Ensembl GeneSeqView
Introduction
Ensembl 'GeneSeqView' allows users to highlight features in the gene structure.
Gene Sequence Information
Ensembl genes are annotated by the Ensembl automatic analysis pipeline (Curwen et al., 2004) using either a GeneWise (Birney et al., 2004) model from a species-specific or vertebrate protein, a set of aligned species-specific cDNAs followed by GenomeWise for ORF prediction or from GENSCAN exons supported by protein, cDNA and EST evidence. GeneWise models are further combined with available aligned cDNAs to annotate UTRs.
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Gene - Gene names are obtained by comparing its translations to entries in UniProt/Swiss-Prot, NCBI RefSeq and UniProt/TrEMBL. For further details see the 'Similarity Matches' section of 'Transcript Reports' below. A single name is selected for display, and the source is shown. Preferentially, a gene symbol approved by the species-specific nomenclature committee is chosen (e. g. the appropriate HUGO HGNC symbol for human). Failing that, a UniProt/Swiss-Prot identifier, a NCBI RefSeq accession number or a UniProt/TrEMBL accession number is assigned.
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Ensembl Gene ID - Ensembl stable gene identifiers are mapped between releases. In case a gene model changes dramatically, the old stable identifier may be retired and a new one assigned. However, the Ensembl Archive tracks all stable identifiers and should provide mappings to the current gene predictions.
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Genomic Location
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Top-level - The top-level sequence (e. g. chromosome) location this gene has been annotated on is indicated. A link to 'ContigView' zooms into a region in corresponding to the gene.
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Sequence-level - The sequence-level (e. g. BAC clone) location the start of this gene has been annotated on is indicated. A gene prediction may span more than one sequence-level entities. A link to 'ContigView' zooms into a region covered by the sequence-level entity.
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A number of options are available to highlight gene structure:
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Flanking sequence .- You can select the extent of the flanking regions upstream/downstream of the gene.
Exons .- Exons from Ensembl, Vega (manually annotated), ab initio can be highlighted.
Exons on strand .- Exons on the forward, reverse or both strands can be highlighted.
Show variations .- All SNPs or no SNPs can be shown.
Line numbering .- Relative to the sequence, to the coordinate system or no positions can be shown.