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Due to the anti-parallel nature of DNA, this means the 3' end of the template strand is upstream of the gene and the 5' end is downstream. Some genes on the same DNA molecule may be transcribed in opposite directions. This means the upstream and downstream areas of the molecule may change depending on which gene is used as the reference.
The upstream signaling pathway is triggered by the binding of a signaling molecule, a ligand, to a receiving molecule, a receptor. Receptors and ligands exist in many different forms, and only recognize/bond to particular molecules. Upstream extracellular signaling transduce a variety of intracellular cascades. [1]
For example, in a typical gene a start codon (5′-ATG-3′) is a DNA sequence within the sense strand. Transcription begins at an upstream site (relative to the sense strand), and as it proceeds through the region it copies the 3′-TAC-5′ from the template strand to produce 5′-AUG-3′ within a messenger RNA (mRNA).
As promoters are typically immediately adjacent to the gene in question, positions in the promoter are designated relative to the transcriptional start site, where transcription of DNA begins for a particular gene (i.e., positions upstream are negative numbers counting back from -1, for example -100 is a position 100 base pairs upstream).
Upstream and downstream (DNA), determining relative positions on DNA; Upstream and downstream (transduction) determining temporal and mechanistic order of cellular and molecular events of signal transduction
Upstream transcription factors are proteins that bind somewhere upstream of the initiation site to stimulate or repress transcription. These are roughly synonymous with specific transcription factors , because they vary considerably depending on what recognition sequences are present in the proximity of the gene.
Silencers are DNA sequences found in the 5′ flanking region of eukaryotic genes, assisting in the silencing of a gene. They can be found upstream, downstream, or within the gene of interest. [3] When repressors bind silencers, they act in a similar fashion as enhancers and bend over to prevent the interaction of RNA polymerase with promoters ...
Gene structure is the organisation of specialised sequence elements within a gene.Genes contain most of the information necessary for living cells to survive and reproduce. [1] [2] In most organisms, genes are made of DNA, where the particular DNA sequence determines the function of the gene.