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Topic: Stop codon

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Open reading frame

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	EvolvingCode.net - stop codon (Site not responding. Last check: 2007-10-20)
		"Stop" is one of the ways that biologists indicate the codon assignment of "stop translating".
		In the standard genetic code, three codons are assigned to "Stop": UAA, UAG and UGG.
		Stop codons are also known as "termination codons", or even "nonsense codons", though this latter usage is misleading, and really dates back to a time when it wasn't clear what exact function these stop codons performed.
	phenotype.biosci.umbc.edu /index.php?page=stop_codon (98 words)

	TFAP2C - Transcription factor AP-2 gamma
		Termination of translation in eukaryotes is catalyzed by eRF1, the stop codon recognition factor, and eRF3, an eRF1 and ribosome-dependent GTPase.
		We suggest that for eRF1 the stop codon decoding is of a non-linear (non-protein-anticodon) type and explores a combination of positive and negative determinants.
		RT was found to bind the eukaryotic translational release factor 1 (eRF1), the protein that recognizes stop codons and, in complex with eRF3, causes termination and polypeptide release from the ribosome.
	www.ihop-net.org /UniPub/iHOP/gi/92667.html (1755 words)

	Endless possibilities: translation termination and stop codon recognition -- Bertram et al. 147 (2): 255 -- Microbiology
		at UAA and UAG codons, and RF2 at UAA and UGA codons (Craigen
		or co-crystallization of the stop codon and RF.
		UAG stop codon readthrough, with glutamine insertion at the
	mic.sgmjournals.org /cgi/content/full/147/2/255 (7120 words)

	Translation and the Genetic Code
		The multiple STOP codons in the gene suggest that it does not code for a protein, consistent with it being a gene for a tRNA.
		Again, by chance the new AUG start codon is in frame with the rest of the HIS3 polypeptide and is not interrupted by chance stop codons in the same reading frame.
		Again, by chance the AUC start codon is in frame with the rest of the HIS3 polypeptide and is not interrupted by chance stop codons in the same reading frame.
	faculty.washington.edu /pallanck/spring.2002/probset5ans.html (2645 words)

	Accumulation of a mRNA decay intermediate by ribosomal pausing at a stop codon -- Bjornsson and Isaksson 24 (9): 1753 ...
		Stop codons that are placed early in coding regions have been shown to influence mRNA stability, in contrast to stop codons which are introduced further downstream (9 - 11).
		The test codon was either a stop codon (UGA or UAG) or a sense codon (UGG or UUA), with a variable codon context defined by the two flanking codons at positions 161 and 163 (17).
		These codon contexts are identical to two of the UGA codon contexts used (Figs 1 and 2).
	nar.oxfordjournals.org /cgi/content/full/24/9/1753 (4088 words)

	[No title]
		By "potential gene" I mean the portion of an orf from the first start codon to the stop codon at the end.
		The length is measured from the first base of the start codon to the last base before the stop codon.
		They represent a codon as a 12-bit pattern, with 4 bits for each base, one bit for each possible value of the bases, T, G, C or A. Thus the bit pattern 0010 0101 1100 represents the base pattern [C] [A or G] [G or T].
	www.sacs.ucsf.edu /Resources/glimmer/long-orfs.readme (788 words)

	Polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational ...
		as the "anticodon" in deciphering stop codons in mRNA.
		Because the increase in the termination at cognate stop codons was unexpected, we estimated the "altered" frequency of termination
		Similar to the sense codon decoding within the ribosome, the stop codon recognition is designed to be extremely accurate.
	www.pnas.org /cgi/content/full/99/4/1819 (4781 words)

	[No title] (Site not responding. Last check: 2007-10-20)
		As all of the 3 stop codons begin with a U we know that the wildtype VAL codon must therefore have been GUU not the other 3 possibilities and that the STOP codon in the mutant is UGA ANSWERS A.
		The translated portion of the mRNA is 672 nucleotides long = 672/3 codons = 224 codons 224 codons code for a polypeptide of 223 amino-acids (1 codes for the STOP signal) The molecular mass of this polypeptide is 223 x 120 daltons = 26,760 daltons C i).
		GAG................Glu The suppressor mutants were therefore producing an altered tRNA which reacted to the UAG codon as though it were for eg an AAG codon (ie the anticodon on a mutated tRNA for lysine was altered to bind to UAG codons) [enda] 10.
	www.rpi.edu /locker/53/001053/CHAP8.DAT (1821 words)

	Stop codon selection in eukaryotic translation termination: comparison of the discriminating potential between human ...
		For example, the stop codons UAA and UAG are translated into glutamine in several species (UGA = stop variant code), whereas in the hypotrich genus Euplotes, UGA is translated into cysteine (Caron and Meyer, 1985; Preer et al., 1985; Harper and Jahn, 1989; for a recent review, see Lozupone et al., 2001).
		However, for the S64D mutated eRF1, there is a discrepancy between the presence of a cross-link with the three stop codons (Figure 1) and the alteration of release activity in the in vitro release assay (Frolova et al., 2002).
		Indeed, the restriction of stop codon recognition to UAA and UAG, a characteristic of Euplotes eRF1 supported by in vitro release assays (Kervestin et al., 2001), was obtained only when the entire N-terminal domain of Euplotes eRF1 was present (Figure 4).
	www.nature.com /cgi-taf/dynapage.taf?file=/emboj/journal/v22/n7/full/7595057a.html (7828 words)

	Ribosomal Binding Site of Release Factors RF1 and RF2. A NEW TRANSLATIONAL TERMINATION ASSAY IN VITRO -- Grentzmann and ...
		Stop codon occupation of the A-site was not
		The presence of a sense codon in the A-site inhibits
		Recognition of stop codons depends on participation of termination factors, which was initially suggested by Ganoza (39).
	www.jbc.org /cgi/content/full/272/19/12300 (3102 words)

	test (Site not responding. Last check: 2007-10-20)
		For this reason, it is safer to anchor an ORF to a stop codon and look for the farthest START codon that is 1) upstream and 2) in the same frame.
		As soon as we encounter a start codon, we'll set an internal variable to True, indicating that we are now expecting a STOP codon next.
		Codon indexes are not very useful on their own.
	users.cs.dal.ca /~cblouin/BIOCX010/tutorials/lab3 (1407 words)

	The Genetic Code
		RNA codons occur in messenger RNA (mRNA) and are the codons that are actually "read" during the synthesis of polypeptides (the process called translation).
		These are the codons as they are read on the sense (5' to 3') strand of DNA.
		The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/C/Codons.html (620 words)

	July 11, 2001 – Genetic code
		Nonsense mutation — a base change that turns a codon for an aa into a stop codon which results in premature truncation of the protein.
		Release factor II (RFII) is responsible for binding to A-site and recognizes 2 specific stop codons.
		Translation now occurs until the second stop codon is reached and a full length RFII produced.
	www.dartmouth.edu /~bio23/lect7.html (817 words)

	Role of Ribosome Release in Regulation of tna Operon Expression in Escherichia coli -- Konan and Yanofsky 181 (5): 1530 ...
		and UAA stop codons, basal expression of the operon was 20 and
		The UGA stop codon (shown in boldface type) in both constructs was also changed to UAG or UAA.
		In strain PDG1184, the tnaC stop codon was replaced by a leucine codon, UUA (17).
	jb.asm.org /cgi/content/full/181/5/1530 (4636 words)

	Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation -- Lithwick and Margalit 13 (12): 2665 ...
		RNA, codon bias, and the identity of the stop codon.
		The identity of the stop codon and the base-pairing
		The bias in codon usage is expressed by the CAI measure.
	www.genome.org /cgi/content/full/13/12/2665 (4898 words)

	[Genome] Stop codon inclusion in gene annotations (Site not responding. Last check: 2007-10-20)
		It interpreded the stop codon as not part of the coding region.
		In response to the validator Ensembl, SGP and Geneid switched their handling of stop codons to the way I guess twinscan (which we got the same time the validator appeared more or less) did it.
		The GTF2 format > (http://genes.cs.wustl.edu/GTF2.html) does not include the stop codon in > the terminal exon, while the Genbank format does, and the GFF format > does not specify what to do.
	www.cse.ucsc.edu /pipermail/genome/2003-February/001995.html (326 words)

	stop codon
		Background: The presence of a stop codon is an indispensable signal for termination of mRNA translation.
		The genetic code includes three stop codons: UAA, UAG and UGA.
		Note: if the cDNA of the target gene is cloned upstream to a fusion tag/protein, stop codons between the target protein and the fusion partner must be omitted.
	www.ls.huji.ac.il /~expression/vector/stop.html (84 words)

	EMBOSS: getorf
		Advanced (Unprompted) qualifiers: -[no]methionine boolean START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein.
		START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein.
		If you have selected one of the options to report a regions around a START or STOP codon, then note that any such region that crosses the beginning or end of the sequence will not be reported.
	biochem.dental.upenn.edu /EMBOSS-HELP/getorf.html (1612 words)

	ORF-open reading frame?? - BioForum
		ORF is a piece of DNA that begins with an initiation (methionine ATG) codon and ends with a nonsense codon.
		Open reading frame: A long sequence of DNA that has no stop codon (no signal to stop reading) and therefore may encode part or all of a protein.
		The default is that an ORF should start with a start codon (ATG or GTG) go on for at least 300 codons (900bp) and end in a stop codon (TAA TGA TAG).
	www.protocol-online.org /forums/index.php?showtopic=3701 (685 words)

	Stop codon
		During translation termination, one of the three stop codons which normally terminate an open reading frame is recognised by proteins called release factors, which bind the ribosome to trigger release of the nascent peptide.
		eRF1 acts as the stop codon discriminator, recognising the stop codon and triggering peptidyl-release.
		Using novel molecular genetic screens in Saccharomyces, we are currently developing an understanding of how the release factor complex recognises the three different stop codons (UAA, UAG and UGA), and yet discriminates between them and the 61 sense codons (Bertram et al., 2000).
	www.abdn.ac.uk /~mbi094/stop.htm (264 words)

	FEBS Abstract (Site not responding. Last check: 2007-10-20)
		These analogs contained UUC codon for Phe followed by a stop codon UAA, UGA or UAG with a perfluoroaryl azido group at either atom C5 of the uridine or N7 of the guanosine residue of the stop codon.
		Crosslinking of eRF1 to mRNA analogs was entirely dependent on the presence of a stop codon in the mRNA analogs.
		When the reactive group was at the second or third (but not the first) nucleotide of the stop codon, eRF1 substantially shielded 18S rRNA from the crosslinking to the mRNA analog.
	www.blackwellpublishing.com /febsabstracts2004/abstract.asp?id=17307 (385 words)

	Genetic Code
		The start codon sets the reading frame: AUG is the first triplet, and subsequent triplets are read in the same reading frame.
		To be recognized as a stop codon, the triplet must be in the same reading frame as the start codon.
		Note that there are three nucleotides, UAG (indicated by asterisks) that would otherwise constitute a stop codon, except that the codon is out of frame and is not recognized as a stop.
	www.emunix.emich.edu /~rwinning/genetics/code3.htm (433 words)

	Codon Tables
		In searching for a mutation that would allow a type of phage mutant to grow, Seymour Benzer said that whoever identified the mutation would get to name it after themself (in some versions of the story, it would be named after the discoverer's mother).
		Thus, the UAG codon, known as a nonsense codon (later known as a stop codon), was named the amber codon.
		Later, the other two stop codons were called "ochre" (UAA) and "opal" (UGA) (sometimes called, "umber") to maintain the color metaphor.
	sosnick.uchicago.edu /codon_table.html (185 words)

	GTP Hydrolysis by eRF3 Facilitates Stop Codon Decoding during Eukaryotic Translation Termination -- Salas-Marco and ...
		implicated in stop codon binding (19, 31, 46).
		Stop codon selection in eukaryotic translation termination: comparison of the discriminating potential between human and ciliate eRF1s.
		Class-1 translation termination factors: invariant GGQ minidomain is essential for release activity and ribosome binding but not for stop codon recognition.
	mcb.asm.org /cgi/content/full/24/17/7769 (7104 words)

	Stop codon suppression via inhibition of eRF1 expression -- CARNES et al. 9 (6): 648 -- RNA
		Stop codon suppression via inhibition of eRF1 expression -- CARNES et al.
		stop codons, its activity is critical for translation termination.
		Skuzeski, J.M., Nichols, L.M., Gesteland, R.F., and Atkins, J.F. The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons.
	www.rnajournal.org /cgi/content/full/9/6/648 (3075 words)

	Stop codon recognition in ciliates: Euplotes release factor does not respond to reassigned UGA codon -- Kervestin et ... (Site not responding. Last check: 2007-10-20)
		Stop codon recognition in ciliates: Euplotes release factor does not respond to reassigned UGA codon -- Kervestin et al.
		Stop codon recognition in ciliates: Euplotes release factor does not respond to reassigned UGA codon
		the mechanism for decoding stop codons remains unknown.
	emboreports.npgjournals.com /cgi/content/abstract/2/8/680 (545 words)

	The soybean retroelement SIRE1 uses stop codon suppression to express its envelope-like protein -- Havecker and Voytas ... (Site not responding. Last check: 2007-10-20)
		to the stop codon, occurs in murine leukaemia virus.
		Brown, C.M., Dinesh-Kumar, S.P. and Miller, W.A. (1996) Local and distant sequences are required for efficient readthrough of the barley yellow dwarf virus PAV protein gene stop codon.
		Namy, O., Hatin, I. and Rousset, J.P. (2001) Impact of the six nucleotides downstream of the stop codon on translation termination.
	emboreports.npgjournals.com /cgi/content/full/4/3/274 (2431 words)

	[Biopython-dev] unambiguous DNA
		In fact, it doesn't map to a stop codon, so the current biopython code wouldn't try to create a '*' character.
		The Codon table only needs to implement the "get" function for "translate" (it needs __getitem__ for "translate_to_stop").
		The AmbiguouCodonTable takes a regular Codon table and two tables of values for the nucleotide and protein ambiguity codes, and produces a CodonTable which tries to find the minimal ambiguity needed to cover the input ambiguity.
	www.biopython.org /pipermail/biopython-dev/2000-August/000072.html (540 words)

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