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Xenopus (Silurana) tropicalis (western clawed frog) genome view
Annotation Release 101 statistics   Switch to previous build

  BLAST search Xenopus tropicalis sequences
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At present, none of the contigs from the current public WGS assembly have been placed on chromosomes so you cannot browse the sequence data by chromosome. You can find sequenced regions of interest by:

  • querying Map Viewer for a known gene name or symbol, e.g. fgf8
  • querying Map Viewer for accession numbers or Unigene cluster number, e.g. NM_001100263 or Str.17301
  • searching Gene for Xenopus genes that have been annotated on the genome
  • searching by sequence using BLAST against the genome. Results from a BLAST sequence alignment can be displayed in Map Viewer by following the link in "Related Information" to the right of the alignment.

     Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Silurana; Xenopus (Silurana) tropicalis
October 2013, Xenopus (Silurana) tropicalis Annotation Release 101

This is a full annotation run for the 7.44X assembly submitted in December 2012 by the US DOE Joint Genome Institute (JGI-PGF) for Xenopus (Silurana) tropicalis, the western clawed frog. This is the first amphibian genome to be sequenced, with an estimated haploid genome size of approximately 1500 Mb. None of the contigs have been placed on chromosomes in this first version of the assembly. Data for Xenopus laevis, the African clawed frog, has also been mapped to the Xenopus (Silurana) tropicalis assembly. The mitochondrial genome for Xenopus (Silurana) tropicalis, also sequenced by JGI, is available in Sequence Viewer (NC_006839.1).

The NCBI Map Viewer provides graphical displays of features on the Xenopus (Silurana) tropicalis genome sequence assembly. 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 aligned transcripts from Xenopus (Silurana) tropicalis (rnaStr) and Xenopus laevis (rnaXl). The gene on sequence map includes both known genes and putative genes based on supported Gnomon gene predictions. The complete set of Gnomon predicted gene models can be viewed on the ab initio map. Further documentation is provided on the Xenopus genome data and search tips page and through the links below to describe the resource features and methods used, tutorials, and statistics. The previous build, build 1.1, can also be accessed.

    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. Xenopus (Silurana) tropicalis Annotation Release 101 reflects this change; the old nomenclature style would designate this as NCBI build 2.1.

    Annotation Release numbers:xxxxxxxxxxxx
    • 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.

    Available Documentation:

    Last modified: Oct 28, 2013

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