Overview

We propose chicken gene atlases that are enriched in long non-coding RNA (lncRNAs) genes and a few protein-coding genes by gathering gene models from several genome annotations, including in particular EMBL-EBI Ensembl and NCBI RefSeq. The gene-enriched atlases are available for three genome assemblies: GalGal5, GRCg6a, and the most recent GRCg7b.

Each gene of these atlases is provided with "functional" and "genomic" information (see table below). "Functional" annotation includes various features like the official short gene Name, full gene name, human and mouse orthologous name (iD, HGNC name), expression profiles in various tissues (~40 for the last version associated to the GRCg7), tissue specificity score, etc. "Genomic" information provides the position of the genes and transcripts, the exon and intron numbers, the closest gene, the overlap with a miRNA gene, etc.

In addition, a vcf file is provided with a set of ~9.9M SNPs called from RNA-seq data.

Resulting annotations

INRAE
French National Institute for Agricultural Research

FAANG
Functional Annotation of Animal Genomes