オープンリーディングフレーム
WordNet
- without undue constriction as from e.g. tenseness or inhibition; "the clarity and resonance of an open tone"; "her natural and open response"
- a clear or unobstructed space or expanse of land or water; "finally broke out of the forest into the open" (同)clear
- information that has become public; "all the reports were out in the open"; "the facts had been brought to the surface" (同)surface
- a tournament in which both professionals and amateurs may play
- become available; "an opportunity opened up" (同)open_up
- become open; "The door opened" (同)open_up
- cause to open or to become open; "Mary opened the car door" (同)open_up
- make available; "This opens up new possibilities" (同)open_up
- start to operate or function or cause to start operating or functioning; "open a business" (同)open_up
- not sealed or having been unsealed; "the letter was already open"; "the opened package lay on the table" (同)opened
- used of mouth or eyes; "keep your eyes open"; "his mouth slightly opened" (同)opened
- not brought to a conclusion; subject to further thought; "an open question"; "our position on this bill is still undecided"; "our lawsuit is still undetermined" (同)undecided, undetermined, unresolved
- affording unobstructed entrance and exit; not shut or closed; "an open door"; "they left the door open" (同)unfastened
- (set theory) of an interval that contains neither of its endpoints
- accessible to all; "open season"; "an open economy"
- affording free passage or access; "open drains"; "the road is open to traffic"; "open ranks"
- begin or set in action, of meetings, speeches, recitals, etc.; "He opened the meeting with a long speech"
- display the contents of a file or start an application as on a computer
- have an opening or passage or outlet; "The bedrooms open into the hall"
- having no protecting cover or enclosure; "an open boat"; "an open fire"; "open sports cars"
- make the opening move; "Kasparov opened with a standard opening"
- not having been filled; "the job is still open"
- not requiring union membership; "an open shop employs nonunion workers"
- open to or in view of all; "an open protest"; "an open letter to the editor"
- ready for business; "the stores are open"
- enclose in a frame, as of a picture
- a framework that supports and protects a picture or a mirror; "the frame enhances but is not itself the subject of attention"; "the frame was much more valuable than the miror it held" (同)framing
- a single one of a series of still transparent pictures forming a cinema, television or video film
- one of the ten divisions into which bowling is divided
- the framework for a pair of eyeglasses
- a single drawing in a comic_strip
- an application that divides the users display into two or more windows that can be scrolled independently
- make up plans or basic details for; "frame a policy" (同)compose, draw_up
- enclose in or as if in a frame; "frame a picture" (同)frame in, border
- construct by fitting or uniting parts together (同)frame up
- formulate in a particular style or language; "I wouldnt put it that way"; "She cast her request in very polite language" (同)redact, cast, put, couch
- first or beginning; "the memorable opening bars of Beethovens Fifth"; "the plays opening scene"
- opportunity especially for employment or promotion; "there is an opening in the sales department"
- a recognized sequence of moves at the beginning of a game of chess; "he memorized all the important chess openings" (同)chess opening
- a vacant or unobstructed space that is man-made; "they left a small opening for the cat at the bottom of the door"
- becoming open or being made open; "the opening of his arms was the sign I was waiting for"
- the act of opening something; "the ray of light revealed his cautious opening of the door"
- an open or empty space in or between things; "there was a small opening between the trees"; "the explosion made a gap in the wall" (同)gap
- the first performance (as of a theatrical production); "the opening received good critical reviews" (同)opening_night, curtain raising
- a ceremony accompanying the start of some enterprise
- the initial part of the introduction; "the opening established the basic theme"
- the act of measuring with meters or similar instruments; "he has a job meter reading for the gas company" (同)meter reading
- a datum about some physical state that is presented to a user by a meter or similar instrument; "he could not believe the meter reading"; "the barometer gave clear indications of an approaching storm" (同)meter reading, indication
- written material intended to be read; "the teacher assigned new readings"; "he bought some reading material at the airport" (同)reading material
- a particular interpretation or performance; "on that reading it was an insult"; "he was famous for his reading of Mozart"
- the cognitive process of understanding a written linguistic message; "his main reading was detective stories"; "suggestions for further reading"
- provided with a frame; "there were framed snapshots of family and friends on her desk"
PrepTutorEJDIC
- …‘を'『開く』,開ける;…‘の'ふた(おおい)をとる / …‘を'『切り開いて作る』,開拓する;…‘を'全開通させる《+『名』+『up,』+『名』+『up』》 / …‘を'『広げる』《+『up』+(『out』)+『名,』+『名』+『up』(『out』)》 / …‘を'『始める』 / …‘を'開業する,開店する,開場する / (人に)〈心など〉‘を'打ち明ける,〈秘密など〉‘を'漏らす《+『名』+『to』+『名』》 / (新思想などに)〈心・目〉‘を'開く《+『名』+『to』+『名』》 / 〈戸などが〉『開く』,あく / 〈花・つぼみが〉開く《+『out』》 / 〈学校などが〉『始まる』;〈店などが〉開く / 〈道路などが〉開通する / (…に)向かって開いている,(…に)通じている《+『out』『on』(『upon,to,onto』)+『名』》 / 《副詞[句]を伴って》〈風景などが〉広がる,ひらける / 本を開く;(…)ページを開く《+『to』(《英》『at』)+『名』》 / (窓・口などが)『開いた』,開いている;(包みなどが)広げられて / (花が)咲いた / (店などが)『開いている』,開業している;(催し物が)『公開の』,だれでも入れる / 《名詞の前にのみ用いて》ふたのしてない,屋根のない,おおいのない / 広く開いた,さえぎるものがない / 公然の / 率直な,遠慮しない / さらされている,無防備の / 《補語にのみ用いて》(職・地位などが)空位の;(時間などが)あいている / (問題・議事などが)未解決の / 凍結しない,雪や霜の降らない;温和な / (漁・猟が)解禁の / (音声が)開口音の;開音節の / 《the~》戸外,野外 / 空き地;(樹木のない)開けた場所,平野
- 〈C〉(建造物・機械などの)『骨組み』《+『of』+『名』》 / 〈C〉(戸・窓などの)『枠』;額縁《+『of』+『名』》《複数形で》めがねの枠 / 〈C〉『体格』 / 〈C〉(…の)構造,体制《+『of』+『名』》 / 〈C〉(簡略な)温室,温床 / 〈C〉(ボーリングで)フレーム(10回で1ゲームを構成するその各回);各回の得点を記入する枠 / 〈C〉(映画のフイルムの)一こま / 《修飾語を伴って》《a~》気持ち,気分 / (組み合わせて)…‘を'『形作る』,組み立てる;(ある目的などに合うように)〈人・物〉‘を'作り上げる / 〈考え・構想など〉‘を'心に抱く / 〈絵など〉‘を'粋に入れる,縁どる / 〈言葉など〉‘を'言う / 《話》〈人〉‘に'ぬれぎぬを着せる
- 〈C〉(森・垣根・壁などの)空いている所;空き地;すき間,穴 / 〈C〉(物語・会議などの)始め,出だし,冒頭(beginning) / 〈C〉(…の地位の)空き,就職口《+『for』(『at, in』)+『名』》(vacant) / 〈C〉(劇などの)初演 / 〈U〉(…が)開くこと,あくこと《+『of』+『名』》 / 〈C〉(…の)よい機会,好機《+『for』+『名』》 / 初めの,開始の
- 〈U〉『読書』 / 〈U〉(読書によって得た)知識,学識 / 〈U〉朗読;〈C〉朗読会 / 〈U〉読みもの;《複数形で》(…の)選集,文選《+『from』+『名』》 / 〈C〉(劇の役・楽曲・文章などの)解釈《+『of』+『名』》 / 〈C〉(計器などの)示度 / 読書する / 読書用の
Wikipedia preview
出典(authority):フリー百科事典『ウィキペディア(Wikipedia)』「2016/04/28 12:31:01」(JST)
[Wiki en表示]
Sample sequence showing three different possible reading frames. Start codons are highlighted in purple, and stop codons are highlighted in red.
In molecular genetics, an open reading frame (ORF) is the part of a reading frame that has the potential to code for a protein or peptide. An ORF is a continuous stretch of codons that do not contain a stop codon (usually UAA, UAG or UGA).[1] An AUG codon within the ORF (not necessarily the first) may indicate where translation starts. The transcription termination site is located after the ORF, beyond the translation stop codon, because if transcription were to cease before the stop codon, an incomplete protein would be made during translation.[2] In eukaryotic genes with multiple exons, ORFs may span exons. These would be spliced into an ORF in the mRNA.
Contents
- 1 Biological significance
- 2 Six-frame translation
- 3 ORF finding tools
- 4 See also
- 5 References
- 6 External links
Biological significance
One common use of open reading frames is as one piece of evidence to assist in gene prediction. Long ORFs are often used, along with other evidence, to initially identify candidate protein coding regions in a DNA sequence.[3] The presence of an ORF does not necessarily mean that the region is ever translated. For example, in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons.[3] A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode a typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions.[3] By itself even a long open reading frame is not conclusive evidence for the presence of a gene.[3] On the other hand, it has been proven that some short ORFs (sORFs) that lack the classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides.[4]
Six-frame translation
Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames. The double helix of a DNA molecule has two anti-parallel strands so, with the two strands having three reading frames each, there are six possible frame translations.
Example of a six-frame translation
ORF finding tools
- 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 deduced amino acid sequence can be saved in various formats and searched against the sequence database using the BLAST server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software.(sequence analyser)
- ORF Investigator: ORF Investigator is a program which not only gives information about the coding and non coding sequences but also can perform pairwise global alignment of different gene/DNA regions sequences. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, and provides their locations in the sequence. The pairwise global alignment between the sequences makes it convenient to detect the different mutations, including single nucleotide polymorphism. Needleman and Wunsch algorithms are used for the gene alignment. The ORF Investigator is written in the portable Perl programming language, and is therefore available to users of all common operating systems.
- ORFPredictor: OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects.
See also
- Coding region
- Reading frame
- Sequerome - A sequence profiling tool that links each BLAST record to the NCBI ORF enabling complete ORF analysis of a BLAST report.
- Putative gene
References
- ^ "Open reading frame". U.S. National Library of Medicine. 2015-10-19. Retrieved 2015-10-22.
- ^ Slonczewski, Joan; John Watkins Foster (2009). Microbiology: An Evolving Science. New York: W.W. Norton & Co. ISBN 978-0-393-97857-5. OCLC 185042615.
- ^ a b c d Deonier, Richard; Simon Tavaré; Michael Waterman (2005). Computational Genome Analysis: an introduction. Springer-Verlag. p. 25. ISBN 0-387-98785-1.
- ^ Zanet, J.; Benrabah, E.; Li, T.; Pelissier-Monier, A.; Chanut-Delalande, H.; Ronsin, B.; Bellen, H. J.; Payre, F.; Plaza, S. (2015). "Pri sORF peptides induce selective proteasome-mediated protein processing". Science 349 (6254): 1356–1358. doi:10.1126/science.aac5677. ISSN 0036-8075.
External links
- ORF Investigator ORF finding and Gene alignment program developed by Vivek Dhar Dwivedi and Sarad Kumar Mishra.
- [1] - A web page where you can buy the book 'Gene Cloning and DNA analysis' by BROWN, T. A (2010)
- Translation and Open Reading Frames
- NCBI ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide sequences.
- ORF finder - A web based interactive tool for predicting and analysing ORFs from nucleotide sequences - hosted at bioinformatics.org
- hORFeome V5.1 - A web based interactive tool for CCSB Human ORFeome Collection
- ORF Marker - A free, fast and multi-platform desktop GUI tool for predicting and analyzing ORFs
- StarORF - A multi-platform, java based, GUI tool for predicting and analyzing ORFs and obtaining reverse complement sequence
- ORFPredictor - A webserver designed for ORF prediction and translation of a batch of EST or cDNA sequences
UpToDate Contents
全文を閲覧するには購読必要です。 To read the full text you will need to subscribe.
English Journal
- Identification, cDNA Cloning, and Characterization of Luteinizing Hormone Beta Subunit (lhb) Gene in Catla catla.
- Rather MA1, Bhat IA1, Sharma R1.
- Animal biotechnology.Anim Biotechnol.2016 Jul 2;27(3):148-56. doi: 10.1080/10495398.2016.1140055.
- Reproductive hormones play a significant role in the gonadal development and gametogenesis process of animals. In the present study luteinizing hormone beta, (lhb) subunit gene was cloned and characterized from the brain of Catla catla. The lhb full-length of cDNA sequence is 629 bp which consists o
- PMID 26980432
- Characterization of a dual-CRD galectin in the silkworm Bombyx mori.
- Rao XJ1, Wu P2, Shahzad T2, Liu S2, Chen L2, Yang YF2, Shi Q2, Yu XQ3.
- Developmental and comparative immunology.Dev Comp Immunol.2016 Jul;60:149-59. doi: 10.1016/j.dci.2016.03.001. Epub 2016 Mar 2.
- Galectins (S-type lectins) are an ancient family of lectins with the β-galactoside binding activity. In mammals, galectins play essential roles in many biological processes, such as development, immune homeostasis and tumor progression. However, few studies have been devoted to their functions in i
- PMID 26944801
- A novel ubiquitin-protein ligase E3 functions as a modulator of immune response against lipopolysaccharide in Pacific oyster, Crassostrea gigas.
- Cheng Q1, Wang H2, Jiang S2, Wang L3, Xin L2, Liu C2, Jia Z2, Song L4, Zhu B5.
- Developmental and comparative immunology.Dev Comp Immunol.2016 Jul;60:180-90. doi: 10.1016/j.dci.2016.02.027. Epub 2016 Feb 27.
- Ubiquitination is an important post-translational protein modification and plays a crucial role in various processes such as cell cycle, signal transduction, and transcriptional regulation. In the present study, a novel ubiquitin (Ub)-protein ligase E3 (designed as CgE3Rv1) was identified from Crass
- PMID 26928091
Japanese Journal
- cDNA cloning and characterization of a rhamnose-binding lectin SUL-I from the toxopneustid sea urchin Toxopneustes pileolus venom
- Hatakeyama Tomomitsu,Ichise Ayaka,Yonekura Tomokazu,Unno Hideaki,Goda Shuichiro,Nakagawa Hideyuki
- Toxicon 94, 8-15, 2015-02
- … The SUL-I gene contains an open reading frame of 927 nucleotides corresponding to 308 amino acid residues, including 24 residues of a putative signal sequence. …
- NAID 120005526604
- α-Amylase from Mon Thong durian (Durio zibethinus Murr. cv. Mon Thong)-nucleotide sequence analysis, cloning and expression
- , , [他], , , ,
- Plant Biotechnology 32(1), 1-10, 2015
- … DzAmy3) was successfully isolated and its gene contain a 2,679 base pair open reading frame, which encodes 892 amino acids with a calculated molecular mass of 93.7 kDa and an isoelectric point of 5.77. …
- NAID 130005061607
- Characterization of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan
- , , ,
- Journal of Veterinary Medical Science advpub(0), 2015
- … The fusion (F) protein gene of APMV/Shimane67 contained 1,638 nucleotides in a single open reading frame encoding a protein of 545 amino acids. …
- NAID 130005061025
Related Pictures
★リンクテーブル★
[★]
- 関
- coding、coding region、contagious ecthyma、contagious pustular dermatitis、open reading frame、protein coding region
- 同
- open reading frame
[★]
- 英
- coding region、open reading frame、ORF、coding
- 関
- オープンリーディングフレーム、コーディング、コード領域、符号化、読み取り枠、読み枠
[★]
- 関
- CDS、coding、open reading frame、ORF
[★]
- 英
- open reading frame, ORF
- 同
- 読み取り枠、翻訳領域、読み枠
[★]
- 関
- open reading frame、ORF
[★]
上流オープンリーディングフレーム
- 関
- uORF
[★]
- 読書。読書能力。朗読。朗読会。(議会の)読み会
- (書物による)学問研究。読書量。学識
- 判断、解釈。(脚本の)演出。(楽曲の)演奏。(写本・原稿などの)読み方(version)、異文
- 読物
- (晴雨計、温度計などの)示度、示数、記録
- 読書の/読書用の、読むための。読書する、本好きの。勤勉な
[★]
- 関
- aperture、liberal、opening、orificial
[★]
- 関
- aperture、open、orificial
[★]
[★]
- 関
- open reading frame