ZFIN Data Reports from: 29 Jun 2015

Warranty Disclaimer and Copyright Notice  
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 210 KB 2,939
1 2 3 4
Anatomy ID Anatomy Name Start Stage ID End Stage ID
Zebrafish Anatomy Term Relationships
Show 174 KB 5,598
1 2 3
Parent Item ID Child Item ID Relationship Type ID
Zebrafish Anatomy Term Synonyms
Show 146 KB 2,765
1 2 3
Anatomy OBO ID Anatomy Name Anatomy Synonym
Zebrafish Development Stage Terms
Show 315 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 149 KB 1,856
1 2 3 4 5 6 7 8 9
Antibody ID Name Clonal Type Heavy Chain Light Chain Immunogen Organism Host Organism Source SO ID
Antibody Expressions in wild-type
Show 323 KB 5,782
1 2 3 4 5
Antibody ID AnatomyStructure ID AnatomyStructure Name Substructure ID Substructure Name
Disease Disease/Models
Show 8 KB 116
1 2 3 4 5 6 7
Fish ZDB ID Environment ZDB ID is_a_model DO Term ID DO Term Name Publication ZDB ID PubMed ID
Fish Fish Components
Show 7 MB 68,047
1 2 3 4 5 6 7 8 9
Fish Name Fish Unique Name Affector ID Affector Symbol Affector Type Affector Gene Symbol Affector Gene ID Construct Name Construct ZDB ID
Gene Expression Expression data for wildtype fish
Show 26 MB 168,862
1 2 3 4 5 6 7 8 9 10 11 12 13
Gene ID Gene Symbol Genotype Super Structure ID Super Structure Name Sub Structure ID Sub Structure Name Start Stage End Stage Assay Publication ID Probe ID Antibody ID
Expression Environment Description
Show 677 KB 10,757
1 2 3 4 5 6
Environment ID Condition Group Condition Content Value Unit Comment
Expression Experiment-Figure
Show 17 MB 294,447
1 2 3
Expression ID Expression Result ID Figure ID
Zebrafish Gene Expression by Stage and Anatomy Term
Show 26 MB 283,199
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 1 MB 9,951
1 2 3 4 5 6 7 8 9
Antibody ID Antibody Name Gene ID (Optional) Gene Symbol (Option) Expression Type Expression ID Publication ID Genotype ID Environment ID
ZFIN Genes with Expression Assay Records
Show 10 MB 87,654
1 2 3 4 5 6 7 8 9 10
Gene ID Gene Symbol EST ID (Optional) EST Symbol (Optional) Expression Type Expression ID Publication ID Genotype ID Environment ID Probe Quality (optiona 0 - 5 rating)
Genetic Marker Relationships Genetic Marker Relationships
Show 10 MB 100,581
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 9 MB 154,915
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 41,193
1 2
Former ZFIN ID Current ZFIN ID
SNP Data
Show 138 MB 2,438,425
1 2 3 4
Marker ID Marker Symbol SNP rs accession number Publication ZDB ID
Genomic Feature Data All Genomic Features
Show 4 MB 40,233
1 2 3 4 5 6 7 8 9 10
Genomic Feature ID Feature SO ID Genomic Feature Abbreviation Genomic Feature Name Genomic Feature Type Mutagen Mutagee Construct ID Construct name Construct SO ID
Construct Components
Show 1 MB 9,716
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 Features and their affected genes
(alleles, deficiencies, translocations)
Show 2 MB 25,261
1 2 3 4 5 6 7
Genomic Feature ID Feature SO ID Genomic Feature Abbreviation Gene Symbol Gene ID Gene SO ID Genomic Feature - Marker Relationship
Transgenic Insertions
Show 2 MB 27,566
1 2 3 4 5 6 7
Genomic Feature ID Genomic Feature Abbreviation Genomic Feature Name Feature SO ID Construct ID Construct Name Construct SO ID
Genotype Data Genotype Backgrounds
Show 446 KB 7,517
1 2 3
Genotype ID Genotype Name Background
Genotype Features
Show 4 MB 24,036
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 21 KB 220
1 2 3 4 5
Genotype ID Genotype Name Genotye Unique Name Affected Gene Symbol Corresponding ZFIN Gene ID
Genotype-Publication relation
Show 1 MB 37,585
1 2
Genotype ID Publication ID
Image Data Image-Figure translations
Note: Images are not provided due to copyright restrictions
Show 4 MB 94,272
1 2 3
Image ID Figure ID Image Preparation
Knockdown Reagent Data CRISPR
Show 15 KB 117
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 8,110
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 32 KB 232
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 36,444
1 2 3 4 5 6
ZFIN ID Symbol Panel Symbol Chromosome Location Metric
Orthology Data Drosophila and Zebrafish Orthology
Show 5 KB 59
1 2 3 4 5 6
ZFIN ID ZFIN Symbol ZFIN Name Fly Symbol Fly Name Flybase ID
Human and Zebrafish Orthology
Show 1 MB 15,845
1 2 3 4 5 6 7
ZFIN ID ZFIN Symbol ZFIN Name Human Symbol Human Name OMIM ID Gene ID
Mouse and Zebrafish Orthology
Show 1 MB 13,278
1 2 3 4 5 6 7
ZFIN ID ZFIN Symbol ZFIN Name Mouse Symbol Mouse Name MGI ID Gene ID
Phenotypic Zebrafish genes with Human Orthology
Show 116 KB 2,727
1 2 3 4 5
ZFIN ID ZFIN Symbol Entrez Zebrafish Gene ID Human Gene Symbol Entrez Human Gene ID
Phenotype Data Genotype-Figure relation
Show 916 KB 24,969
1 2
Genotype ID Figure ID
Genotypes with Phenotypes
Show 20 MB 92,835
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
Genotype ID Genotype 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
Phenotype Environment Description
Show 709 KB 11,746
1 2 3
Environment ID Condition Group Condition
Phenotype for Zebrafish genes with fin phenotype
Show 293 KB 1,164
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
# Gene Symbol Gene ID 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 Genotype ID Genotype Name Knockdown Reagent ID Stage Start Stage End Genotype Experiment ID Publication ID Figure ID
Phenotype for Zebrafish genes with Human Orthology
Show 4 MB 37,080
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 18 MB 73,936
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
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 Genotype ID Genotype Display Name Knockdown Reagent ID Start Stage ID End Stage ID Genotype Environment ID Publication ID Figure ID
Previous Names Previous Names
Show 10 MB 138,997
1 2 3 4 5
Current ZFIN ID Current Name Current Symbol Previous Name SO ID
Publications Gene-Publication relation
Show 19 MB 351,317
1 2 3 4 5
Gene Symbol Gene ID Publication ID Publication Type PubMed ID
ZFIN Bibliography
Show 4 MB 18,754
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 5 MB 73,726
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 607 KB 23,354
1 2
Publication ZFIN ID PubMed ID (none or blank when not available)
Sequence Coordinates Assembly: Ensembl
Show 161 MB 1,049,576
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Complete Assembly Clones: Ensembl
Show 3 MB 33,167
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Transgenic Insertion: ENSEMBL
Show 2 MB 15,223
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Antibodies: Ensembl
Show 68 KB 637
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Expression: Ensembl
Show 1 MB 10,244
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes with Phenotype: Ensembl
Show 289 KB 2,667
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Genes: Ensembl
Show 4 MB 23,629
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
ZFIN Knockdown Reagents: Ensembl
Show 1 MB 8,766
1 2 3 4 5 6 7 8 9
Chromosome Source Type Start End Score Strand Phase Attributes
Sequence Data Transcripts
Show 5 MB 53,216
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 4 MB 102,384
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 41,500
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 22,038
1 2 3 4
ZFIN ID Gene SO ID Symbol Ensembl ID
ZFIN Marker associations to GenBank sequence data
Show 5 MB 121,919
1 2 3 4
ZFIN ID SO ID Name GenBank ID
ZFIN Marker associations to GenPept protein data
Show 1 MB 41,912
1 2 3
ZFIN ID Symbol GenePept ID
ZFIN Marker associations to InterPro protein data
Show 133 MB 2,821,538
1 2 3 4
ZFIN ID SO ID Symbol InterPro ID
ZFIN Marker associations to NCBI Gene data
Show 1 MB 22,965
1 2 3 4
ZFIN ID SO ID Symbol NCBI Gene ID
ZFIN Marker associations to RefSeq sequence data
Show 3 MB 75,251
1 2 3 4
ZFIN ID SO ID Symbol RefSeq ID
ZFIN Marker associations to Sanger Vega data
Show 2 MB 37,499
1 2 3 4
ZFIN ID SO ID Symbol Vega ID
ZFIN Marker associations to UniGene sequence data
Show 948 KB 21,148
1 2 3 4
ZFIN ID SO ID Symbol UniGene ID
ZFIN Marker associations to UniProt protein data
Show 2 MB 50,225
1 2 3 4
ZFIN ID SO ID Symbol UniProt ID
Wildtype Lines Wildtype Lines
Show 1 KB 30
1 2 3
Genotype ID Genotype Name Genotype Abbreviation
ZFIN Identifiers ZFIN Identifiers
Show 20 MB 224,682
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
Show
Anatomical Ontologies Zebrafish Anatomical Ontology in OBO Format Obofoundry zebrafish_anatomy.obo monthly OBO file format