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彻底搞清楚promoter,exon,intron,andUTR•启动子:RNA聚合酶特异性识别和结合的DNA序列。•promoter自然不属于intron和Exon的任何一个，属于noncodingsequence。•noncodingRNA是现在研究的热点之一。我们常见的MiRNA,SiRNA,antisenseRNAtech,这些都是属于ncRNA的范围。只要你在进一步问下：这些RNA是哪里来的？你就知道部分答案，跟那些看似跟编码蛋白没有关系的DNA序列有关系。这部分DNA有个统称就junkDNA，垃圾ＤＮＡ或者冗余DNA，他们编码的RNA就属于ncRNA.RNAi就是迄今最经典的ncRNA功能典范。•AnexonisasequenceofDNAthatisexpressed(transcribed)intoRNAandthenoften,butwithmanynoteworthyexceptions[1],translatedintoprotein.Adjacentexonsmaybeseparatedbyanintron,whichislaterremovedfromtheRNAtranscriptviathesplicingmechanism.(FromWikipedia)•UTR（UntranslatedRegions)即非翻译区，是信使RNA（mRNA）分子两端的非编码片段。•5'-UTR从mRNA起点的甲基化鸟嘌呤核苷酸帽延伸至AUG起始密码子，3'-UTR从编码区末端的终止密码子延伸至多聚A尾巴（Poly-A）的末端。转录（Transcription）是遗传信息从DNA到RNA的转移。即以双链DNA中的一条链为模板，以ATP、CTP、GTP和UTP4种核苷三磷酸为原料，在RNA聚合酶催化下合成RNA的过程。PromotergeneCDSDNA：PremRNA：CDSCDSMaturemRNA：CDSCDSCDSPolyAXXXXXXAUGXXXX………………..…....UGAXXXXXXXXXXAAUAAAAAAAAAAstartcodon:AUGstopcodons：UGA,UAG,UAA5'UTR3'UTRPolyAATGXXXXXXXXX…..XXXXXXXTGAORF(openreadingframe)cDNA：TSS:transcriptionstartsiteCDS(Codingsequence)PolyA是后来加上去的。Gene里没有cDNA中有。5'UTR3'UTR3'UTR5'UTRcapIntron1Exon1Exon2Intron2Exon3Grayarea:5'UTR(1-45)TSS:transcriptionstartsiteGreenarea:intronIntron1(73-1216)CDS(46-72)Startcodon:ATG5'UTR3'UTRExon1Intron1Example1IL17Ainterleukin17A[Homosapiens]Location:6p12Sequence:Chromosome:6;NC_000006.11(52051185..52055436)gene1..4252mRNAjoin(1..72,1217..1419,2669..4252)CDSjoin(46..72,1217..1419,2669..2906)Exon2Intron2Exon3Example1IL17Ainterleukin17A[Homosapiens]Location:6p12Sequence:Chromosome:6;NC_000006.11(52051185..52055436)gene1..4252mRNAjoin(1..72,1217..1419,2669..4252)CDSjoin(46..72,1217..1419,2669..2906)Grayarea:3'UTR(2907-4252)Greenarea:intronIntron2(1420-2668)CDS(2669-4252)Endcodon:TAAExample2:Cx3cr1chemokine(C-X3-C)receptor1[Musmusculus]Location:9F4;9Sequence:Chromosome:9;NC_000075.6(120048693..120068282,complement)gene1..19590mRNAjoin(1..78,15940..19590)CDS15949..17013Grayarea:5'UTR(15940-15948)inexon2Greenarea:Intron1(79-15939)CDS(15949-17013)Startcodon:ATGEndcodon:TGA5'UTR3'UTRExon1Intron1互补链上Grayarea:3'UTR(17014-19590)inexon2Exon2常见问题：问：Promoter在DNA序列中是算内含子还是外显子？答：都不是。属于noncodingsequence。问：UTR在DNA序列中是算内含子还是外显子？答：外显子。问：起始密码子ATG在gene的哪个位置？答：外显子内，CDS以ATG开始。问：每个基因之间都有一定的间隔序列，这些基因间的间隔序列应该不属于内含子吧？答：是的。属于noncodingsequence。问：如何寻找启动子区域和预测转录因子结合位点？答：见我的帖子