1.1 (GCA_000409795.2), was produced by the Vervet Genomics Consortium. This species is particularly important when studying high blood pressure and AIDS, since it is a host for simian immunodeficiency virus (SIV). BAM files and RNAseq-based gene models are available also for this species.
- Data matrix configuration extended to all species with RNASeq data
- Added new studies and updated other studies for human from DGVa
- Updated human phenotype from ClinVar and Decipher
- Updated mouse phenotype from IMPC
A complete list of the changes can be found on the Ensembl website.
Find out more at the Ensembl Release Webinar e77 (Thu, October 16, 2014 4:00 PM – 4.30 PM GMT). Register for free here: http://tinyurl.com/ensembl-oct-release