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Topic: Open reading frame

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	Open Reading Frame
		A reading frame, in biology, consists of three-nucleotide codon sets in either DNA or RNA that are contiguous and non-overlapping.
		Sometimes short open reading frames occur outside the genes, simply by chance, and these are generally examined and discarded.
		Open reading frames are crucial to genetic sequencing.
	www.iscid.org /encyclopedia/Open_Reading_Frame (202 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.
		An open reading frame is any segment of that stretch of DNA that begins with a start codon and ends with a stop codon when both the start codon and the stop codon are in the same reading frame.
	www.protocol-online.org /forums/index.php?showtopic=3701 (1140 words)

	GeneLooper High-Throughput
		In general, for a full-length mRNA, the longest open reading frame is the region coding for its protein.
		The sequence before the first ATG of the longest ORF is called 5’ untranslated region (5’UTR), and the sequence after the stop in the same frame is called the 3’ untranslated region (3’UTR).
		The incomplete ORF detection method allows one to study the coding regions of partial cDNAs, for example, to screen those with relatively long incomplete ORF because they are more likely to be genuine transcripts coding for proteins.
	www.geneharbor.com /products/genelooper/orf_detect.html (320 words)

	Open reading frame - Wikipedia, the free encyclopedia
		In a gene, ORFs are located between the start-code sequence (initiation codon) and the stop-code sequence (termination codon).
		In fact, the existence of an ORF, especially a long one, is usually a good indication of the presence of a gene in the surrounding sequence.
		In this case, the ORF is part of the sequence that will be translated by the ribosomes and the ORF will be long and continue over gaps, or introns.
	en.wikipedia.org /wiki/Open_reading_frame (385 words)

	Open Reading Frame?
		An open reading frame (ORF) is a portion of a gene's sequence that contains a sequence of bases, uninterrupted by stop sequences, that could potentially encode a protein.
		ORF identification involves scanning each of the six reading frames and determining which one(s) contains a stretch of DNA sequence bounded by a start and stop codon, yet containing no start or stop codons within it; a sequence meeting these conditions could correspond to the actual single product of the gene.
		The identification of an ORF provides the first evidence that a new sequence of DNA is part or all of a gene encoding for a particular protein.
	www.physicsforums.com /showthread.php?t=42688 (455 words)

	Programmed Translational Frameshift in the Bacteriophage P2 FETUD Tail Gene Operon -- Christie et al. 184 (23): 6522 -- ...
		Distal to gene E+E' is an open reading frame encoding a polypeptide
		Boxes indicate the extent of the open reading frame (orf) and overlap in the genes equivalent to P2 E (white) and the -1 reading frame E' (light gray), as well as show the beginning of T (dark gray, which in all cases is in the same frame as E).
		The TAA stop codon for open reading frame 26 (orf26) (HP1 and HP2) or orf30 (K139) is underlined, as is the TGA stop codon that defines the extent of overlap in the -1 reading frame.
	jb.asm.org /cgi/content/full/184/23/6522 (6572 words)

	Characterization of the bvgR Locus of Bordetella pertussis -- Merkel et al. 180 (7): 1682 -- The Journal of Bacteriology
		12 open reading frames in the Synechocystis genome, 9 open reading
		coli genome, and 2 open reading frames in the
		FCCORF_WOSU, unidentified open reading frame in the fcc 5' region of Wolinella succinogenes (Y10581); DEFORF_CALO, unidentified open reading frame in the def 3' region of Calothrix sp.
	jb.asm.org /cgi/content/full/180/7/1682 (5901 words)

	UMR cDNA Resource Center (Site not responding. Last check: 2007-10-21)
		The open reading frame was amplified by the PCR from human whole brain cDNA (Clontech).
		The open reading frame was amplified by the PCR from human whole brain cDNA.
		The open reading frame was amplified by the PCR from human lung cDNA (Clontech).
	www.cdna.org /Clones?GROUP=88 (693 words)

	Open Reading Frame
		I had a section on this in my "open access" essay for 3QD, but I cut it out in the interest of brevity, because the open source section was just there for background and I assumed most people reading 3QD would be at least somewhat familiar with it.
		I take it as read that for-profit ventures charge what the market will bear, but when the market in question is largely scientists and their allies (librarians, clinicians, &c.), it seems logical that the market should look for data on which to base decisions about just what it will bear.
		If one feels that the social benefits of open access are clearly and completely overwhelming, then one is compelled to push for whatever solutions might point in that direction and let the chips fall where they may. But to righteously ignore the fact that some of those chips may fall very heavily indeed is irresponsible.
	www.sennoma.net (3482 words)

	Reading frame - Wikipedia, the free encyclopedia
		In biology, a reading frame is a contiguous and non-overlapping set of three-nucleotide codons in DNA or RNA.
		There are 3 possible reading frames in a mRNA strand and six in a double stranded DNA molecule.
		In rare cases a translating ribosome may shift from one frame to another, a translational frameshift.
	en.wikipedia.org /wiki/Reading_frame (178 words)

	reading frame
		reading frame The reading frame defines which sets of three nucleotides are read as triplets, and hence as codons, in DNA transcription.
		The SLC25A12 gene comprises a 2,037-base-pair open-reading frame, encoding the 678 amino acid mitochondrial aspartate/glutamate carrier, which resides in the...
		An open reading frame of Campylobacter jejuni with similarity to the ispD and ispF genes of Escherichia coli was cloned into an expression vector directing the...
	www.mongabay.com /igapo/biotech/reading_frame.html (156 words)

	ORF Finder
		The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
		This tool identifies all open reading frames using the standard or alternative genetic codes.
		The ORF Finder should be helpful in preparing complete and accurate sequence submissions.
	www.ncbi.nlm.nih.gov /gorf/gorf.html (104 words)

	Genome Biology \| Full text \| Novel gene and gene model detection using a whole genome open reading frame analysis in ...
		This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
		The ORF library was used as the search database for X!Tandem, an open source program that matches tandem mass spectra to a peptide sequence from a given database of protein sequences [13,14].
		Putative ORFs were generated on both DNA strands of the chromosome in all three reading frames.
	genomebiology.com /2006/7/4/R35 (5897 words)

	ABC of Bioinformatics
		Because a codon is a three-letter word, every region of DNA has six possible reading frames, three in each direction.
		In the following example, the three reading frames in the forward direction are shown with the translated amino acids below each DNA seqeunce.
		Frame 1 starts with the "a", Frame 2 with the "t" and Frame 3 with the "g".
	www.shokhirev.com /nikolai/abc/bioinf/bioinf.html (697 words)

	Murine Cytomegalovirus with a Transposon Insertional Mutation at Open Reading Frame M35 Is Defective in Growth In Vivo ...
		The transposon sequence is shown as a solid bar, while the coding sequence of open reading frame M35 is represented by an open arrow.
		P-radiolabeled probe was derived from the plasmid that contained the transposon and the M35 open reading frame sequence.
		In vitro and in vivo characterization of a murine cytomegalovirus with a transposon insertional mutation at open reading frame M43.
	jvi.asm.org /cgi/content/full/77/14/7746 (7392 words)

	Functional properties of a 16 kDa protein translated from an alternative open reading frame of the core-encoding ...
		Functional properties of a 16 kDa protein translated from an alternative open reading frame of the core-encoding genomic region of hepatitis C virus -- Basu et al.
		open reading frame of the HCV core-encoding genomic region.
		The +1 reading frame in the F protein is shown as an open box.
	vir.sgmjournals.org /cgi/content/full/85/8/2299 (4054 words)

	Murine Cytomegalovirus Open Reading Frame M27 Plays an Important Role in Growth and Virulence in Mice -- Abenes et al. ...
		The transposon sequence is shown as a solid bar, while the coding sequence of open reading frame M27 is represented by an open arrow.
		Construction of an MCMV mutant containing the transposon insertion at open reading frame M27 and the rescued virus that restored the mutation.
		Identification and characterization of a murine cytomegalovirus gene with homology to the UL25 open reading frame of human cytomegalovirus.
	jvi.asm.org /cgi/content/full/75/4/1697 (7108 words)

	Antigenic Domains of the Open Reading Frame 2-Encoded Protein of Hepatitis E Virus -- Khudyakov et al. 37 (9): 2863 -- ...
		The antigenic composition of the hepatitis E virus (HEV) protein encoded by open reading frame 2 (ORF2) was determined by
		Mapping of linear B cell epitopes on open reading frame 2- and 3-encoded proteins of hepatitis E virus using synthetic peptides.
		Comparative characterization of antigenic epitopes in the immunodominant region of the protein encoded by open reading frame 3 in Burmese and Mexican strains of hepatitis E virus.
	jcm.asm.org /cgi/content/full/37/9/2863 (5379 words)

	Efficiencies of translation in three reading frames of unusual non-ORF sequences isolated from phage display -- GOLDMAN ...
		The nucleotide sequence for the parental H10 segment, cloned in the 0-frame, is given in full, as are amino acid translations for all three reading frames below the nucleotide sequence.
		E-tag epitope (AAAGAP) delineates the reading frame of the fused
		UGA codons in the respective reading frames are indicated as well as the frame encoding the partial E-tag epitope.
	www.fasebj.org /cgi/content/full/14/3/603 (4916 words)

	AbOrygen - Intuitive bioinformatics
		Open Reading Frame (ORF) analysis enables you to find and display open reading frames bordered by potential start and stop codons.
		A double-click on the result in the project window will open a table with tabs for each frame.
		The result from Open Reading Frame analysis can be displayed in the editor and graphical windows.
	www.aborygen.com /products/biOpen/tools-for-biOpen/orf.php (76 words)

	Genetic Code (Site not responding. Last check: 2007-10-21)
		The start codon sets the reading frame: AUG is the first triplet, and subsequent triplets are read in the same reading frame.
		A reading frame between a start codon and an in-frame stop codon is called an open reading frame.
		The first AUG read in that direction sets the reading frame, and subsequent codons are read in frame, until the stop codon, UAA, is encountered.
	www.emunix.emich.edu /~rwinning/genetics/code3.htm (433 words)

	Restoration of Open Reading Frame Resulting from Skipping of an Exon with an Internal Deletion in the COL7A1 Gene
		Restoration of open reading frame resulting from exon skipping has been documented as a mechanism of rescuing an mRNA transcript containing mutations.
		In this study, we describe a mutation in a family with dystrophic epidermolysis bullosa consisting of a 16-bp deletion within exon 87 of the type VII collagen gene (COL7A1) and predicted to lead to a frameshift and downstream premature termination codon.
		Restoration of open reading frame by exon skipping represents a previously undescribed mechanism of action of intraexonic deletion mutations.
	info.med.yale.edu /labinvest/abstracts/98months/9812dec/1298_003.html (196 words)

	Inefficient Reinitiation Is Responsible for Upstream Open Reading Frame —Mediated Translational Repression of the ...
		The Lc uORF is represented as the open boxes, the downstream ORF as the fl boxes, scanning ribosomes (40S) as unfilled circles, and ribosomal subunits (40S and 60S) that are translating or have translated the uORF as stippled circles.
		Damiani, R.D., Jr., and Wessler, S.R. (1993) An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators.
		The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene
	www.plantcell.org /cgi/content/full/10/10/1733 (7296 words)

	Assignment 4 Part 1
		A single screen shot of the Blast output from ORF Finder showing the name of the best hits for the open reading frame 10 pts.
		An explanation of how you have insured that the complete eIF-2B coding region is in the same translation reading frame as the MCF protein.
		You must be sure that you identify the coding region of the eIF-2B subunit and design a way to clone it into the vector in the correct translation reading frame with MCP.
	udel.edu /~schmidtc/html/assignment_4_part_1.html (371 words)

	The T open reading frame of human immunodeficiency virus type 1.
		The T open reading frame of human immunodeficiency virus type 1.
		Sequence analysis of multiple isolates of the human immunodeficiency virus type 1 (HIV-1) reveals the existence of a conserved open reading frame, designated T, that partially overlaps the tat, rev, and vpu coding sequences.
		Here we show that in vitro translation of RNA derived from this region of the viral genome yields a 17 kDa fusion protein, the result of a minus one frameshift event in the overlap between the tat and T open reading frames.
	www.aegis.com /aidsline/1990/aug/M9080462.html (390 words)

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