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Taeniopygia guttata (zebra finch) genome view
Annotation Release 101 statistics

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August 2013, Zebra finch Annotation Release 101

This is a full annotation run for the first assembly submitted in October 2008 by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis. The zebra finch 5.5X draft genome assembly was the second avian genome to be sequenced and, like the chicken genome, the finch genome has a haploid genome size of 1200 Mb. The zebra finch genome, similar to the genomes of chicken and many other Aves, is composed of chromosomes of vastly different sizes identified as either macro- or microchromosomes. The Taeniopygia guttata genome has 40 pairs of autosomes and a pair of sex chromosomes, referred to as Z and W to distinguish them from mammalian sex chromosomes. In birds, the male is homozygous (ZZ) while the female is heterozygous (ZW).

    Data for other avian species has also been mapped to the zebra finch assembly. Separate maps for chicken Gallus gallus UniGene clusters and mRNAs, as well as mRNAs from avian species other than zebra finch and chicken are available.

Announcement: To avoid confusion between the independent notions of a genome assembly and its annotation, NCBI is now using Annotation Release numbers to designate annotation versions. Zebra finch Annotation Release 101 reflects this change; the old nomenclature style would designate this as "NCBI build 2.1".

Annotation Release numbers:
  • are integer values that increment each time the genome annotation is updated.
  • have initial values starting at 100 or higher.
  • are incremented independently for each organism. This means that different organisms may have the same release number (e.g., Human 105, Mouse 105), but the two annotation runs are not connected. In addition, differences in the release number for different organisms does not imply one annotation release is more up-to-date than another (e.g., Mouse 104 could be a newer dataset than Human 105).
  • are used for the set of annotations calculated on one or more genome assemblies for the same species. For instance, Human Annotation Release 104 includes annotation for a new alternate assembly, CHM1_1.0, and updated annotation for the reference assembly, HuRef assembly, and the CRA_TCAGchr7v2 chromosome 7 assembly.
Therefore, a specific genome annotation dataset is associated with three primary identifiers: the assembly accession, the annotation release number, and the NCBI taxonomy ID or species name.

August 2013 Update: NCBI released an update for the zebra finch genome annotation. The chromosome sequence is unchanged. A previous version of the reference genome assembly, NCBI Build 1.1, can still be accessed for Map Viewer display and for BLAST.

    The NCBI Map Viewer provides graphical displays of features on the zebra finch genomic sequence assembly as well as genetic and physical maps.

    Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map), the WGS sequences (the 'Component' map), and the location of genes, STSs, ESTs, and Gnomon predicted gene models.

    You can find genes or markers of interest by submitting a query against the whole genome, or a chromosome at a time. Results are indicated both graphically, as tick marks on the ideogram, and in a tabular format. The results table includes links to a chromosome graphical view where the gene or marker can be seen in the context of additional data. For genes, a particularly useful display includes the Gene, Ab initio (e.g., the Gnomon predicted models), and UniGene sequence maps. You can also browse a chromosome by clicking on a chromosome link in the ideogram above. Use the "Maps & Options" window, available on individual chromosome displays, to configure your display.

    Please note that other genomes can also be viewed in the NCBI Map Viewer resource. The Map Viewer Home Page provides a current list. Consider also reviewing the resources listed on the Genomic Biology site.

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