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Sus scrofa (pig) genome view
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  BLAST search against pig sequences


     Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus; Sus scrofa

In September 2011, the Swine Genome Sequencing Consortium released a mixed BAC and WGS-based assembly of the porcine genome (Sscrofa10.2). It includes assemblies for chromosomes 1-18, X and Y. Most of the genome sequence was derived from a female of the Duroc breed; some BACs from other breeds were also included. The NCBI Sus scrofa build 3.1 includes the Sscrofa10.2 assembly and a complete mitochondrial genome derived from a Landrace pig.

The NCBI Map Viewer provides graphical displays of features on the porcine genome sequence assembly. Map features that can be seen along the sequence include NCBI contigs (the 'Contig' map), the BAC and WGS sequences (the 'Component' map), and the location of genes, STSs, ESTs, and Gnomon-predicted gene models. Extensive documentation is provided to describe the resource features and methods used, tutorials, and statistics.

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, Model Transcripts (i.e. the Gnomon predicted models), and rnaSsc (i.e. pig ESTs and mRNAs) 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.

The NCBI Map Viewer also presents a graphical view of the MARC linkage map for Sus scrofa. Each of the markers on the genetic map has a link to NCBI's UniSTS resource, which provides regular updates of positioning of these markers on sequences available in DDBJ/EMBL/GenBank. It is thus possible to navigate from these markers to information in Gene, GenBank, RefSeq, HomoloGene and UniGene.

Please note that other genomes can also be viewed in the NCBI Map Viewer resource. The Map Viewer Home Page provides a current list.

Available Documentation:


Last modified: Jun 16 2011





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