The watermark can change any nucleotide base in noncoding DNA to a start codon
("ATG" (Methionine)) or three stop codons ("TAG" (Amber), "TAA" (Ochre), "TGA" (Opal)), indicating the start/stop of the coding DNA region .
targeted (SCoT) polymorphism is based on the short conserved nucleotide sequence that flanks the conserved region surrounding the translation-initiation codon, ATG.
However, an overlap can also occur between uORFs and the coding sequence, in which alternative translation of an upstream in-frame start codon
of a gene can possibly produce an extended protein product .
(b) Porin lesion type: + and - indicate the position upstream and downstream of start codon
; numbers between parentheses correspond the nucleotide insertion position; ISn indicate the mutation in the promoter region and presence of insertion sequences, respectively.
Translation proceeds sequentially along the mRNA molecule from the start codon
nearest the ribosome-binding site terminating at stop codons and reinitiating at the next start codon
The stop codon of this ORF is fused to the start codon
of the gene of interest (thus having TAATG), which is assembled downstream.
The codon AUG codes for the initiation of the translation process and is therefore also known as start codon
. Also a codon can be changed in several ways; such change is known as mutation.
All these polymorphisms are numbered relative to the adenine of the translation start codon
. The sequencing results and SNPs found are shown in Figure 1.
ORF 2 was originally reported to commence at nucleotide position 4,390 at a canonical AUG start codon
. However, it was later revealed empirically to actually start at codon GCU (genome position 4423-4425) which encodes for an alanine (Valles and Hashimoto 2008).
He posed the question of whether a gene was a "functional unit carrying the information necessary for the synthesis of a macromolecule" or "the unit of recombination." Textbooks of my college era discussed genes in terms of proposed models of cistrons, recons, and mutons; were missing the start codon
in charts of the genetic code; and listed "nonsense" for what we know as stop codons (Keeton, 1967).
According to the stop and start codons
, exon can be classified as: (i) a single exon gene which starts with a start codon
and ends with a stop codon, (ii) an initial exon that begins with a start codon
and ends with a donor site, (iii) a terminal exon that starts with an acceptor site and ends with a stop codon, (iv) and an internal exon that starts with an acceptor site and ends with a donor site .
The first exon is untranslated, and the start codon
(AUG) is located at the beginning of exon 2 (1).
This polymorphism, resulting from a T[right arrow]C transition, introduces codon 4 as the start codon
resulting in a shorter isoform of the VDR.
The GSTP1 313A[right arrow]G (rs1695), NQO1 609C[right arrow]T (rs1800566), MBL2 codon 54A[right arrow]G (rs1800450), ABCB1 3435C[right arrow]T (rs1045642), MTHFR 677C[right arrow]T (rs1801133), and VDR start codon
FokI polymorphism (rs2228570) were genotyped by DNAPrint Genomics (Sarasota, FL) in a multiplex PCR followed by single base extension.
Sequence analysis revealed that the clone with molecular size of about 4.9 kb (F3'H-G2) contained the first exon corresponding to 1 to 472 bp of sf3'hl cDNA and approximately 1.5 kb upstream from the start codon
. The two clones from the genomic library, F3'H-G1 and F3'H-G2, have an overlapping region of 644 bp and the DNA sequence of this region was identical in these two clones.