The source of gene annotations in BovineMine are NCBI (RefSeq) and Ensembl.
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 v1.7 (release-updates) integrates the bovine reference genome assembly (ARS-UCD2.0) with other biological data sets including genes, gene expression, Gene Ontology, pathways, orthologs, genomic variants and QTL.This release includes a new dataset of curated selective sweeps in bovine breeds.
Genes |
Expression |
Proteins |
Homology |
Function |
Entire Gene Set |
Alias and DBxref |
Variation |
The source of gene annotations in BovineMine are NCBI (RefSeq) and Ensembl.
Query for genes:
Bovine gene expression values (FPKM and TPM) were computed using publically available RNAseq. See the Data Source page for the Bioprojects incldued.
Query for expression:
Most protein information is from UniProt and InterPro. NCBI (RefSeq) and Ensembl protein ids and sequences are also available.
Query for proteins:
Homologue datasets are from Ensembl Compara and OrthoDB.
Query for homology:
Gene Ontology annotation is from UniProt, Ensembl and RefSeq. Pathway datasets are from KEGG and Reactome.
Query for function:
These template queries allow retrieval of an entire dataset associated with the specified gene set.
Query for entire gene set:
These template queries enable the retrieval of database cross references (DBxref) and alias. DBxref are provided for gene ids across Ensembl and RefSeq. Aliases are provided for SNP ids.
Query for alias and dbxref:
dbSNP rsID SNP Alias IDs and Sources Cross References SNP Alias IDs Database Cross Reference ID (e.g RefSeq to Ensembl) Database CrossReference ID and Locations Genes and Database Cross Reference IDs Transcripts + Genes + Database Cross Reference IDsVariation datasets include SNP, SNP effects on Ensembl genes , SNP id aliases (SNPchiMp), AnimalQTLdb, and Selective Sweeps in bovine breeds. In the BovineMine database, a selective sweep region is called "haplotype block" in order to satisfy the InterMine requrement of using current Sequence Ontology terms for all genome features.
Query for variation:
Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
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