Danio rerio
Photo courtesy of NHGRI (Press Photos)

The Jul. 2010 zebrafish (Danio rerio) Zv9 assembly (GCA_000002035.2) was produced by The Wellcome Trust Sanger Institute, UK. For more information about this assembly, see Zv9 in the NCBI Assembly database.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the zebrafish genome. Note that some position queries (e.g. "huntington") may return matches to the mRNA records of other species. In these cases, the mRNAs are mapped to their homologs in zebrafish. See the User's Guide for more information.

Request:
Genome Browser Response:

chr1 Displays all of chromosome 1

chr1:1-200000 Displays first two hundred thousand bases of chromosome 1

chr1:100000+2000 Displays a region of chr 1 that spans 2000 bases, starting with position 100000

U30710 Displays region containing zebrafish mRNA with GenBank accession number U30710

AA658622 Displays region containing zebrafish EST with GenBank accession AA658622

ENSDART00000025573 Displays region containing Ensembl gene prediction transcript ENSDART00000025573

p53 Lists mRNAs related to the p53 tumor suppressor

pseudogene mRNA Lists transcribed pseudogenes but not cDNAs, in GenBank

homeobox caudal Lists mRNAs for caudal homeobox genes in GenBank

zinc finger Lists many zinc finger mRNAs

kruppel zinc finger Lists only kruppel-like zinc fingers

huntington Lists mRNAs associated with Huntington's disease

porter Lists mRNAs deposited by scientists named Porter

Amsterdam,A. Lists mRNAs deposited by co-author A. Amsterdam

Use this last format for author queries. Although GenBank requires the search format Amsterdam A, internally it uses the format Amsterdam,A.

Assembly details

The Zv9 assembly comprises a sequence length of 1.4 Gb in 26 chromosomes and 1,107 scaffolds. This assembly is based on a clone path sorted with the high-density meiotic map SATMAP (Clark et al., in preparation). The data freeze was taken on 1 April 2010. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involved sequence alignemnts as well as cDNA, marker and BAC/Fosmid end sequence placements. For more details about the Zv9 assembly, see the Sanger Institute page for the Danio rerio Sequencing Project.

In this assembly, scaffolds that are based on clone contigs or could be associated with chromosome placements through marker information are named Zv9_scaffoldn. WGS contigs that could not be placed on chromosomes are named Zv9_NAn. Linkage group numbers were translated directly into chromosome numbers (e.g. linkage group 1 = chromosome 1). The zebrafish mitochondrial sequence is also available as the virtual chromosome, chrM (GenBank accession NC_002333.2)

The Sanger Institute notes that this assembly release is still preliminary. The regions of the assembly covered by WGS contigs are of lower quality.

Downloads of the zebrafish data and annotations can be obtained from the UCSC FTP site or Downloads page. This data set has specific conditions for use. The danRer7 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

GenBank Pipeline Details
For the purposes of the GenBank alignment pipeline, this assembly is considered to be: well-ordered.

Request:	Genome Browser Response:

chr1		Displays all of chromosome 1
chr1:1-200000		Displays first two hundred thousand bases of chromosome 1
chr1:100000+2000		Displays a region of chr 1 that spans 2000 bases, starting with position 100000

U30710		Displays region containing zebrafish mRNA with GenBank accession number U30710
AA658622		Displays region containing zebrafish EST with GenBank accession AA658622
ENSDART00000025573		Displays region containing Ensembl gene prediction transcript ENSDART00000025573

p53		Lists mRNAs related to the p53 tumor suppressor
pseudogene mRNA		Lists transcribed pseudogenes but not cDNAs, in GenBank
homeobox caudal		Lists mRNAs for caudal homeobox genes in GenBank
zinc finger		Lists many zinc finger mRNAs
kruppel zinc finger		Lists only kruppel-like zinc fingers
huntington		Lists mRNAs associated with Huntington's disease

porter		Lists mRNAs deposited by scientists named Porter
Amsterdam,A.		Lists mRNAs deposited by co-author A. Amsterdam

Use this last format for author queries. Although GenBank requires the search format Amsterdam A, internally it uses the format Amsterdam,A. Assembly details The Zv9 assembly comprises a sequence length of 1.4 Gb in 26 chromosomes and 1,107 scaffolds. This assembly is based on a clone path sorted with the high-density meiotic map SATMAP (Clark et al., in preparation). The data freeze was taken on 1 April 2010. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involved sequence alignemnts as well as cDNA, marker and BAC/Fosmid end sequence placements. For more details about the Zv9 assembly, see the Sanger Institute page for the Danio rerio Sequencing Project. In this assembly, scaffolds that are based on clone contigs or could be associated with chromosome placements through marker information are named Zv9_scaffoldn. WGS contigs that could not be placed on chromosomes are named Zv9_NAn. Linkage group numbers were translated directly into chromosome numbers (e.g. linkage group 1 = chromosome 1). The zebrafish mitochondrial sequence is also available as the virtual chromosome, chrM (GenBank accession NC_002333.2) The Sanger Institute notes that this assembly release is still preliminary. The regions of the assembly covered by WGS contigs are of lower quality. Downloads of the zebrafish data and annotations can be obtained from the UCSC FTP site or Downloads page. This data set has specific conditions for use. The danRer7 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release. GenBank Pipeline Details For the purposes of the GenBank alignment pipeline, this assembly is considered to be: well-ordered.