Ensembl GeneRegulationView
Introduction
Ensembl 'GeneRegulationView' provides information about regulatory elements.
Ensembl Gene Regulation Report
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.
-
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.
-
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.
-
Genomic Location
-
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.
-
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.
-
-
Description - The description of the gene is taken from the UniProt/Swiss-Prot entry the predicted gene is mapped to, or, if none available, from a NCBI RefSeq or UniProt/TrEMBL entry. If a predicted gene has not been mapped to any such entries, no description will be given. If its translation is however part of an Ensembl protein family cluster, the consensus annotation of that family may be informative. See the links to Ensembl 'FamilyView' in the 'Protein Family' section on Ensembl 'ProteinView' pages.
Regulatory Factors
For human genes, we include both CisRed and miRanda features, and in future will include other types. In Drosophila we include FlyReg features too. In the table we include location, lenght, consensus sequence, link to the distribution of the factor in the genome, and analysis