BovReg
The BovReg consortium aims to provide a comprehensive map of functionally active genomic features in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. This constitutes key knowledge for biology-driven genomic prediction needed by scientific and industry livestock communities.
BovReg brings together a critical mass of experts in ruminant research and beyond encompassing bioinformatics, molecular and quantitative genetics, animal breeding, reproductive physiology, ethics and social science. 20 partners from the EU, Canada and Australia form a global interdisciplinary team, which builds on previous and running national and EU-funded projects and many established industry cooperations. Datasets will be shared and coordinated with other FAANG initiatives via the FAANG data coordination centre.
Ensembl is a partner in the BovReg project, and we annotate the protein-coding and non-coding RNA gene structures using a re-engineered version of our Gene Annotation System (Aken et al, 2017). After QC, genomes and annotations are made available via our FTP site (see table below) before subsequently being made available in the Ensembl Genome Browser.
| Species | Accession | Assembly submitted by | Annotation | Proteins | Transcripts | Softmasked genome | Repeat library | Other data | View in browser |
|---|---|---|---|---|---|---|---|---|---|
| Bos taurus | GCA_002263795.2 | USDA ARS | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | ensembl.org |
| Bos gaurus | GCA_014182915.1 | USDA, ARS, USMARC | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org |
| Bos grunniens | GCA_005887515.1 | Lanzhou University | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Bos indicus x Bos taurus | GCA_003369695.2 | University of Adelaide | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |
| Bos mutus | GCA_000298355.1 | BGI-shenzhen | GTF, GFF3 | FASTA | FASTA | FASTA | Repeatmodeler | FTP dumps | ensembl.org |
| Bos mutus (Datong Yak) | GCA_007646595.3 | Lanzhou University | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | rapid.ensembl.org |
| Bos indicus x Bos taurus | GCA_003369685.2 | University of Adelaide | GTF, GFF3 | FASTA | FASTA | FASTA | – | FTP dumps | ensembl.org |