ZFIN Data Reports from: 17 Jul 2025

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ZFIN data reports are updated every day of the week at 10:10pm PST with the exception of the externally hosted files. The format for each file is described below. All files use tab as the field delimiter. The 'Download File' link will display the file in your browser. Click the download button to save the file onto your local system (includes timestamp and header info). If you choose to link to a ZFIN data page from your web site, append the ZFIN ID to the URL http://zfin.org/
e.g. http://zfin.org/ZDB-GENE-980526-166
for the 'shha' gene. Please direct questions or requests for additional data to ZFIN.
View Archive Files
Category Download File Download
w Header		 Column Headers File Size Number of Records
Anatomical Ontologies Zebrafish Anatomy Term
Show 220 KB 3,105
1 2 3 4
Anatomy ID Anatomy Name Start Stage ID End Stage ID
Zebrafish Anatomy Term
Show 220 KB 3,105
1 2 3 4
Anatomy ID Anatomy Name Start Stage ID End Stage ID
Zebrafish Anatomy Term
Show 220 KB 3,105
1 2 3 4
Anatomy ID Anatomy Name Start Stage ID End Stage ID
Zebrafish Anatomy Term Relationships
Show 181 KB 5,985
1 2 3
Parent Item ID Child Item ID Relationship Type ID
Zebrafish Anatomy Term Relationships
Show 181 KB 5,985
1 2 3
Parent Item ID Child Item ID Relationship Type ID
Zebrafish Anatomy Term Synonyms
Show 156 KB 2,993
1 2 3
Anatomy OBO ID Anatomy Name Anatomy Synonym
Zebrafish Anatomy Term Synonyms
Show 156 KB 2,993
1 2 3
Anatomy OBO ID Anatomy Name Anatomy Synonym
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Development Stage Terms
Show 317 KB 13,380
1
Entire Staged Anatomy (tab indented)
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Zebrafish Stage Series
Show 2 KB 45
1 2 3 4 5
Stage ID Stage OBO ID Stage Name Begin Hours End Hours
Antibody Data Antibody Expressions in wild-type
Show 584 KB 10,519
1 2 3 4 5
Antibody ID AnatomyStructure ID AnatomyStructure Name Substructure ID Substructure Name
Fish Data Experiment Details
Show 1 MB 27,991
1 2 3 4 5 6
Experiment ID ZECO Term ID ZFA Term ID GO Cellular Component Term ID Chebi Term ID NCBI Taxon Term ID
Fish Components
Show 13 MB 87,420
1 2 3 4 5 6 7 8 9 10 11 12
Fish ID Fish Name Gene ID Gene Symbol Affector ID Affector Symbol Construct ID Construct Symbol Background ID Background Name Genotype ID Genotype Name
Fish Components
Show 13 MB 87,420
1 2 3 4 5 6 7 8 9 10 11 12
Fish ID Fish Name Gene ID Gene Symbol Affector ID Affector Symbol Construct ID Construct Symbol Background ID Background Name Genotype ID Genotype Name
Innocuous/Phenotypic Construct Details
Show 2 MB 27,687
1 2 3 4 5
Construct ID Construct Name Innocuous/Phenotypic Feature ID Feature Name
Gene Expression Expression data for wildtype fish
Show 40 MB 238,587
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Gene ID Gene Symbol Fish Name Super Structure ID Super Structure Name Sub Structure ID Sub Structure Name Start Stage End Stage Assay Assay MMO ID Publication ID Probe ID Antibody ID Fish ID
Expression Environment Description
Show 1 MB 14,692
1 2 3 4 5 6 7 8 9 10 11
Environment ID ZECO Term Name ZECO Term ID (ZECO:ID) Chebi Term Name Chebi Term ID (Chebi:ID) ZFA Term Name ZFA Term ID (ZFA:ID) Affected Structure Subterm Name Affected Structure Subterm ID (GO-CC:ID) NCBI Taxon Name NCBI Taxon ID (NCBI Taxon:ID)
Expression Environment Description
Show 1 MB 14,692
1 2 3 4 5 6 7 8 9 10 11
Environment ID ZECO Term Name ZECO Term ID (ZECO:ID) Chebi Term Name Chebi Term ID (Chebi:ID) ZFA Term Name ZFA Term ID (ZFA:ID) Affected Structure Subterm Name Affected Structure Subterm ID (GO-CC:ID) NCBI Taxon Name NCBI Taxon ID (NCBI Taxon:ID)
Expression Experiment-Figure
Show 20 MB 499,391
1 2 3
Expression ID Expression Result ID Figure ID
Expression Experiment-Figure
Show 20 MB 499,391
1 2 3
Expression ID Expression Result ID Figure ID
Expression Experiment-Figure
Show 20 MB 499,391
1 2 3
Expression ID Expression Result ID Figure ID
Expression phenotypes with single chemical in environment in WT fish
Show 2 MB 6,268
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
Gene Symbol Gene ID RO Term RO ID Superstructure Name Superstructure ID Substructure Name Substructure ID Phenotype Keyword Name Phenotype Keyword ID Phenotype Tag Start Stage Name Start Stage ID End Stage Name End Stage ID Assay Assay MMO ID Probe ID Antibody Name Antibody ID Fish ID Environment ID Figure ID Publication ID PubMed ID Fish Name ZECO ID(s) ZECO Name(s) ChEBI ID ChEBI Name
Expression phenotypes with single chemical in environment in WT fish
Show 2 MB 6,268
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
Gene Symbol Gene ID RO Term RO ID Superstructure Name Superstructure ID Substructure Name Substructure ID Phenotype Keyword Name Phenotype Keyword ID Phenotype Tag Start Stage Name Start Stage ID End Stage Name End Stage ID Assay Assay MMO ID Probe ID Antibody Name Antibody ID Fish ID Environment ID Figure ID Publication ID PubMed ID Fish Name ZECO ID(s) ZECO Name(s) ChEBI ID ChEBI Name
Zebrafish Gene Expression by Stage and Anatomy Term
Show 38 MB 499,528
1 2 3 4 5 6 7
Expression Result ID Expression ID Start Stage ID End Stage ID Anatomy Super Term ID Anatomy Sub Term ID Expression Found
Zebrafish Gene Expression by Stage and Anatomy Term
Show 38 MB 499,528
1 2 3 4 5 6 7
Expression Result ID Expression ID Start Stage ID End Stage ID Anatomy Super Term ID Anatomy Sub Term ID Expression Found
ZFIN Genes with Expression Assay Records
Show 23 MB 177,145
1 2 3 4 5 6 7 8 9 10 11
Gene ID Gene Symbol EST ID (Optional) EST Symbol (Optional) Expression Type Expression Type MMO ID Expression ID Publication ID Fish ID Environment ID Probe Quality (optional 0 - 5 rating)
ZFIN Genes with Expression Assay Records
Show 23 MB 177,145
1 2 3 4 5 6 7 8 9 10 11
Gene ID Gene Symbol EST ID (Optional) EST Symbol (Optional) Expression Type Expression Type MMO ID Expression ID Publication ID Fish ID Environment ID Probe Quality (optional 0 - 5 rating)
Genetic Marker Relationships Genetic Marker Relationships
Show 15 MB 143,184
1 2 3 4 5 6 7
Gene ID Gene SO ID Gene Symbol Marker ID Marker SO ID Marker Symbol Relationship
Genetic Marker Relationships
Show 15 MB 143,184
1 2 3 4 5 6 7
Gene ID Gene SO ID Gene Symbol Marker ID Marker SO ID Marker Symbol Relationship
Genetic Markers Genetic Marker
Show 12 MB 199,577
1 2 3 4 5
Marker ID Marker Symbol Marker Name Marker Type SO ID
Genetic Marker
Show 12 MB 199,577
1 2 3 4 5
Marker ID Marker Symbol Marker Name Marker Type SO ID
Genetic Marker
Show 12 MB 199,577
1 2 3 4 5
Marker ID Marker Symbol Marker Name Marker Type SO ID
Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)
Show 1 MB 38,831
1 2
Former ZFIN ID Current ZFIN ID
Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)
Show 1 MB 38,831
1 2
Former ZFIN ID Current ZFIN ID
Genomic Feature Data All Genomic Features
Show 8 MB 79,441
1 2 3 4 5 6 7 8 9 10 11 12
Genomic Feature ID Feature SO ID Genomic Feature Abbreviation Genomic Feature Name Genomic Feature Type Mutagen Mutagee Construct ID Construct name Construct SO ID TALEN/CRISPR ID TALEN/CRISPR Name
Construct Components
Show 2 MB 19,000
1 2 3 4 5 6 7 8 9
Construct ID Construct Name Construct Type Component ID Component Name Component Type Relationship Construct SO ID Component SO ID
Construct Components
Show 2 MB 19,000
1 2 3 4 5 6 7 8 9
Construct ID Construct Name Construct Type Component ID Component Name Component Type Relationship Construct SO ID Component SO ID
Genomic Feature Data for CZRC
Show 12 MB 78,629
1 2 3 4 5 6 7 8 9 10 11 12 13 14
Genomic Feature ID Genomic Feature Name Affected Gene Affected Gene ID Synonyms Genomic Feature Type Protocol Notes Lab of Origin Lab ID Location Construct Name Construct ID Downloaded Time
Genomic Feature Data for CZRC
Show 12 MB 78,629
1 2 3 4 5 6 7 8 9 10 11 12 13 14
Genomic Feature ID Genomic Feature Name Affected Gene Affected Gene ID Synonyms Genomic Feature Type Protocol Notes Lab of Origin Lab ID Location Construct Name Construct ID Downloaded Time
Genomic Features and their affected genes
(alleles, deficiencies, translocations)
Show 10 MB 56,684
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42
Genomic Feature ID Feature SO ID Genomic Feature Abbreviation Gene Symbol Gene ID Gene SO ID Genomic Feature - Marker Relationship Feature Type DNA/cDNA Change SO ID Reference Nucleotide Mutant Nucleotide Base Pairs Added Base Pairs Removed DNA/cDNA Change Position Start DNA/cDNA Change Position End DNA/cDNA Reference Sequence DNA/cDNA Change Localization DNA/cDNA Change Localization SO ID DNA/cDNA Change Localization Exon DNA/cDNA Change Localization Intron Transcript Consequence Transcript Consequence SO ID Transcript Consequence Exon Transcript Consequence Intron Protein Consequence Protein Consequence SO ID Reference Amino Acid Mutant Amino Acid Amino Acids Added Amino Acids Removed Protein Consequence Position Start Protein Consequence Position End Protein Reference Sequence Zv9 Chromosome Zv9 Start Zv9 End GRCz10 Chromosome GRCz10 Start GRCz10 End GRCz11 Chromosome GRCz11 Start GRCz11 End
Transgenic Insertions
Show 3 MB 34,794
1 2 3 4 5 6 7 8
Genomic Feature ID Genomic Feature Abbreviation Genomic Feature Name Feature SO ID Construct ID Construct Name Construct SO ID Allele Of
Human Disease Disease Models that Include Chemical
Show 119 KB 615
1 2 3 4 5 6 7 8 9 10 11 12
Fish ZDB ID Environment ZDB ID is_a_model DO Term ID DO Term Name Publication ZDB ID PubMed ID Evidence Code ZECO ID(s) ZECO Name(s) ChEBI ID(s) ChEBI Name(s)
Disease Models that Include Chemical
Show 119 KB 615
1 2 3 4 5 6 7 8 9 10 11 12
Fish ZDB ID Environment ZDB ID is_a_model DO Term ID DO Term Name Publication ZDB ID PubMed ID Evidence Code ZECO ID(s) ZECO Name(s) ChEBI ID(s) ChEBI Name(s)
Gene to Disease via Orthology
Show 1 MB 9,006
1 2 3 4 5 6 7 8 9 10
Zebrafish Gene ID Zebrafish Gene Symbol Human Ortholog Entrez Gene Id Human Ortholog Symbol DO Term Name DO Term ID OMIM Term Name OMIM ID Evidence Code Publication
Gene to Disease via Orthology
Show 1 MB 9,006
1 2 3 4 5 6 7 8 9 10
Zebrafish Gene ID Zebrafish Gene Symbol Human Ortholog Entrez Gene Id Human Ortholog Symbol DO Term Name DO Term ID OMIM Term Name OMIM ID Evidence Code Publication
Human Disease Attributions
Show 357 KB 4,835
1 2 3 4 5
DO Term ID DO Term Name Publication ZDB ID PubMed ID Evidence Code
Image Data Image-Figure translations
Note: Images are not provided due to copyright restrictions
Show 9 MB 187,256
1 2 3
Image ID Figure ID Image Preparation
Image-Figure translations
Note: Images are not provided due to copyright restrictions
Show 9 MB 187,256
1 2 3
Image ID Figure ID Image Preparation
Knockdown Reagent Data Morpholino
Show 1 MB 12,320
1 2 3 4 5 6 7 8 9
Target ID Target SO ID Target Symbol Morpholino ID Morpholino SO ID Morpholino Symbol Morpholino Sequence Publication(s) Note
Morpholino
Show 1 MB 12,320
1 2 3 4 5 6 7 8 9
Target ID Target SO ID Target Symbol Morpholino ID Morpholino SO ID Morpholino Symbol Morpholino Sequence Publication(s) Note
Mapping Data Mapping Data from the 6 Zebrafish Mapping Panels
Show 1 MB 36,499
1 2 3 4 5 6 7
ZFIN ID Symbol SO ID Panel Symbol Chromosome Location Metric
Orthology Data Drosophila and Zebrafish Orthology
Show 15 KB 77
1 2 3 4 5 6 7 8 9 10 11 12
ZFIN ID ZFIN Symbol ZFIN Name Fly Symbol Fly Name Flybase ID Gene ID Evidence Pub ID ZFIN Abbreviation Name ECO ID ECO Term Name
Drosophila and Zebrafish Orthology
Show 15 KB 77
1 2 3 4 5 6 7 8 9 10 11 12
ZFIN ID ZFIN Symbol ZFIN Name Fly Symbol Fly Name Flybase ID Gene ID Evidence Pub ID ZFIN Abbreviation Name ECO ID ECO Term Name
Mouse and Zebrafish Orthology
Show 6 MB 31,770
1 2 3 4 5 6 7 8 9 10 11 12
ZFIN ID ZFIN Symbol ZFIN Name Mouse Symbol Mouse Name MGI ID Gene ID Evidence Pub ID ZFIN Abbreviation Name ECO ID ECO Term Name
Phenotypic Zebrafish genes with Human Orthology
Show 208 KB 4,788
1 2 3 4 5
ZFIN ID ZFIN Symbol Entrez Zebrafish Gene ID Human Gene Symbol Entrez Human Gene ID
Phenotype Data Fish with Abnormal and Normal Phenotypes
Show 49 MB 217,122
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Fish ID Fish Name Start Stage ID Start Stage Name End Stage ID End Stage Name Affected Structure or Process 1 subterm ID Affected Structure or Process 1 subterm Name Post-composed Relationship ID Post-composed Relationship Name Affected Structure or Process 1 superterm ID Affected Structure or Process 1 superterm Name Phenotype Keyword ID Phenotype Keyword Name Phenotype Tag Affected Structure or Process 2 subterm ID Affected Structure or Process 2 subterm name Post-composed Relationship (rel) ID Post-composed Relationship (rel) Name Affected Structure or Process 2 superterm ID Affected Structure or Process 2 superterm name Publication ID Environment ID
Fish-Figure relation
Show 2 MB 75,853
1 2
Fish ID Figure ID
Fish-Figure relation
Show 2 MB 75,853
1 2
Fish ID Figure ID
Fish-Figure relation
Show 2 MB 75,853
1 2
Fish ID Figure ID
Gene Expression Phenotypes
Show 14 MB 48,258
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
Gene Symbol Gene ID RO Term RO ID Superstructure Name Superstructure ID Substructure Name Substructure ID Phenotype Keyword Name Phenotype Keyword ID Phenotype Tag Start Stage Name Start Stage ID End Stage Name End Stage ID Assay Assay MMO ID Probe ID Antibody Name Antibody ID Fish ID Environment ID Figure ID Publication ID PubMed ID
Gene Expression Phenotypes
Show 14 MB 48,258
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25
Gene Symbol Gene ID RO Term RO ID Superstructure Name Superstructure ID Substructure Name Substructure ID Phenotype Keyword Name Phenotype Keyword ID Phenotype Tag Start Stage Name Start Stage ID End Stage Name End Stage ID Assay Assay MMO ID Probe ID Antibody Name Antibody ID Fish ID Environment ID Figure ID Publication ID PubMed ID
Phenotypes with Chemicals in Environment
Show 9 MB 29,337
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
Fish ID Fish Name Affected Genomic Region IDs Affected Genomic Region Abbreviations Construct IDs Construct Abbreviations Start Stage ID Start Stage Name End Stage ID End Stage Name Affected Structure or Process 1 Subterm ID Affected Structure or Process 1 Subterm Name Post-composed Relationship A ID Post-composed Relationship A Name Affected Structure or Process 1 Superterm ID Affected Structure or Process 1 Superterm Name Phenotype Keyword ID Phenotype Keyword Name Phenotype Tag Affected Structure or Process 2 Subterm ID Affected Structure or Process 2 Subterm Name Post-composed Relationship B ID Post-composed Relationship B Name Affected Structure or Process 2 Superterm ID Affected Structure or Process 2 Superterm Name Publication ID PubMed ID Environment ID ZECO ID ZECO Name ChEBI ID ChEBI Name ZFA Term ID ZFA Term Name GO-CC ID GO-CC Name NCBI Taxon ID NCBI Taxon Name
Publications ZFIN Bibliography
Show 13 MB 50,986
1 2 3 4 5 6 7 8
Publication ID pubMed ID (none or blank when not available) Authors Title Journal Year Volume Pages
ZFIN Bibliography
Show 13 MB 50,986
1 2 3 4 5 6 7 8
Publication ID pubMed ID (none or blank when not available) Authors Title Journal Year Volume Pages
ZFIN Bibliography
Show 13 MB 50,986
1 2 3 4 5 6 7 8
Publication ID pubMed ID (none or blank when not available) Authors Title Journal Year Volume Pages
Sequence Coordinates Assembly: Ensembl
Show 158 MB 1,152,227
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Assembly: Ensembl
Show 158 MB 1,152,227
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Assembly: Ensembl
Show 158 MB 1,152,227
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Assembly: Ensembl
Show 158 MB 1,152,227
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Complete Assembly Clones: Ensembl
Show 4 MB 51,655
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Complete Assembly Clones: Ensembl
Show 4 MB 51,655
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Complete Assembly Clones: Ensembl
Show 4 MB 51,655
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Complete Assembly Clones: Ensembl
Show 4 MB 51,655
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Phenotype: Ensembl
Show 1 MB 5,085
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Phenotype: Ensembl
Show 1 MB 5,085
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Knockdown Reagents: Ensembl
Show 5 MB 40,500
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Knockdown Reagents: Ensembl
Show 5 MB 40,500
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Sequence Data ZFIN Marker associations to Ensembl IDs
(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)
Show 1 MB 26,952
1 2 3 4
ZFIN ID Gene SO ID Symbol Ensembl ID
ZFIN Marker associations to Ensembl IDs
(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)
Show 1 MB 26,952
1 2 3 4
ZFIN ID Gene SO ID Symbol Ensembl ID

Externally Hosted Files:

The 'File Name'-links point to the latest version. To obtain previous versions you have to check the archive of the external source.
Category Description External Source File Name Update Frequency Format / Header
Gene Ontology Data Gene Ontology (GO) Annotations of Zebrafish Markers
(see also GO Annotation File format at the Gene Ontology Consortium) 		geneontology.org gene_association.zfin.gz weekly
Anatomical Ontologies Zebrafish Anatomical Ontology in OBO Format Obofoundry zebrafish_anatomy.obo quarterly OBO file format
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