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ZIRC

ZFIN Data Reports from: 16 May 2013

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
197 KB 2,748
Zebrafish Anatomy Term Relationships
161 KB 5,169
Zebrafish Anatomy Term Synonyms
85 KB 1,637
Zebrafish Development Stage Terms
315 KB 13,380
Zebrafish Stage Series
2 KB 45
Antibody Data Antibodies
97 KB 1,216
Antibody Expressions in wild-type
222 KB 4,002
Fish Fish Components
8 MB 49,283
Gene Expression Expression data for wildtype fish
18 MB 144,996
Expression Environment Description
463 KB 7,236
Expression Experiment-Figure
13 MB 228,991
Expression for Zebrafish genes with fin phenotype
422 KB 2,809
Zebrafish Gene Expression by Stage and Anatomy Term
20 MB 221,779
ZFIN Antibody Expression Assay Records
739 KB 5,958
ZFIN Genes with Expression Assay Records
8 MB 66,203
Genetic Marker Relationships Genetic Marker Relationships
9 MB 87,251
Genetic Markers Genetic Marker
8 MB 138,039
Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)
1 MB 32,623
SNP Data
123 MB 2,158,820
Genomic Feature Data All Genomic Features
2 MB 31,119
Genomic Features and their affected genes
(alleles, deficiencies, translocations)
1 MB 17,577
Genotype Data Genotype Backgrounds
443 KB 6,845
Genotype Features
3 MB 18,384
Genotype Features (removed or displaced genes)
18 KB 195
Genotype-Publication relation
1 MB 30,525
Image Data Image-Figure translations
Note: Images are not provided due to copyright restrictions
4 MB 85,996
Mapping Data Mapping Data from the 6 Zebrafish Mapping Panels
1 MB 26,654
Morpholino Data Morpholino
811 KB 5,875
Orthology Data Drosophila and Zebrafish Orthology
4 KB 56
Human and Zebrafish Orthology
1 MB 13,903
Mouse and Zebrafish Orthology
1 MB 11,140
Phenotypic Zebrafish genes with Human Orthology
88 KB 2,069
Phenotype Data Genotype-Figure relation
666 KB 18,086
Genotypes with Phenotypes
14 MB 68,604
Genotypes with Phenotypes (obo format)
10 MB 70,660
Phenotype Environment Description
443 KB 7,320
Phenotype for Zebrafish genes with fin phenotype
189 KB 812
Phenotype for Zebrafish genes with Human Orthology
2 MB 26,410
Phenotype of Zebrafish Genes
13 MB 57,675
Previous Names Previous Names
8 MB 113,502
Publications ZFIN Bibliography
3 MB 14,258
ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs
3 MB 57,015
ZFIN Publication IDs: ZFIN IDs to PubMed IDs
475 KB 18,095
Sequence Coordinates Assembly: Ensembl
174 MB 1,097,064
Complete Assembly Clones: Ensembl
3 MB 33,167
Transgenic Insertion: ENSEMBL
2 MB 15,223
ZFIN Genes with Antibodies: Ensembl
51 KB 484
ZFIN Genes with Expression: Ensembl
1021 KB 9,245
ZFIN Genes with Phenotype: Ensembl
219 KB 2,023
ZFIN Genes: Ensembl
3 MB 20,321
ZFIN Morpholinos: Ensembl
530 KB 4,530
Sequence Data Transcripts
3 MB 41,200
ZFIN Gene IDs indirectly and directly associated with Sequence Accessions via cDNA & EST
3 MB 82,659
ZFIN Gene IDs indirectly associated with Sequence Accessions via cDNA & EST
1 MB 41,503
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 18,466
ZFIN Marker associations to GenBank sequence data
5 MB 113,619
ZFIN Marker associations to Gene sequence data
1 MB 22,523
ZFIN Marker associations to GenPept protein data
2 MB 42,952
ZFIN Marker associations to InterPro protein data
106 MB 2,245,810
ZFIN Marker associations to RefSeq sequence data
1 MB 34,564
ZFIN Marker associations to Sanger Vega data
1 MB 30,210
ZFIN Marker associations to UniGene sequence data
1 MB 23,161
ZFIN Marker associations to UniProt protein data
2 MB 46,551
Wildtype Lines Wildtype Lines
1006 bytes 29
ZFIN Identifiers ZFIN Identifiers
15 MB 196,384

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