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dbZeneMark, a Database of Retroviral Insertions in the Zebrafish Genome

Find Retroviral Insertions in Your Favorite Genes . . .

Select from the methods below to look for mutations in your genes of interest. For genes not yet annotated, we recommend that you use the BLAST search method.

  • Look through BLAST searches. Search the zebrafish genome using your query sequence. The result page has links to bring you to the "ContigView" of the genome browser for the region that matches your query sequence.
  • Look through chromosomal locations. If you know the location(s) of your gene(s) in the zebrafish genome (Zv7, August 2007), enter the coordinates in the boxes on the right hand side under the name "Jump directly to sequence position".
  • Look through Ensembl gene IDs. If you have the Ensembl gene IDs, use the search box located on the upper right corner of this page.
  • Look through our insertions list* . This list contains genes that have retrovirus inserted in them or in their upstream 5kb region.
  • Look through keyword searches* (e.g. "phosphatase").
    Enter keyword(s):  
*Important: Since genome sequencing and gene annotation for zebrafish are still underway, it is strongly advised that researchers use the BLAST server in this site or Ensembl gene IDs, genomic locations to identify the locations of genes of interest. Follow the resultant links to go to the "ContigView" page and examine the genomic context of the genes and see any retrovirus insertions in the region.

Mapping Statistics (as of September 28, 2007)

Unique ZeneMark tags mapped on Zv7 with 1-3 hits: 237,225
Unique ZeneMark tags unambiguously mapped on Zv7: 202,628
Total Ensembl genes: 25,473
Ensembl genes with insertions: 11,606*
Ensembl exons with insertions: 6,086*
Ensembl introns with insertions: 18,470*
Ensembl first introns with insertions: 3,997*

* Based on the 202,628 insertions unambiguously mapped on Zv7.

Browse Retroviral Insertions by Chromosomes

Click on a chromosome for a closer view

Zebrafish karyotype selector

Jump directly to sequence position

Chromosome: or region
From (bp):
To (bp):

About ZeneMark® Database

The ZeneMark® Database contains retroviral insertions mapped on the most recent zebrafish genomic sequences (Zv7, August 2007). Its front end is a web-based genome browser built on the Ensembl technology.

Note: If the insertional mutations to your interest is not found at this time, please come back later to see if we have added new insertions.