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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. Ans. From the Ensembl human genome browser, search for the SSBP4 gene. • 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). • • • • • • • • • • • • • • • • • 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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