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Search HymenopteraMine. Enter names, identifiers or keywords for genes, proteins, ontology terms, authors, etc. (e.g. NM_001011573.1, 406079, vitellogenin, Vg, LOC102653843, Polistes, GO:0006633, V9I9E1_APICE).

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About v1.5 and Templates

HymenopteraMine v1.5 (Release-Updates) integrates genomic data for bees, ants and parasitoid jewel wasp. Expression and variation data are provided for A. mellifera. The tabs below show query template categories. "Alias and DBxref" templates are for id conversion between same-species gene sets. "Entire Gene Set" templates are for querying an organism's entire gene set.

Gene models in HymenopteraMine come from multiple sources including NCBI RefSeq 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:

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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 protein:

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HymenopteraMine includes orthologue predictions from two sources: OrthoDB v10.1 and a new source called HGD-Ortho, which was computed at HGD using the Orthologer pipeline (provided by OrthoDB). HGD-Ortho includes all HymenopteraMine species, while OrthoDB v10.1 includes a subset species. Both datasets provide orthologous groups that are descended from a single ancestral gene, based on a specified last common ancestral taxon. For OrthoDB, HymenopterMine has two last common ancestor ortholog sets, Hymenoptera and Holometabloa (which includes Drosophila melanogaster). HGD-Ortho includes ortholog sets based on the following last common ancestral taxa: Aculeata, Apidae, Apis, Apoidea, Bombus, Chalcidoidea, Formicidae, Formicinae, Halictidae, Holometabola, Hymenoptera, Ichneumonoidea, Myrmicinae, Parasitoida. Any orthologous group from either data source can include duplicated genes that emerged after divergence from the last common ancestor. All pairwise relationships within an orthologous group are called orthologues even if some might be classified as paralogues in an analysis of a more recent last common ancestor. 

Query for homology:

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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:

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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:

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Please contact us if you would like any additional template queries or if you have a concern about a query not completing.