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Category:Resource:ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters
Abbrev ABS  +
Availability Acknowledgement requested +, GNU General Public License +, V2 +
CurationStatus curated  +
DefiningCitation http://genome.imim.es/datasets/abs2005/index.html  +
Definition Public database of known binding sites ide Public database of known binding sites identified in promoters of orthologous vertebrate genes that have been manually curated from bibliography. We have annotated 650 experimental binding sites from 68 transcription factors and 100 orthologous target genes in human, mouse, rat or chicken genome sequences. Computational predictions and promoter alignment information are also provided for each entry. For each gene, TFBSs conserved in orthologous sequences from at least two different species must be available. Promoter sequences as well as the original GenBank or RefSeq entries are additionally supplied in case of future identification conflicts. The final TSS annotation has been refined using the database dbTSS. Up to this release, 500 bps upstream the annotated transcription start site (TSS) according to REFSEQ annotations have been always extracted to form the collection of promoter sequences from human, mouse, rat and chicken.<br /> For each regulatory site, the position, the motif and the sequence in which the site is present are available in a simple format. Cross-references to EntrezGene, PubMed and RefSeq are also provided for each annotation. Apart from the experimental promoter annotations, predictions by popular collections of weight matrices are also provided for each promoter sequence. In addition, global and local alignments and graphical dotplots are also available.<br /> l dotplots are also available.<br />
ExampleImage ABS.PNG +
Grant Category:Contract LSHG-CT-2003-503265   +
Has default formThis property is a special property in this wiki. Resource  +
Has role Database +
Id nif-0000-21006  +
Is part of Center for Genomic Regulation; Barcelona; Spain +
Keywords Gene +, Alignment +, Annotation +, Binding +, Computational +, Genome +, Nucleotide +, Ortholog +, Prediction +, Promoter +, Sequence +, Target +, Transcription +, Transcriptional factor +, Binding site +, Promoter sequence +, Protein motif +, Benchmark +, Transcription factor binding site +
Label Resource:ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters  +
Modification dateThis property is a special property in this wiki. 21 May 2014 17:48:25  +
ModifiedDate 21 May 2014  +
PMID 16381947  +
Page has default formThis property is a special property in this wiki. Resource  +
RelatedTo Resource:IntegromeDB +
Species Human +, Mouse +, Chicken +, Rat +, Vertebrata +
SuperCategory Resource  +
Supporting Agency European Commission +, (FP6) +
Synonym A database of Annotated regulatory Binding Sites from orthologous promoters  +
Categories Resource
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