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New Search (in the same window)
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.
||a disintegrin and metalloproteinase domain 23
|| ||ht_-3163 h_-363
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.