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Zebrafish Genome Browser at UCSC:
A joint collaboration between UCSC and the Zebrafish Genome Initiative at Children's Hospital Boston provides several useful tracks of genome data, including:
- Mapping & Sequencing: Position / Conigs / Scaffolds / RH Map / BAC End Pairs & Singles / Gap / GC Percent
- Genes & Gene Prediction: RefSeq Genes / Ensembl Genes
- mRNA & EST: ZF mRNAs & ESTs / spliced ESTs / WZ EST Clusters / nonZF mRNAs
- Expression & Regulation: Affy ZF
- Comparative Genomics: Fugu Chain & Net / Human Proteins / HG Blast
- Variation & Repeats: RepeatMasker / SimpleRepeats
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The UCSC Browser for the Tropical 5D Zebrafish Line T5D (also known as Microsporidia Free 5-D line SPF 5-D)
Zebrafish Genome Resources at NCBI:
This page provides information about genomic resources available from NCBI and the zebrafish research community, including sequence, mapping, clone information, and NCBI's independent gene annotation.
SNPFisher : Variant Report Compiler:
Variation data for FLI, TL, and WIK. The SNPfisher website includes the SNPfisher Variant Reporter tool, which provides the genomic position, alternate allele read frequency, strain specificity, restriction enzyme recognition site changes and flanking primers for all SNPs and Indels in a user-defined gene or region of the zebrafish genome. The SNPfisher site also contains links to display our SNP data in the UCSC genome browser.
FishMap Zebrafish Genomics Knowledge base:
A community resource for Zebrafish Genomics.
Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S. FishMap Zv8 update--a genomic regulatory map of zebrafish. Zebrafish. 2010 Jun;7(2):179-80.
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BLAST hits of Human Genes from Sanger sequence maintained by Zon lab:
Each human gene annotated on the Santa Cruz site was compared by BLAST against the Sanger Institute zebrafish genome sequence. These data can be used to help identify zebrafish orthologues of human or Fugu genes.
Zebrafish BLAST server at MGH:
MGH site provides a BLAST search of a gene or marker of interest to the assembled sequence contigs of the zebrafish genomic shotgun sequence from the Sanger project.
RH, meiotic and integrated maps of the genome:
Centralized site for all meiotic and radiation hybrid maps of the zebrafish genome.
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Detailed information on the mutants resulting from the large insertional mutagenesis screen described in Amsterdam, et al. (2004) Identification of 315 genes essential for early zebrafish development. Proceeding of the National Academy of Sciences 101: 12792-12797
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