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Search results (if any) are listed below.
Tip: This table lists computational prediction of CREB binding sites (CREs).
To quickly search the same gene in another data set (e.g. ChIP-chip, 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 CRE Prediction CRE Flag Full Site Half Site Conserved CRE CREcluster pHMM+Pos Chrom Strand Pos Note Link
1 BDNF brain-derived neurotrophic factor NM_001709627MGC34632 CRE_NoTATA H  H_-1235 ht_-3119 H_-1235_509  chr11 - 27686285 "all, CREBtarget" HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression
2 BDNF brain-derived neurotrophic factor NM_170733627MGC34632 CRE_NoTATA H ht  H_-58 ht_-1942 H_-58_509  chr11 - 27687462 "all, CREBtarget" HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression
3 BDNF brain-derived neurotrophic factor NM_170734627MGC34632 CRE_NoTATA H  h_308 H_-2031 ht_-3915 H_-2031_509  chr11 - 27685489 "all, CREBtarget" HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression
4 BDNF brain-derived neurotrophic factor NM_170731627MGC34632 others h  h_-1520    chr11 - 27707584 "all, " HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression
5 BDNF brain-derived neurotrophic factor NM_170732627MGC34632 others h  h_-2570    chr11 - 27706534 "all, " HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression
6 BDNF brain-derived neurotrophic factor NM_170735627MGC34632 others h  h_-1538 H_-3877    chr11 - 27683643 "all, " HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression

Computational prediction of functional CREs on promoters of human RefSeq genes.


The names for most columns are self-explanatory; Details about columns for computational results are listed below:
CRE Prediction: Genes with predicted functional CRE by any of the three methods (conserved CRE, CRE cluster, or positional conserved pHMM hits) are chosen and further separated into two groups, CRE_TATA and CRE_NoTATA based on the presence of TATA boxes. The rest of the genes are simply labeled as "others". When a gene (defined as unique LocusLink number) has multiple entries (GenBank Accession numbers) due to different splicing forms, the best prediction for CRE is chosen

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 "|".

pHMM+Pos: If there is a positional conserved CRE identified by pHMM search in human and mouse orthologs, it will be shown here. The values shown are 1) models used(F: full site model; H: half site model) in human and mouse, respectively; 2) Human match score and position; 3) Mouse match and position. Here the position is relative to the start codon.

Chrom/Strand/Pos: Chromosomal position of the TSS and the strand of the transcript based on hg16 human genome assembly from the UCSC Genome Bioinformatics Site.