GC Box
The GC box is a proximal promoter element found in some eukaryotic genes. It has a consensus sequence, GGGCGG, from which its name is derived. During transcription, it is bound by general transcription factors.
CAAT Box
The CAAT box, also known as the CCAAT box, is a proximal promoter element found in some eukaryotic genes. It has a consensus sequence, GGCCAATCT, from which its name is derived. During transcription, it is bound by general transcription factors. The CAAT box is neccesary for robust transcription in the genes which possess it, and mutations of the CAAT box will often serve to lower the gene's rate of transcription.
TFIIB Recognition Element (BRE)
The BRE is a cis-regulatory element found either upstream or downstream of the TATA box. During transcription, BRE is recognized and bound by the general transcription factor TFIIB. Along with other GTFs, TFIIB helps form the pre-initiation complex.
TATA Box / Goldberg-Hogness box
The TATA box is a conserved DNA region in the core promoter characterized by alternating repeats of adenine and thymine base pairs, TATATA..., from which its name is derived. It is 25-30 bps upstream of the +1 site.
During transcription, the TATA box is bound by the general transcription factor TFIID, which assists in recruiting other GTFs to the site of transcription.
Initiator Element (inr)
The initiator element is a core promoter element which overlaps the transcription start site. During transcription, it facilitates the binding of general transcription factors and RNAPII.
The +1 Site
The +1 site is the transcription start site. During transcription, RNAPII's active site is aligned with the +1 site. Everything downstream of the +1 site is transcribed into RNA by RNAPII.
Motif Ten Element (MTE)
The motif ten element is a core promoter element. In genes whose core promoters lack a TATA box, it assists in transcription.
Downstream Promoter Element (DPE)
The downstream promoter element is a core promoter element. In genes whose core promoters lack a TATA box, it helps recruit transcription machinery.
Kozak Sequence & Translation Start Site
Translation of an RNA into a protein begins at a specific site on the RNA transcript. This site is marked by a 'start codon', AUG, which codes for methylamine.
Because there may be many such codons in a single RNA transcript, the AUG serving as the start codon is identified by an accompanying sequence called the Kozak sequence.
The Kozak sequence is a consensus sequence surrounding the start codon.
STOP Codon
The stop codon tells translation machinery to end translation of an RNA transcript. There are 3 stop codons: UAG, UAA, and UGA.
When a stop codon is encountered by a ribosome, a release factor (RF1 or RF2, depending on the specific codon encountered) is recruited to the ribosomal A-site. The RF catalyzes the hydrolysis of the bond linking the growing polypeptide chain to the tRNA at the ribosomal P-site, thus releasing the polypeptide.
Another RF, RF3, forms a complex with guanine triphosphate (GTP), and binds to the ribosome. The RF3-GTP complex releases the other RF, the mRNA, and the tRNA at the P-site. This ends translation.
3' Untranslated Region
The 3'-UTR contains the polyadenylation sequence. In DNA, this is a series of thymine repeats (TTTATT). During transcription, the poly-A sequence serves as a cleavage signal, effectively ending transcription; as RNAPII transcribes the poly-A sequence (reading AAUAAA), an endonuclease enzyme is attracted to the site, where it cuts the bonds between the pre-mRNA and RNAPII.
In pre-mRNA, the 3' untranslated region serves to promote certain post-transcriptional modifications. The poly-A sequence attracts the poly-A polymerase enzyme, which attaches a poly-A tail to the transcript's 3' end. The poly-A tail is a string of adenines terminated by a hydroxyl group, and it is bound by poly-A binding proteins.
5' Untranslated Region
In mRNA, the 5' untranslated region serves to promote post-transcriptional gene regulation. Namely, short sequences in the 5'-UTR form riboswitches, which bind to molecules called ligands. Binding induces the mRNA to adopt a terminator structure, preventing translation.
Proximal Promoter Elements
The proximal promoter elements comprise part of the eukaryotic promoter. The proximal promoter elements are adjacent to and upstream from the core promoter, and typically contain binding sites for regulatory transcription factors, whereby they regulate gene expression.
Core Promoter
The core promoter comprises part of the eukaryotic promoter. Assisted by the binding of general transcription factors to various core promoter elements, it demarcates where the transcription machinery, namely RNAPII, initiates transcription of the gene.
Consensus Sequence
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Shine-Delgarno Sequence & Start Codon
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3' Untranslated Region
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5' Untranslated Region
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