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 |
| Antibodies |
|---|
Antibodies
| ZFIN ID | Name | Clonal Type | Heavy Chain | Light Chain | Immunogen Organism | Host Organism |
Antibody Expressions in wild-type fish
| ZFIN ID | Anatomy Structure ID | AnatomyStructure Name | Substructure Term ID | Substructure Term Name |
| Previous Names |
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Previous names
| Current ZFIN ID | Current Name | Current Symbol | Previous Name |
| Mapping Data |
|---|
Mapping Data from the 6 Zebrafish Mapping Panels
| ZFIN ID | Symbol | Panel Symbol | Chr | Location | Metric |
| Sequence Coordinates in gff3 format |
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ZFIN Genes
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
Transcripts and Genes
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
ZFIN Genes with Expression
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
ZFIN Genes with Phenotype
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
ZFIN Genes with Antibodies
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
ZFIN Morpholinos
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
Assembly
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
Complete Assembly Clones
| Chromosome | Source | Type | Start | End | Score | Strand | Phase | Attributes |
Chromosome sequence-region definitions (useful for GBrowse)
| Sequence-region | Chromosome | Start | End |
| 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 Gene sequence information
| ZFIN ID | Symbol | 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 |
Transcripts
| ZFIN ID | Name | Gene ZFIN ID | Clone ZFIN ID | Transcript type | Transcript status |
ZFIN Gene IDs indirectly and directly 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 | Gene ID |
Mouse and Zebrafish Orthology
| ZFIN ID | ZFIN Symbol | ZFIN Name | Mouse Symbol | Mouse Name | MGI ID | Gene ID |
Drosophila and Zebrafish Orthology
| ZFIN ID | ZFIN Symbol | ZFIN Name | Fly Symbol | Fly Name | Flybase ID |
Phenotypic Zebrafish genes with Human Orthology
| ZFIN ID | ZFIN ID | ZFIN Symbol | Entrez Zebrafish Gene ID | Human Gene Symbol | Entrez Human Gene 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 | Probe Quality (optional 0 - 5 rating) |
ZFIN Antibody Expression Assay Records
| Antibody ID | Antibody name | Gene ID (optional) | Gene Symbol (optional) | Expression Type | Expression ID | Publication ID | Genotype ID | Environment ID |
Expression Environment Description
| Environment ID | Condition Group | Condition Content | Value | Unit | Comment |
Expression Experiment-Figure
| Expression ID | Expression Result ID | Figure ID |
Expression data for wildtype fish
| Gene ID | Gene abbreviation | Genotype | Super Structure ID | Super Structure Name | Sub Structure ID | Sub Structure Name | Start Stage | End Stage | Assay |
Zebrafish Gene Expression by Stage and Anatomy Term
| Expression Result ID | Expression ID | Begin Stage ID | End Stage ID | Anatomy Super Term ID | Anatomy Sub Term ID | Expression Found |
| Genotype Data |
|---|
Genotype Features
| Genotype 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)
| Genotype ID | Genotype Name | Genotype Unique Name | Affected Gene Symbol | Corresponding ZFIN Gene ID |
Genotype Backgrounds
| Genotype ID | Genotype Name | Background |
Genotype-Publication relation
| Genotype ID | Publication ID |
| Wildtype Lines |
|---|
Wildtype Lines
| Genotype ID | Genotype Name | Genotype Abbreviation |
| Publications |
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ZFIN Publication IDs: ZFIN IDs to PubMed ids
| Publication ZFIN ID | PubMed ID. None or blank when not available |
ZFIN Bibliography
| Publication ZFIN ID | PubMed ID. None or blank when not available | Authors | Title | Journal | Year | Volume | Pages |
ZFIN Marker ID's-UniProtKB ID's to ZFIN Pub IDs & PubMed ids
| ZFIN Marker ID | UniProtKB ID | ZFIN Pub ID | PubMedID | ZFIN Annotation(GO/Phenotype/Expression) |
| Phenotype Data |
|---|
Genotypes with Phenotypes
| Genotype ID | Genotype Name | Start Stage ID | Start Stage Name | End Stage ID | End Stage Name | Affected Structure or Process 1 superterm ID | Affected Structure or Process 1 superterm Name | Affected Structure or Process 1 subterm ID | Affected Structure or Process 1 subterm Name | Phenotype Keyword ID | Phenotype Keyword Name | Phenotype Modifier | Affected Structure or Process 2 superterm ID | Affected Structure or Process 2 superterm Name | Affected Structure or Process 2 subterm ID | Affected Structure or Process 2 subterm Name | Publication ID | Environment ID |
Genotypes with Phenotypes (obo format)
| Genotype ID | Genotype Name | Start Stage Obo ID | End Stage Obo ID | Affected Structure or Process 1 superterm obo ID | Affected Structure or Process 1 subterm obo ID | Phenotype Keyword obo ID | Phenotype Modifier | Affected Structure or Process 2 superterm obo ID | Affected Structure or Process 2 subterm obo ID | Publication ZFIN ID | Environment ZFIN ID |
Phenotype Environment Description
| Environment ID | Condition Group | Condition Content | Value | Unit | Comment |
Genotype-Figure relation
| Genotype ID | Figure ID |
Phenotype for Zebrafish genes with Human Orthology
| ZFIN Gene ID | Entrez Zebrafish Gene ID | Entrez Human Gene ID | ZFIN Gene Symbol | Affected Structure or Process 1 superterm obo ID | Affected Structure or Process 1 superterm name ID | Affected Structure or Process 1 subterm obo ID | Affected Structure or Process 1 subtrem name ID | Affected Structure or Process 2 superterm obo ID | Affected Structure or Process 2 superterm name | Affected Structure or Process 2 subterm obo ID | Affected Structure or Process 2 subterm name | Phenotype Keyword obo ID | Phenotype Quality | Phenotype Tag |
| 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 OBO 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 |
| Morpholino Data |
|---|
Morpholino
| Gene ID | Gene Symbol | MO ID | MO Symbol | MO Sequence | Note |
| Images |
|---|
Note:Images are not provided due to copyright restrictions
Image-Figure translations
| Image ID | Figure ID | Image Preparation |