The source of gene annotations in BovineMine are NCBI (RefSeq), Ensembl and the Bovine Genome Database.
Query for genes:
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)
Enter a list of identifiers.
BovineMine v1.4 (release updates) integrates the bovine reference genome assembly (UMD3.1.1) with many other biological data sets, including genomes of other species. The sheep (Oar_v3.1) 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.
Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
Genes |
Expression |
Proteins |
Function |
Homology |
Interactions |
Variation |
Entire Gene Set |
Alias and DBXref |
The source of gene annotations in BovineMine are NCBI (RefSeq), Ensembl and the Bovine Genome Database.
Query for genes:
BovineMine provides gene expression data for Bos taurus from NCBI SRA.
Query for expression:
Transcripts Expression Transcript Expression Transcripts + Expression Expression, Metadata and BRENDA Tissue Ontology Bovine Homologues Bovine Transcripts Bovine Expression Transcripts Expression Transcripts ExpressionProteins from NCBI (RefSeq), Ensembl and UniProt.
Query for proteins:
BovineMine provides Gene Ontology annotation from GOA@UniProt, protein domain information from InterPro, and pathways data from Reactome and BioCyc.
Query for function:
BovineMine provides homologue information from TreeFam, Ensembl Compara, OrthoDB and Homologene.
Query for homology:
BovineMine provides physical interactions from BioGRID.
Query for interactions:
BovineMine provides QTL information from Animal QTLdb and SNP information from dbSNP.
Query for variation:
BovineMine provides templates for querying data in bulk.
Query for entire gene set:
Genes and Chromosomal location Transcripts + Genes + Database Cross Reference IDs Gene IDs Genes and Database Cross Reference IDs All proteins Proteins (UniProt) and Publications. Genes + mRNA + Protein Genes and Transcript idsAlias and database cross references for features.
Query for alias and dbxref:
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