ZFIN Data Reports from: 30 Mar 2023

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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 219 KB 3,091
1 2 3 4
Anatomy ID Anatomy Name Start Stage ID End Stage ID
Zebrafish Anatomy Term Relationships
Show 180 KB 5,958
1 2 3
Parent Item ID Child Item ID Relationship Type ID
Zebrafish Anatomy Term Synonyms
Show 156 KB 2,983
1 2 3
Anatomy OBO ID Anatomy Name Anatomy Synonym
Zebrafish Development Stage Terms
Show 316 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
Antibody Data Antibodies
Show 370 KB 4,277
1 2 3 4 5 6 7 8 9 10
Antibody ID Name Clonal Type Heavy Chain Light Chain Immunogen Organism Host Organism SO ID AB Registry ID Source
Antibody Expressions in wild-type
Show 531 KB 9,558
1 2 3 4 5
Antibody ID AnatomyStructure ID AnatomyStructure Name Substructure ID Substructure Name
Fish Data Experiment Details
Show 933 KB 24,209
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 11 MB 77,025
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
Genotype Backgrounds
Show 687 KB 10,497
1 2 3 4
Genotype ID Genotype Name Background Background Name
Genotype Features
Show 8 MB 44,863
1 2 3 4 5 6 7 8 9 10 11 12 13
Genotype ID Genotype Name Genotye Unique Name Allele ID Allele Name Allele Abbreviation Allele Type Allele Display Type Gene or Construct Symbol Corresponding ZFIN Gene ID/Construct ID Allele Zygosity Construct Name Construct ZdbId
Genotype Features (removed or displaced genes)
Show 46 KB 426
1 2 3 4 5
Genotype ID Genotype Name Genotye Unique Name Affected Genomic Region Symbol Corresponding ZFIN Gene ID
Innocuous/Phenotypic Construct Details
Show 2 MB 26,425
1 2 3 4 5
Construct ID Construct Name Innocuous/Phenotypic Feature ID Feature Name
Gene Expression Expression data for wildtype fish
Show 39 MB 230,608
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 931 KB 13,271
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 455,665
1 2 3
Expression ID Expression Result ID Figure ID
Zebrafish Gene Expression by Stage and Anatomy Term
Show 37 MB 455,801
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 Antibody Expression Assay Records
Show 2 MB 20,609
1 2 3 4 5 6 7 8 9 10
Antibody ID Antibody Name Gene ID (Optional) Gene Symbol (Option) Expression ID Expression Type Expression Type MMO ID Publication ID Fish ID Environment ID
ZFIN Genes with Expression Assay Records
Show 21 MB 155,717
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 12 MB 120,917
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 11 MB 177,036
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 38,382
1 2
Former ZFIN ID Current ZFIN ID
SNP Data
Show 148 MB 2,673,006
1 2 3 4
Marker ID Marker Symbol SNP rs accession number Publication ZDB ID
Genomic Feature Data All Genomic Features
Show 8 MB 74,741
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 16,227
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 74,672
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 8 MB 55,206
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
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
Transgenic Insertions
Show 3 MB 33,232
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 Gene to Disease via Orthology
Show 1 MB 8,682
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/Models
Show 457 KB 4,586
1 2 3 4 5 6 7 8
Fish ZDB ID Environment ZDB ID is_a_model 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 7 MB 152,162
1 2 3
Image ID Figure ID Image Preparation
Knockdown Reagent Data CRISPR
Show 1 MB 8,087
1 2 3 4 5 6 7 8 9
Gene ID Gene SO ID Gene Symbol CRISPR ID CRISPR SO ID CRISPR Symbol CRISPR Target Sequence Publication(s) Note
Morpholino
Show 1 MB 10,989
1 2 3 4 5 6 7 8 9
Gene ID Gene SO ID Gene Symbol Morpholino ID Morpholino SO ID Morpholino Symbol Morpholino Sequence Publication(s) Note
TALEN
Show 115 KB 844
1 2 3 4 5 6 7 8 9 10
Gene ID Gene SO ID Gene Symbol TALEN ID TALEN SO ID TALEN Symbol TALEN Target Sequence 1 TALEN Target Sequence 2 Publication(s) Note
Mapping Data Mapping Data from the 6 Zebrafish Mapping Panels
Show 1 MB 36,500
1 2 3 4 5 6 7
ZFIN ID Symbol SO ID Panel Symbol Chromosome Location Metric
Orthology Data Drosophila and Zebrafish Orthology
Show 8 KB 76
1 2 3 4 5 6 7 8 9
ZFIN ID ZFIN Symbol ZFIN Name Fly Symbol Fly Name Flybase ID Gene ID Evidence Pub ID
Human and Zebrafish Orthology
Show 5 MB 43,222
1 2 3 4 5 6 7 8 9 10
ZFIN ID ZFIN Symbol ZFIN Name Human Symbol Human Name OMIM ID Gene ID HGNC ID Evidence Pub ID
Mouse and Zebrafish Orthology
Show 4 MB 31,315
1 2 3 4 5 6 7 8 9
ZFIN ID ZFIN Symbol ZFIN Name Mouse Symbol Mouse Name MGI ID Gene ID Evidence Pub ID
Phenotypic Zebrafish genes with Human Orthology
Show 189 KB 4,386
1 2 3 4 5
ZFIN ID ZFIN Symbol Entrez Zebrafish Gene ID Human Gene Symbol Entrez Human Gene ID
Phenotype Data Ameliorated Phenotypes
Show 1 MB 6,369
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
Antibody Labeling Phenotypes
Show 1 MB 3,983
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
Antibody Name Antibody ID SO Term SO 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 Fish ID Environment ID Figure ID Publication ID PubMed ID
Exacerbated Phenotypes
Show 220 KB 872
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 with Phenotypes
Show 42 MB 185,888
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 64,897
1 2
Fish ID Figure ID
Gene Expression Phenotypes
Show 10 MB 35,447
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
Phenotype Environment Description
Show 1 MB 17,420
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)
Phenotype for Zebrafish genes with Human Orthology
Show 7 MB 59,181
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
Gene ID Entrez Zebrafish Gene ID Entrez Human Gene ID ZFIN Gene Symbol Affected Structure or Process 1 subterm OBO ID Affected Structure or Process 1 subterm name Post-Composed Relationship ID Post-Composed Relationship Name Affected Structure or Process 1 superterm OBO ID Affected Structure or Process 1 superterm name Phenotype Keyword OBO ID Phenotype Quality Phenotype Tag Affected Structure or Process 2 subterm OBO ID Affected Structure or Process 2 subterm name Post-Composed Relationship ID Post-Composed Relationship Name Affected Structure or Process 2 superterm OBO ID Affected Structure or Process 2 superterm name
Phenotype of Zebrafish Genes
Show 35 MB 143,964
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
ID Gene Symbol Gene ID 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 Fish ID Fish Display Name Start Stage ID End Stage ID Fish Environment ID Publication ID Figure ID
Previous Names Previous Names
Show 13 MB 192,512
1 2 3 4 5
Current ZFIN ID Current Name Current Symbol Previous Name SO ID
Publications Fish-Publication relation
Show 5 MB 124,085
1 2
Fish ID Publication ID
Gene-Publication relation
Show 34 MB 621,705
1 2 3 4 5
Gene Symbol Gene ID Publication ID Publication Type PubMed ID
Genotype-Publication relation
Show 3 MB 97,144
1 2 3
Publication ID PubMed ID Genotype ID
ZFIN Bibliography
Show 11 MB 42,453
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 Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
Show 7 MB 113,415
1 2 3 4 5
ZFIN Marker ID SO ID UniProtKB ID PubMed ID ZFIN Annotation (GO/Phenotype/Expression)
ZFIN Publication IDs: ZFIN IDs to PubMed IDs
Show 1 MB 53,161
1 2
Publication ZFIN ID PubMed ID (none or blank when not available)
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
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
Transgenic Insertion: ENSEMBL
Show 2 MB 15,224
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Gene Models
Show 66 MB 622,707
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Antibodies: Ensembl
Show 218 KB 994
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Expression: Ensembl
Show 2 MB 12,641
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 4,605
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Knockdown Reagents: Ensembl
Show 2 MB 23,411
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Sequence Data Transcripts
Show 5 MB 55,177
1 2 3 4 5 6 7
ZFIN ID SO ID Name Gene ID Clone ID Transcript Type Transcript Status
ZFIN Gene IDs indirectly and directly associated with Sequence Accessions via cDNA & EST
Show 6 MB 130,779
1 2 3 4
ZFIN ID SO ID Gene Symbol Sequence Accession
ZFIN Gene IDs indirectly associated with Sequence Accessions via cDNA & EST
Show 1 MB 41,471
1 2 3
ZFIN ID Gene Symbol Sequence Accession
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 26,780
1 2 3 4
ZFIN ID Gene SO ID Symbol Ensembl ID
ZFIN Marker associations to GenBank sequence data
Show 7 MB 169,355
1 2 3 4
ZFIN ID SO ID Name GenBank ID
ZFIN Marker associations to GenPept protein data
Show 1 MB 42,963
1 2 3
ZFIN ID Symbol GenePept ID
ZFIN Marker associations to InterPro protein data
Show 320 MB 6,965,712
1 2 3 4
ZFIN ID SO ID Symbol InterPro ID
ZFIN Marker associations to NCBI Gene data
Show 1 MB 23,309
1 2 3 4
ZFIN ID SO ID Symbol NCBI Gene ID
ZFIN Marker associations to RefSeq sequence data
Show 4 MB 88,989
1 2 3 4
ZFIN ID SO ID Symbol RefSeq ID
ZFIN Marker associations to Sanger Vega data
Show 2 MB 38,875
1 2 3 4
ZFIN ID SO ID Symbol Vega ID
ZFIN Marker associations to UniProt protein data
Show 2 MB 57,289
1 2 3 4
ZFIN ID SO ID Symbol UniProt ID
Wildtype Lines Wildtype Lines
Show 1 KB 32
1 2 3 4
Fish ID Fish Name Fish Abbreviation Genotype ID
ZFIN Alliance Data (1.0.1.0) AGM
Show 16 MB 536,697
1
Allele
Show 23 MB 739,874
1
Basic Gene Information
Show 27 MB 983,682
1
Disease
Show 980 KB 37,121
1
Expression
Show 382 MB 13,428,888
1
Phenotype
Show 135 MB 4,769,275
1
STR
Show 3 MB 113,090
1
Variant
Show 10 MB 356,123
1
ZFIN Alliance Data (1.0.1.1) AGM
Show 16 MB 561,586
1
Allele
Show 31 MB 1,118,064
1
Basic Gene Information
Show 27 MB 1,001,394
1
Construct
Show 3 MB 113,459
1
Disease
Show 1 MB 54,547
1
Expression
Show 388 MB 13,649,108
1
HTP Dataset
Show 11 KB 223
1
HTP Dataset Sample
Show 164 KB 5,700
1
Phenotype
Show 190 MB 6,622,583
1
STR
Show 3 MB 119,480
1
Variant
Show 10 MB 356,142
1
ZFIN Alliance Data (1.0.1.4) AGM
Show 18 MB 619,352
1
Allele
Show 33 MB 1,167,359
1
Basic Gene Information
Show 28 MB 1,010,670
1
Construct
Show 3 MB 131,437
1
Disease
Show 3 MB 116,101
1
Expression
Show 398 MB 14,065,360
1
HTP Dataset
Show 11 KB 223
1
HTP Dataset Sample
Show 163 KB 5,700
1
Phenotype
Show 299 MB 10,446,154
1
Reference
Show 168 MB 3,139,752
1
Reference Exchange
Show 18 MB 743,212
1
Resource
Show 1 MB 33,420
1
STR
Show 4 MB 135,172
1
Variant
Show 21 MB 730,638
1
ZFIN Identifiers ZFIN Identifiers
Show 23 MB 265,311
1 2
ID Alternate Identifiers

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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