BovineMine includes gene annotations from RefSeq, Ensembl and the Bovine Genome Database. Use "ALIAS AND DBXREF" templates to convert identifiers.
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 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.
Genes |
Expression |
Proteins |
Function |
Homology |
Interactions |
Variation |
ALIAS AND DBXREF |
ENTIRE GENE SET |
BovineMine includes gene annotations from RefSeq, Ensembl and the Bovine Genome Database. Use "ALIAS AND DBXREF" templates to convert identifiers.
Query for genes:
BovineMine includes B. taurus transcript expression values, which we compute based on aligned RNAseq reads. SRA Metadata and BRENDA tissue ontology terms are also included.
Query for expression:
BovineMine includes protein information from UniProt and protein domain information for UniProt proteins from InterPro. Although UniProt uses protein isoform identifiers as primary identifiers, it maps UniProt ids to RefSeq genes rather than to specific Refseq transcript identifiers. Therefore, BovineMine maps UniProt ids to RefSeq genes. Queries relating RefSeq genes to UniProt may produce multiple results per gene due to the presence of protein isoforms.
Query for proteins:
BovineMine includes GO annotations for B. taurus, C. hircus, O. aries and model organisms. It also includes Reactome, KEGG and BioCyc pathways for B. taurus and model organisms.
Query for function:
BovineMine includes homologues from Ensembl Compara, Homologene, OrthoDB and TreeFam.
Query for homology:
BovineMine includes gene interactions from IntAct for B. taurus, O. aries and model organisms, and from BioGrid for B. taurus and model organisms.
Query for interactions:
BovineMine includes bovine sequence variants from dbSNP and dbVar, and bovine SNP array identifiers ("SNP Alias IDs") from SNPchiMp. We compute variant effects on bovine Ensembl and RefSeq genes using the Ensembl Variant Effect Predictor.
Query for variation:
The templates in this category allow you to convert primary gene set identifiers (e.g RefSeq to Ensembl and vice versa).
Query for alias and dbxref:
The templates in this category allow you to perform simple queries on an entire gene or protein set.
Query for entire gene set:
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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Chromosomal location