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A consensus logo is a simplified variation of a sequence logo that can be embedded in text format. Like a sequence logo, a consensus logo is created from a collection of aligned protein or DNA/RNA sequences and conveys information about the conservation of each position of a sequence motif or sequence alignment [ 1 ] [ 4 ] .
The sequence at -35 (the -35 element) has the consensus sequence TTGACA. The above consensus sequences, while conserved on average, are not found intact in most promoters. On average, only 3 to 4 of the 6 base pairs in each consensus sequence are found in any given promoter.
Through mutational analysis by Lo and Smale, the "functional" consensus sequence of Inr in humans was inferred to be YYA +1 NWYY. [a] Human genome-wide CAGE data suggests a very simple consensus of YR +1. Vo ngoc et al. have characterized the Inr at focused core promoters (those with a single or a narrow cluster of start sites) and found BBCA ...
It is also commonly called the -10 sequence or element, because it is centered roughly ten base pairs upstream from the site of initiation of transcription. The Pribnow box has a function similar to the TATA box that occurs in promoters in eukaryotes and archaea : it is recognized and bound by a subunit of RNA polymerase during initiation of ...
Figure 1. TATA box structural elements. The TATA box consensus sequence is TATAWAW, where W is either A or T. In molecular biology, the TATA box (also called the Goldberg–Hogness box) [1] is a sequence of DNA found in the core promoter region of genes in archaea and eukaryotes. [2]
EPD (Eukaryotic Promoter Database) is a biological database and web resource of eukaryotic RNA polymerase II promoters with experimentally defined transcription start sites. [1] Originally, EPD was a manually curated resource relying on transcript mapping experiments (mostly primer extension and nuclease protection assays ) targeted at ...
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances.KEGG is utilized for bioinformatics research and education, including data analysis in genomics, metagenomics, metabolomics and other omics studies, modeling and simulation in systems biology, and translational research in drug development.
In molecular biology, a downstream promoter element (DPE) is a core promoter element. Like all core promoters, the DPE plays an important role in the initiation of gene transcription by RNA polymerase II. The DPE was first described by T. W. Burke and James T. Kadonaga in Drosophila melanogaster at the University of California, San Diego in ...