List all zebrafish genes annotated to a specific Gene Ontology term.
For a given Gene (or lists of Genes) in zebrafish, returns the OMIM disease phenotypes of the human ortholog.
Specify OMIM human disease phenotype(s) and retrieve zebrafish genes which are orthologs of the associated human genes. This dataset is limited to zebrafish genes for which a human ortholog has been curated by ZFIN.
Search for antibodies.
Find out the definition and parents of a phenotype ontology term. Search by term name or term identifier.
Find terms in any one of the ontologies used in ZFIN: the Gene Ontology (includes Biological Process, Molecular Function, and Cellular Component Ontologies), the Phenotypic Quality Ontology, the Sequence Ontology, the Zebrafish Anatomy Ontology, and the Zebrafish Stage Ontology.
Retrieve ZFIN-curated orthologs for any zebrafish gene.
Search for genes, markers, clones, constructs, and other sequence features in ZebrafishMine.
Sequence alterations include mutations, SSLPs, and SNPs. You can use gene symbol (for example fgf8a), to search for sequence alterations associated with that gene. You can also search by the symbol of the sequence alteration (for example, ti282a).
Find all identifiers for a gene
Find details about a publication. Search by author name and/or PubMed ID.
Find morpholinos and their sequences using the symbol of the targeted gene.
Find publications where ZMP sa alleles have been used.
Find zebrafish that have been used as models for specific human diseases. The human disease names are from the Disease Ontology (http://disease-ontology.org/).
Search for zebrafish anatomy terms in the Zebrafish Anatomy (ZFA) Ontology. This search retrieves the definition and parents of the term.
For a given gene (or list of genes), this query returns the ZFIN-curated zebrafish orthologs of human genes.
For a given zebrafish gene (or list of genes) returns the phenotypes of single mutants of that gene. Does not include phenotypes resulting from morpholinos and other knock-down reagents.
Find all sequence alterations for a publication using an author name and/or a PubMed ID.
For a given zebrafish gene (or list of genes), returns the expression pattern of the gene(s) in wild-type fish, under standard experimental conditions.
Search for morpholinos using the target gene symbol and/or the morpholino name.
Retrieve the curated human ortholog of any zebrafish gene and the associated OMIM disease phenotypes.
Find all genes in a publication. Search by author name or PubMed ID.
For a given zebrafish gene (or list of genes), returns the phenotype resulting from knocking down the gene using morpholinos, CRISPRs or TALENs.
Find zebrafish mutants that have been used to model specific human diseases. The human disease names are from the Disease Ontology.
Search for DNA clones
Use this search to find cross references for gene records in other databases.
This search returns zebrafish genes expressed in an anatomical structure (and its parts), in wildtype (standard) zebrafish, in standard conditions.
Find all non-wildtype genotypes in a publication. Search using author name and/or PubMed ID.
Retrieve all Gene Ontology annotations for a specified gene (or list of genes).
Find zebrafish genes by name or symbol
Use a gene symbol to find protein accession numbers
Find zebrafish models for specific human diseases. These transient models were generated using sequence targeting reagents such as morpholinos, TALENs or CRISPRs. The human disease names are from the Disease Ontology.
List of fish at ZFIN with IDs, names and whether they are "wildtype" lines.
This search returns all zebrafish mutants that were generated using ENU. Results include allele symbol, affected gene symbol, affected gene name, lab of origin, and type of mutation. If details of the type of mutation are not known, the term "sequence_alteration" is displayed in the "Sequence Ontology Term > Name" (type of mutation) column.
This search returns all zebrafish mutants that were generated using ENU, where the affected gene has a protein accession in the ZFIN database. Results include allele symbol, affected gene symbol, affected gene name, lab of origin, type of mutation, protein accessions associated with the gene, and the source of the protein accessions. If details of the type of mutation are not known, the term "sequence_alteration" is displayed in the "Sequence Ontology Term > Name" (type of mutation) column.
This template returns a list of all ZFIN phenotypes. To see all phenotypes for a sample list of publications that contain ameliorated phenotypes, select the checkbox next to "constrain to be IN saved Publication list" and select "AmelioratedPhenoPublicationList" from the pulldown list.
A query to find all sources for all ZFIN objects.
This search returns a list of all zebrafish mutant alleles in ZFIN that are associated with a gene. To find out how many zebrafish genes have mutant alleles, run the search and click on the "View Column Summary" icon in the "Gene Symbol" column.
Use this query to find all children of a given Zebrafish Anatomy Ontology term. The sample query will return all children of "central nervous system".
Labs available at ZFIN
List all zebrafish genes annotated to specific Gene Ontology terms. GO term and Gene Symbol are returned.
A list of the zebrafish anatomy terms and their synonyms when available.
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ZebrafishMine is a collaboration between ZFIN at University of Oregon and the InterMine project at the Cambridge Systems Biology Centre.
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