Gene models in HymenopteraMine come from multiple sources including NCBI RefSeq, Ensembl Rapid Release and consortium official gene sets. Consortium data sources are labeled using the original consortium official gene set names, and may have "HGD" appended, if the data source has ids assigned by HGD. Use "ALIAS AND DBXREF" templates to convert identifiers.
Query for genes:
More queries
HymenopteraMine 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, HymenopteraMine 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:
More queries
HymenopteraMine includes three collections of orthologue predictions: OrthoDB v11, HGD-Ortho and Drosophila-RBH. The latter two were computed at HGD using the Orthologer pipeline (provided by OrthoDB). The Drosophila-RBH dataset consists of one-to-one orthologues between D. melanogaster genes and each hymenopteran species predicted based on reciprocal-best-hit protein alignments. HGD-Ortho and OrthoDB v11 each provide orthologous groups (called âorthologue clustersâ) that are descended from a single ancestral gene, based on a specified last common ancestral taxon. HGD-Ortho includes all HymenopteraMine species, while OrthoDB v11 includes a subset of the species. For OrthoDB, HymenopterMine has four last common ancestor orthologue sets: Apoidea, Formicidae, Hymenoptera and Holometabola (which includes Drosophila melanogaster). HGD-Ortho includes 18 orthologue sets based on different last common ancestral taxa, shown in the Taxonomy tab above. Any orthologue cluster from either data source can include duplicated genes that emerged after divergence from the last common ancestor. All pairwise relationships within an orthologue cluster are called orthologues even if some could be classified as paralogues in an analysis of a more recent last common ancestor.
Query for homology:
More queries
HymenopteraMine includes GO annotations for all species. Other data sources (KEGG, Reactome, BioGRID and IntAct) are available for a subset of organisms, listed on the Data Source page. You can use orthologous relationships to leverage A. mellifera and D. melanogaster information for other species.
Query for function:
More queries
The query templates in this category allow you to perform simple queries on an entire gene or protein set for a species.
Query for entire gene set:
More queries
The query templates in this category allow you to convert identifiers. Use a database cross reference query template to convert between a RefSeq and consortium gene set with HGD ids. Use an alias query template to convert between HGD ids and original consortium ids, HGD ids and OrthoDB ids, or HGD ids for old vs new gene sets (e.g. amel_OGSv3.2 vs amel_OGSv1.0). You must use the appropriate alias query template for converting either gene ids or transcript ids, depending on the species. For the following species, aliases are provided for transcripts rather than genes because the original gene sets did not have gene ids: A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Query for alias and dbxref:
More queries