ZFIN Data Reports |
Warranty Disclaimer and Copyright Notice |
ZFIN data reports are updated every day of the week at 10:10pm PST. The format for each file is described below. Each record contains a ZFIN ID which may be used to link data between files. All files use tab as the field delimiter. The 'download' links will display the file on your browser. Use your browser 'save as' feature to make a local copy of the file. If you choose to link to a ZFIN data page from your web site, append the ZFIN ID to the URL http://zfin.org/cgi-bin/ZFIN_jump?record=
Please direct questions or requests for additional data to ZFIN.
| Table of Contents |
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| Genetic Markers |
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Genetic Markers
| ZFIN ID | Symbol | Name | Marker type |
Previous ZFIN IDS includes former and current ZFIN IDs for merged data
| Former ZFIN ID | Current ZFIN ID |
| Previous Names |
|---|
Previous names
| Current ZFIN ID | Current Name | Current Symbol | Previous Name |
| Mapping Data |
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Mapping Data from the 6 Zebrafish Mapping Panels
| ZFIN ID | Symbol | Panel Symbol | LG | Location | Metric |
| Sequence Data |
|---|
ZFIN Markers associations to GenBank sequence information
| ZFIN ID | Name | GenBank ID |
ZFIN Markers associations to RefSeq sequence information
| ZFIN ID | Symbol | RefSeq ID |
ZFIN Markers associations to Entrez Gene sequence information
| ZFIN ID | Symbol | Entrez Gene ID |
ZFIN Markers associations to UniGene sequence information
| ZFIN ID | Symbol | UniGene ID |
ZFIN Marker associations to UniProt protein IDs
| ZFIN ID | Symbol | UniProt ID |
ZFIN Marker associations to InterPro protein IDs
| ZFIN ID | Symbol | InterPro ID |
ZFIN Marker associations to GenPept protein IDs
| ZFIN ID | Symbol | GenPept ID |
ZFIN Marker associations to Sanger Vega IDs
| ZFIN ID | Symbol | Vega ID |
ZFIN Markers associations to Ensembl IDs in ZFIN
(Only associations with 1:1 relationships between ZFIN marker IDs and Ensembl IDs are stored in ZFIN.
All associations can be obtained using BioMart http://www.ensembl.org/biomart/martview)
| ZFIN ID | Symbol | Ensembl ID |
ZFIN Gene IDs indirectly associated with Sequence Accessions via cDNA & EST
| ZFIN Gene ID | ZFIN Gene Symbol | Sequence Accession |
| Orthology |
|---|
Human and Zebrafish Orthology
| ZFIN ID | ZFIN Symbol | ZFIN Name | Human Symbol | Human Name | OMIM ID | Entrez Gene ID |
Mouse and Zebrafish Orthology
| ZFIN ID | ZFIN Symbol | ZFIN Name | Mouse Symbol | Mouse Name | MGI ID | Entrez Gene ID |
Drosophila and Zebrafish Orthology
| ZFIN ID | ZFIN Symbol | ZFIN Name | Fly Symbol | Fly Name | Flybase ID |
Yeast and Zebrafish Orthology
| ZFIN ID | ZFIN Symbol | ZFIN Name | Yeast Symbol | Yeast Name | SGD ID |
| Genetic Marker Relationships |
|---|
Genetic Marker Relationships
| Gene ID | Gene Symbol | Marker ID | Marker Symbol | Relationship |
| Gene Ontology Data |
|---|
Gene Ontology (GO) Annotations of Zebrafish Markers
(see also GO Annotation File format at the Gene Ontology Consortium)
| Database Desig- nation |
Marker ID | Gene Symbol | Quali- fiers |
GO Term ID |
Refer- ence ID |
GO Evidence Code |
Inferred From | Ontology:
P=Biological Process F=Molecular Function C=Cellular Component |
Marker Name | Marker Synonyms (if any) |
Marker Type:
gene transcript protein |
Taxon | Modifi- cation Date |
Assigned By |
Download from www.geneontology.org
| Gene Expression |
|---|
ZFIN Genes with Expression Assay Records
| Gene ID | Gene Symbol | EST ID(optional) | EST Symbol(optional) | Expression Type | Expression ID | Publication ID | Genotype ID | Environment ID |
Expression Environment Description
| Environment ID | Condition Group | Condition Content | Value | Unit | Comment |
| Genotype Data |
|---|
Genotype Features
| ZFIN ID | Genotype Name | Genotype Unique Name | Allele ID | Allele Name | Allele Abbreviation | Allele Type | Allele Display Type | Gene or Construct Symbol | Corresponding ZFIN Gene ID/Construct ID |
Genotype Features (removed or displaced genes)
| ZFIN ID | Genotype Name | Genotype Unique Name | Affected Gene Symbol | Corresponding ZFIN Gene ID |
Genotype Backgrounds
| ZFIN ID | Genotype Name | Background |
| Wildtype Lines |
|---|
Wildtype Lines
| ZFIN ID | Genotype Name | Genotype Abbreviation |
| Phenotype Data |
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Genotypes with Phenotypes
| Genotype ID | Genotype Name | Start Stage ID | Start Stage Name | End Stage ID | End Stage Name | Affected Structure or Process 1 ID | Affected Structure or Process 1 Name | Affected Structure or Process 2 ID | Affected Structure or Process 2 Name | Phenotype Keyword ID | Phenotype Keyword Name | Phenotype Modifier | Publication ID | Environment ID |
Genotypes with Phenotypes (obo format)
| Genotype ZFIN ID | Genotype Name | Start Stage Obo ID | End Stage Obo ID | Affected Structure or Process 1 obo ID | Affected Structure or Process 2 obo ID | Phenotype Keyword obo ID | Phenotype Modifier | Publication ZFIN ID | Environment ZFIN ID |
Phenotype Environment Description
| Environment ID | Condition Group | Condition Content | Value | Unit | Comment |
| Anatomical Ontologies |
|---|
Zebrafish Anatomical Ontology in OBO Format
Zebrafish Anatomical Terms
| Entire Staged Anatomy (tab indented) |
Download (*note: format changed April 26, 2005)
Zebrafish Anatomy Term Relationships
| Parent Item ID | Child Item ID | Relationship Type ID |
Download (*note: format changed April 26, 2005)
Zebrafish Stage Series
| Stage ID | Stage Name | Begin Hours | End Hours |
Zebrafish Anatomy Term Stages
| Anatomy Item ID | Anatomy Item Name | Begin Stage ID | End Stage ID |
Zebrafish Anatomy Term Synonyms
| Anatomy Item ID | Anatomy Item Name | Anatomy Item Synonym |
Zebrafish Gene Expression by Stage and Anatomy Term
| Expression ID | Begin Stage ID | End Stage ID | Anatomy Item ID | Expression Found |
| Morpholino Data |
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Morpholino
| Gene ID | Gene Symbol | MO ID | MO Symbol | MO Sequence | Note |
| Ontology Translations |
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Gene Ontology IDs: ZFIN to GO ids
(see also GO in OBO format at the Gene Ontology Consortium)
| GO term ZFIN ID | GO term GO ID |
Anatomy Ontology IDs: ZFIN to AO ids
(see also AO File in OBO format at the OBO foundry )
| AO term ZFIN ID | AO term AO ID |
Quality Ontology IDs: ZFIN to Quality ids
(see also Quality file in OBO format at the OBO foundry
| Quality term ZFIN ID | Quality term Quality ID | Quality term name |
| PubMed Translations |
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ZFIN Publication IDs: ZFIN IDs to PubMed ids
| Publication ZFIN ID | PubMed ID or None when not available |