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PubMed Protein Genome Structure PopSet Taxonomy OMIM

	UniGene Links  DDD  FAQ  Query Tips  Other Links  Locus Link  HomoloGene  dbEST  Trace Archive  BLAST  CGAP	SearchPubMed Protein Nucleotide Structure Genome PopSet OMIM Taxonomy Books ProbeSet 3D Domains UniSTS Domains SNP HomoloGene Journals UniGene   Limits Index History Details UniGene Build Procedure - Genome Based   The availability of genomic sequence is helpful for identifying sets of transcript sequences that correspond to distinct transcription loci or to annotated genes, which is the goal of UniGene. The procedure used for genome-based clustering of transcript sequences is described here. Several types of evidence are used to identify a transcription locus' boundaries and to identify which transcripts represent the locus. Although determining gross structure and transcript representation of many genes is not sensitive to the details of transcript mapping, there are cases where the details are important: overlapping genes on opposite strands, or genes located within introns of other genes, for example. To accurately resolve these and similar cases, we identify genes by incorporating evidence in order of confidence, beginning with the strongest data. Annotation of characterized genes annotated on the genomic sequence is recorded. Annotated genes include those supported by experimentally confirmed RefSeqs as well as transcription loci that are predicted to encode a protein realized in a gene model. These annotated exon boundaries and the association of exons with genes form a skeleton that can be extended by subsequent analysis but cannot be contradicted subsequently. Transcribed sequences that can be stringently aligned to genomic sequence with a requirement of splice site consensus are used to enumerate additional exon-intron boundaries. Not all sequence alignments satisfy this stringent requirement. Any sequences sharing an exon-intron boundary that can be identified with only one gene are grouped together. Unspliced sequences, as well as sequences for which the splicing location or orientation is uncertain, are associated with an overlapping exon if one exists, or placed against genome if not. Sequence orientation is used where there is possible ambiguity of gene orientation. Sequences that do not align to genomic sequence are grouped together, and transcribed sequences within an interval smaller than 3000 nt that have a common clone of origin are grouped together. Clusters that do not correspond to an annotated gene and are less than 500 bases 3' of another cluster are likely alternative 3' termini, and are merged into the upstream cluster. This merging is not transitive.

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