The current zebrafish genome build (2.1) is based on the Zv6 assembly provided by the Wellcome Trust Sanger Institute in March 2006. The sequencing strategy produced a mixed assembly of 6.5-7X coverage consisting of whole genome shotgun sequence and BAC sequence.

The mitochondrial sequence presented, NC_002333, is derived from a single individual of strain ABC.

The complete set of zebrafish sequence databases available for BLAST searching is shown in the pop-up menu on the zebrafish BLAST page, which includes a link to the database descriptions.

Provides the tiling path of GenBank accessions used to build each of the "NW_xxxxxxxxx" contigs, described below.

Shows the chromosomal placement of NW_xxxxxxxxx contigs on the assembled genomic sequence. The individual GenBank records used to assemble the contigs are shown on the Component map, described above.

• relaxed (shown with light blue shading on the map)
• 200 bp min length
• 50% or higher G + C content
• 0.60 or higher observed CpG / expected CpG
• post-processing:  merge islands that are <= 100 bp apart
• strict (shown with dark blue shading on the map)
• 500 bp min length
• 50% or higher GC content
• 0.60 or higher observed CpG / expected CpG

Shows the alignment of zebrafish genomic DNA sequences from GenBank that were not used in the assembly of contigs. It includes zebrafish genomic sequences longer than 500 bp that have at least 97% identity to the components for at least 98 base pairs. If a sequence extends beyond a contig, that portion of sequence is not shown. The length of a line represents the upper and lower-most points on the genome assembly to which sequence fragments from a single GenBank record were aligned. When the GenBank DNA map is displayed as the master map, in the default verbose mode, the descriptive text includes several columns: Total Bases, which shows the total number of bases in the GenBank record; Aligned Bases, which shows the total number of bases from that record that were aligned to the genome; % identity for the alignment; % coverage, which shows how much of the Genbank record aligned to the genome as a percentage; Alignment-length ratio, which is the ratio of the alignment length in the genome to the alignment length of the Genbank record; and Strain from which the Genbank record was derived, when available.

Genes that have been annotated on the genomic contigs. This includes known and putative genes placed as a result of alignments of mRNAs to the contigs. If multiple models exist for a single gene, corresponding to splicing variants, the Gene map presents a flattened view of all the exons that can be spliced together in various ways. For example, if one splice variant uses exons 1, 3, 4, and another splice variant uses exons 2, 3, 4, the Gene map shows exons 1, 2, 3, 4. Genes shown on the left of the grey line are transcribed in the - orientation (from the bottom up) and those on the right in the + orientation (from the top down).

Models with Interim GeneIDs (LOC######) may be paralogs, genes not yet curated, duplications because of assembly errors, or pseudogenes. The genome assembly and annotation pipeline assigns Interim GeneIDs when there is no unambiguous solution to what they should be. Interim GeneIDs are associated with RefSeq XM_* accessions (model mRNAs).

Diagrams of the RNAs that are predicted on the genomic contigs. The RefSeq Transcript map and Gene map are built in the same way using the same types of evidence. The Gene map, however, shows a view of all the exons in a gene while the RefSeq Transcript map shows the combinations of exons (i.e., splice variants) that are valid if mRNA sequences indicate alternative splice variants.

• gene symbol
  A search for anxa13 will retrieve the locus annexin A13.
• marker name and alias
• GenBank accession number
• text words
  For example, a search for actin will retrieve all map objects containing that word in their description. If multiple terms are entered. they will automatically be combined with the 'AND' Boolean operator.
  

1. enter a range of interest in the Region text boxes in side bar
2. click on the region of interest in the chromosome thumbnail graphic in the sidebar
3. click on a region of interest in the enlarged Map View of the chromosome

• symbols - you can enter marker names or alternate marker names (aliases) to display a region of the chromosome between those mapped elements. Note that both mapped elements must be present on the maps that share the same coordinate system in order for the range search to work properly.

• numerical positions - can be used if the master map is a genetic map, radiation hybrid map, or sequence map. It is not necessary to specify units. The Map Viewer will interpret the range in the units of the master map. Note that for a sequence map, base pair positions may be entered in any of the following formats: 1000000 or 1,000,000 or 1M or 1000K.

• Find what is mapped to zebrafish chromosome 10 that is protocadherin-related.
  ../map_search.cgi?taxid=7955&query=protocadherin&qchr=10
• Find two STS markers, fa17f05.s1 and fc13a10.x1
  ../map_search.cgi?taxid=7955&advsrch=off&query=fa17f05.s1+OR+fc13a10.x1