2011-04-15T05:18:23-07:00
Resource:ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters
ABS
curated
http://genome.imim.es/datasets/abs2005/index.html
ABS is a 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. A simple and easy-to-use web interface facilitates data retrieval allowing different views of the information.
Annotations have been collected from the literature and are manually curated. 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 very 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 />
Category:Contract LSHG-CT-2003-503265
nif-0000-21006
Resource:ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters
2011-04-15T00:00:00
16381947
A database of Annotated regulatory Binding Sites from orthologous promoters
Synonym
PMID
ModifiedDate
Label
Transcription factor
Protein motif
Promoter sequence
Binding site
Vertebrate
Transcriptional factor
Transcription
Target
Specie
Sequence
Rat
Promoter
Prediction
Orthologous
Nucleotide
Mouse
Human
Genome
Computational
Chicken
Binding
Annotation
Alignment
Gene
Keywords
Center for Genomic Regulation; Barcelona; Spain
Is part of
Id
Database
Has role
Grant
Definition
DefiningCitation
CurationStatus
Abbrev