Given a gene id or gene symbol, retrieve the chromosomal coordinates.

Given a gene id or symbol, retrieve GO terms. Be sure to view the Qualifier column for genes annotated as "NOT".

Given a Gene id, retrieve expression values, metadata and BRENDA Tissue Ontology.

Given a gene id or symbol, retrieve publications.

Given a chromosome id and coordinates, retrieve genes.

Given a SNP rsID, retrieve ids (AnimalQTLdb) of overlapping QTL and traits.

Given a bovine SNP alias ID, such as ssID or an array id, retrieve dbSNP rsID.

Given a bovine SNP rsID, retrieve chromosome location.

Given a bovine SNP rsID, retrieve gene. No rows will be returned if the SNP is not within a gene.

Given a gene id or symbol, retrieve pathways. The pathway data sources retrieved may be affected by the input id (RefSeq, Ensembl or gene symbol).

Given a gene id, retrieve proteins (UniProt) and protein domains.

Given a bovine tissue, retrieve gene expression levels. Optionally constrain by gene expression cutoff and gene source.

Given a gene id, retrieve variants and their consequences.

Given a gene id or symbol in the selected organism, retrieve homologues. Optionally select homologue type.

Given gene id or symbol, retrieve interacting genes.

Given a bovine trait, retrieve QTL id (AnimalQTLdb) and chromosomal location.

Given a chromosome id, retrieve genes and their locations.

Given a GO term (e.g. DNA binding) or GO identifier (e.g. GO:0003677), retrieve genes. Wildcards (*) are allowed (e.g. *muscle*).

Given a gene source (e.g. RefSeq or Ensembl), retrieve all gene ids. Use this to create a single-gene-set background list for enrichment.

Retrieve all QTL ids, with traits and locations of QTL on ARS-UCD1.2. Although there is a pulldown menu, this works only for bovine because QTL are not loaded for other species.

Given a gene id or symbol, retrieve transcript ids, locations and exon locations.

Given a bovine trait, retrieve QTL on the ARS-UCD1.2 assembly from AnimalQTLdb.

Given an organism, retrieve all transcripts with genes and database cross references. Multiple gene sets may be retrieved, and can be filtered in the output.

Given a bovine dbSNP rsID, retrieve SNP Alias IDS and sources.

Given an organism and gene set, retrieve all genes and their locations.

Given an InterPro id, retrieve proteins and genes.

Given a bovine QTL id (AnimalQTLdb) on the ARS_UCD1.2 assembly, retrieve genes within QTL region. You can create a gene list to use in a gene template query. No rows will be returned if there are no genes.

Given a Uniprot accession or ID, retrieve orthologues from the GPLUSE ORIS dataset. This works for bovine, sheep, pig, mouse and human ids.

Given a RefSeq or Ensembl transcript id, retrieve gene id and gene expression values, metadata and BRENDA Tissue Ontology.

Given an organism, retrieve all protein ids (UniProt).

Given a bovine QTL ID from AnimalQTLdb, retrieve SNPs within the QTL region.

Given a bovine QTL id (AnimalQTLdb), retrieve transcripts within QTL region. A list of transcripts can be saved and used in an expression template query. No rows will be returned if there are no transcripts.

Given a protein id (UniProt), retrieve genes and GO.

Given a gene id or symbol in the selected organism, retrieve GO terms and homologues. Optionally select homologue type.

Given a gene id or symbol, retrieve Reactome pathways.

Given a Gene Symbol or ID for a specified organism and gene source, retrieve transcript ids and locations.

Given a gene id or symbol from the selected non-bovine organism, retrieve bovine homologues and pathways. Optionally select homologue type.

Given a gene id in organism 1, retrieve homologues in organism 2 and pathways for the homologues. Optionally select homologue type.

Given a gene id, retrieve database cross reference id (e.g. RefSeq to Ensembl or vice versa).

Given a QTL id from AnimalQTLdb, retrieve trait and Vertebrate Trait Ontology.

Given a bovine Ensembl gene id or symbol, retrieve metabolic reactions and subsystems. These reactions are based on Human Recon2.

Given an organism, retrieve all miRNAs and their locations.

Given a bovine Ensembl gene id, retrieve ORIS (Orthology Inference Using Synteny) orthologues and orthologue cluster id.

Given a gene id or gene symbol, retrieve proteins (UniProt).

Given a gene id, retrieve gene symbol and description.

Given a gene id or symbol, retrieve homologues.

Given a protein id (UniProt), retrieve publications.

Given a chromosome id and coordinates, retrieve miRNAs.

Retrieve all gene ids and database cross reference ids for the specified organism and gene source.

Given a non-human Gene id, retrieve human homologues and pathway information for those homologues. Optionally select homologue type.

Given a genome assembly version, retrieve primary chromosome ids used in BovineMine and alternative ids.

Given a non-bovine Ensembl gene id, retrieve ORIS (Orthology Inference Using Synteny) bovine orthologue.

Given a gene id or symbol, retrieve transcript ids and coding sequences.

Given protein domain name (InterPro), retrieve information about protein domains. Wildcards (*) are allowed.

Given a transcript id, retrieve gene id.

For a given organism, retrieve all mRNAs and proteins along with their lengths. All gene sources are provided.

Given an InterPro protein domain name, retrieve proteins and genes for an organism. Wildcards (*) are allowed.

Given a gene id, retrieve transcript id(s).

Given a trait, retrieve VTO term. Remove trait name constraint to retrieve all traits and VTO terms.

Given a transcript id, retrieve protein id (from gene set, not UniProt).

Given an organism, retrieve UniProt proteins with publications.

Given a gene id or symbol in the selected organism, retrieve human orthologues.

Given a gene ID, retrieve database crossreference gene and locations of both. This is useful for comparing genes across assembly versions for B. taurus and O. aries. If the gene is from RefSeq of an older assembly (UMD3.1.1 or Oar_v3.1), you should append the assembly name to the gene id (e.g. 100048947-UMD3.1.1 or 100034665-Oar_v3.1).

Given a gene id or symbol, retrieve transcript and protein ids (from the gene set, not UniProt).

Given a transcript ID, retrieve gene id and GO terms.

Given a gene alias id, retrieve gene id. This template should be used to convert RefSeq-UMD3.1.1 or RefSeq-Oarv3.1 gene ids to BovineMine gene ids for use in template queries that require gene ids.

Given a gene symbol, retrieve gene id from the specified gene set.

Given a transcript id, retrieve gene id and pathways.

Given a protein id (UniProt), retrieve corresponding gene and location of gene.

For a given organism, retrieve all genes with metabolic reactions and subsystems. These reactions are based on Human Recon2.

Given a gene id, retrieve transcripts and proteins.

Given a transcript id, retrieve protein id.

Given a gene id, retrieve transcripts.

Given a gene source and organism, retrieve all gene ids, gene symbols and transcript ids.

Given a gene ID, retrieve database crossreference gene from a specified gene source and locations of both. This is useful for comparing genes across assembly versions for B. taurus and O. aries. If the gene is from RefSeq of an older assembly (UMD3.1.1 or Oar_v3.1), you should append the assembly name to the gene id (e.g. 100048947-UMD3.1.1 or 100034665-Oar_v3.1).

Retrieve all metabolic reactions and their subsystems for an organism. These reactions are based on Human Recon2.

Given a gene id, retrieve publications.

Given a Bovine Ensembl95 transcript ID, retrieve non-synonymous coding variants.