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Tip: This table lists computational prediction of CREB binding sites (CREs). To quickly search the same gene in another data set (e.g. cAMP induced genes in tissues), click the links from the last column. The locuslink number will be used as query.
|No||Symbol||Gene Name||Accession||LocusLink||Alias Symbols||CREflag||Full Site||Half Site||Conserved CRE||CRE cluster||CREB binding (SACO)||chr||strand||pos||Notes||Link|
|1||Csnk1d||"casein kinase 1, delta"||NM_139060||64462||FT h||FT_-28||ht_-4481 h_-1098 h_854||FT_-28_46||498_3||chr10||-||110211716||"all, CREBtarget, saco"||PC12_Expression_A PC12_Expression_B|
Computational prediction of functional CREs on promoters of Rat RefSeq genes and CREB binding data from SACO
The names for most columns are self-explanatory; Details about columns for computational results are listed below:
CRE Flag: Flags, or markers for the types of CREs on the promoter (-3Kb to 300bp from transcription start site). "F/f" means full site, "H/h" means half site, with upper case representing conserved CRE. "FH" is a full site CRE in the species studied but only appear as half site in other species. "T/t" at the end means the presence of a TATA box less than 300bp downstream of the CRE.
Full Site/Half Site: All occurrences of full site (TGACGTCA) or half site(TGACG/CGTCA) CREs in -5Kb-1Kb region of the transcription start site (TSS). Here the position of each CRE relative to the TSS is shown following its flag.
Conserved CRE: All the conserved full and half site are shown in this column since they are the most likely functional CREs. These CREs are shown similar to the format used by Full site/Half site, with the addition of the distance to closest downstream TATA box, shown as the last number.
CRECluster: Here all the CRE clusters are shown; In a CRE cluster, neighbors must be closer than 50bp to each other; If more than two clusters appear in a promoter, they are separated by "|".
CREB binding (SACO): CREB binding data from Ref 1. If a CREB occupied genomic locus is located in the promoter of a Refseq genes, it will be shown here. The position of the center of the locus relative to TSS is shown, followed by number of GSTs identified for the locus.
Chrom/Strand/Pos: Chromosomal position of the TSS and the strand of the transcript based on rn3 rat genome assembly from the UCSC Genome Bioinformatics Site.
1: Impey S, McCorkle SR, Cha-Molstad H, Dwyer JM, Yochum GS, Boss
JM, McWeeney S,
Dunn JJ, Mandel G, Goodman RH.
Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell. 2004 Dec 29;119(7):1041-54.