NCBI (RefSeq) genes are available for all AquaMine species. Check the Data Source page for the availability of Ensembl genes.
Query for genes:
Search AquaMine. Enter names, identifiers or keywords for genes, proteins, pathways, ontology terms, authors, etc. (e.g. LOC100136597, nlrx1, rab3b, ENSONIG00000000010, 105319044, NM_001124210.1, XP_020363214.1, A0A1S3RVZ0_SALSA, homeobox, glycolysis, AMOG4978at6656).
Enter a list of identifiers.
AquaMine v1.2 (release-updates) integrates reference genome and annotation data of aquatic species important to US aquaculture and fisheries. To get started, try a query template listed under one of the tabs in the bar shown below, or use the Keyword search to retrieve a report page after entering an identifier or descriptive text.
Genes |
Expression |
Proteins |
Homology |
Function |
Entire Gene Set |
Alias and DBxref |
NCBI (RefSeq) genes are available for all AquaMine species. Check the Data Source page for the availability of Ensembl genes.
Query for genes:
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:
AquaMine includes orthologue predictions from three sources: OrthoDB v10.1, AquaMine-Ortho, and Ensembl (from Ensembl Compara and Ensembl Metazoa). The AquaMine-Ortho dataset was computed using the Orthologer pipeline (developed by OrthoDB). Both AquaMine-Ortho and Ortho-DB use RefSeq gene ids; the Ensembl data set uses Ensembl gene ids. AquaMine-Ortho includes all AquaMine species, while OrthoDB v10.1 and Ensembl each include a subset species (see Data Source page). The Ensembl dataset provides pairwise orthologue relationships, and classifies them as ortholog_one2one, ortholog_many2many, ortholog_one2many. OrthoDB and AquaMine-Ortho provide orthologous groups that are descended from a single ancestral gene, based on a specified last common ancestral taxon. Any orthologous group from either data source can include in-paralogues, which result from gene duplication after divergence from the last common ancestor. Click on the Taxonomy tab in the main navigation bar above to view the taxonomy tree and the last common ancestral groups used in AquaMine-Ortho.
Query for homology:
Homologues (OrthoDB or AquaMine-Ortho) Genes Homologues (Ensembl) GO Terms Homologues (OrthoDB or AquaMine-Ortho) GO Terms Homologues (Ensembl) Homologues Homologues (OrthoDB or AquaMine-Ortho) from specified Organism Reciprocal Best HitsGene Ontology annotation is from UniProt. Pathway datasets are from KEGG.
Query for function:
These template queries allow retrieval of an entire dataset for a specified organism or gene set.
Query for entire gene set:
These template queries enable the retrieval of database cross references ids (RefSeq <=> Ensembl).
Query for alias and dbxref:
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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