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ZIRC

ZFIN Data Reports from: 17 Apr 2014

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
205 KB 2,873
Zebrafish Anatomy Term Relationships
169 KB 5,428
Zebrafish Anatomy Term Synonyms
139 KB 2,646
Zebrafish Development Stage Terms
315 KB 13,380
Zebrafish Stage Series
2 KB 45
Antibody Data Antibodies
119 KB 1,496
Antibody Expressions in wild-type
259 KB 4,663
Fish Fish Components
10 MB 61,834
Gene Expression Expression data for wildtype fish
24 MB 153,924
Expression Environment Description
547 KB 8,609
Expression Experiment-Figure
14 MB 253,539
Zebrafish Gene Expression by Stage and Anatomy Term
22 MB 245,024
ZFIN Antibody Expression Assay Records
916 KB 7,413
ZFIN Genes with Expression Assay Records
9 MB 74,872
Genetic Marker Relationships Genetic Marker Relationships
9 MB 94,408
Genetic Markers Genetic Marker
9 MB 147,694
Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)
1 MB 33,152
SNP Data
133 MB 2,346,457
Genomic Feature Data All Genomic Features
4 MB 39,400
Construct Components
1019 KB 7,210
Genomic Features and their affected genes
(alleles, deficiencies, translocations)
2 MB 25,074
Transgenic Insertions
2 MB 26,872
Genotype Data Genotype Backgrounds
435 KB 7,324
Genotype Features
3 MB 21,127
Genotype Features (removed or displaced genes)
18 KB 199
Genotype-Publication relation
1 MB 33,697
Image Data Image-Figure translations
Note: Images are not provided due to copyright restrictions
4 MB 89,533
Knockdown Reagent Data CRISPR
3 KB 26
Morpholino
995 KB 6,628
TALEN
23 KB 172
Mapping Data Mapping Data from the 6 Zebrafish Mapping Panels
1 MB 26,654
Orthology Data Drosophila and Zebrafish Orthology
5 KB 58
Human and Zebrafish Orthology
1 MB 14,985
Mouse and Zebrafish Orthology
1 MB 12,254
Phenotypic Zebrafish genes with Human Orthology
111 KB 2,611
Phenotype Data Genotype-Figure relation
782 KB 21,256
Genotypes with Phenotypes
17 MB 79,412
Genotypes with Phenotypes (obo format)
12 MB 82,012
Phenotype Environment Description
568 KB 9,383
Phenotype for Zebrafish genes with fin phenotype
245 KB 979
Phenotype for Zebrafish genes with Human Orthology
4 MB 35,389
Phenotype of Zebrafish Genes
15 MB 65,010
Previous Names Previous Names
8 MB 125,045
Publications ZFIN Bibliography
3 MB 15,807
ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
4 MB 64,559
ZFIN Publication IDs: ZFIN IDs to PubMed IDs
522 KB 19,845
Sequence Coordinates Assembly: Ensembl
166 MB 1,049,576
Complete Assembly Clones: Ensembl
3 MB 33,167
Transgenic Insertion: ENSEMBL
2 MB 15,223
ZFIN Genes with Antibodies: Ensembl
59 KB 555
ZFIN Genes with Expression: Ensembl
1 MB 9,537
ZFIN Genes with Phenotype: Ensembl
253 KB 2,339
ZFIN Genes: Ensembl
3 MB 20,952
ZFIN Morpholinos: Ensembl
530 KB 4,530
Sequence Data Transcripts
4 MB 48,358
ZFIN Gene IDs indirectly and directly associated with Sequence Accessions via cDNA & EST
4 MB 92,988
ZFIN Gene IDs indirectly associated with Sequence Accessions via cDNA & EST
1 MB 41,501
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)
1 MB 19,196
ZFIN Marker associations to GenBank sequence data
5 MB 119,270
ZFIN Marker associations to GenPept protein data
2 MB 44,668
ZFIN Marker associations to InterPro protein data
118 MB 2,505,048
ZFIN Marker associations to NCBI Gene data
970 KB 20,944
ZFIN Marker associations to RefSeq sequence data
2 MB 60,649
ZFIN Marker associations to Sanger Vega data
2 MB 30,610
ZFIN Marker associations to UniGene sequence data
909 KB 20,239
ZFIN Marker associations to UniProt protein data
2 MB 48,151
Wildtype Lines Wildtype Lines
1006 bytes 29
ZFIN Identifiers ZFIN Identifiers
18 MB 216,516

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 monthly OBO file format