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Search BovineMine. Enter names, identifiers or keywords for genes, proteins, ontology terms, authors, etc. (e.g. RPL24, RCAN1, NM_001040473.2, 282087, ENSBTAG00000013066, IGF2_BOVIN, rs385910977)

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BovineMine v1.5 (release updates) integrates bovine reference genome assemblies (AR-UCD1.2 and UMD3.1.1) with many other biological data sets, including genomes of other species. The sheep (Oar_v3.1 and Oar_v4.0) and goat (ARS1) genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-curated data sets to be applied to ruminants using orthology.

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Bovine gene expression values (FPKM and TPM) were computed using RNAseq from Dominette 01449 and her calves and sire.

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Gene Ontology annotation is from GOA@UniProt and AgBase. Pathway datasets are from KEGG and Reactome. A metabolic reactions dataset computed based on orthology to human RECON2 by the GplusE project is also available.

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Homologue datasets include TreeFam, Ensembl Compara and OrthoDB. A new ortholog dataset called ORIS (Orthology inference using synteny) from the GplusE project is also available.

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Interaction datasets include BioGrid and IntAct.

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Template queries are provided for datasets generated by the GplusE project, which has been the source of funding for BovineMine development. Current datasets include ORIS (Orthology inference using synteny) and metabolic reactions computed for the ORIS dataset based on RECON2.

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