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Genomic Database - Ensembl

Genomic Database - Ensembl. Ka-Lok Ng Department of Bioinformatics Asia University. Ensembl http://www.ensembl.org/index.html Worked example The human protein single-stranded DNA binding protein 4, SSBP4. How can one find the mouse ortholog at Ensemble, without doing a BLAST search.

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Genomic Database - Ensembl

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  1. Genomic Database - Ensembl Ka-Lok Ng Department of Bioinformatics Asia University

  2. Ensemblhttp://www.ensembl.org/index.html • Worked example • The human protein single-stranded DNA binding protein 4, SSBP4. How can one find the mouse ortholog at Ensemble, without doing a BLAST search. • Ans. From the Ensembl human genome browser, search for the SSBP4 gene.

  3. It returns Ensembl Gene: ENSG00000130511 (RefSeq NM_032627.2). Following the link to GeneView in the Orthologue Predication section are the results of sequence comparison between the human gene and genes from other organisms. The mouse gene ENSMUSG00000070003 is a best reciprocal hit to the human. This mouse gene (growth differentiation factor 15) is a putative ortholog of the human SSBP4 corresponding to RefSeq. NM_133772.1 (see the Similarity Section).

  4. NCBI • NCBI Map Viewer • NCBI Map Viewer Help • NCBI Map Viewer Human Maps Help • UCSC • UCSC Genome Browser • UCSC Genome Browser Archive • UCSC Genome Browser Experimental Tracks • UCSC Genome Browser Custom Tracks • Genome Browser User’s Guide • UCSC Genome Browser Mailing List • Ensembl • Project Ensembl • Project Ensembl Preview Browser • Other • Genome Sequencing Projects Funded by NHGRI • The Vertebrate Genome Annotation (VEGA) database

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