如何查找基因的序列(带图表)

1、如何查找基因序列？在Genbank中寻找目的基因1 根据文献搞reasearch肯定要读文献的，如果你曾经在文献中看到过你感兴趣的基因，而 且文中还提到了该基因在Genbank中的ID号，那就好办了，直接打开 httu：/www.ncbinlmnihgov ,在Search后的下拉框中选择Nucleotide,把 Genbank ID号输入GO前面的文本框中，点90”，就可以找到他了。举例说明，例如：在2003年JBC的文章(Conditional Knock-out of Integrin-linked Kinase Demonstrates an Essential Role in Pro

2、tein Kinase B/Akt Activation)中出现了“calreticulin (GenBank accession number gi 16151096)", 那么把鋼6151096”输入GO前面的文本框中，点90”，就可以找到该基因了(当 然包括基因序列等相关信息)。NCBINational Center for Biotedmology InfonnationNational Lihiary oI MedicineNalional InsHiules of HealthPubMed All DalabasesBLASTOMIMBooksTaxBrowser Str

3、uctureSearch NucleotidePubMedProteinf for ,16151096SITE叽|心. . . Nucleotide AlphabetnResourceoes NCBI do?Hot SpotsAbout MAn introdiNCBIGeriBanSequence submission support and softwareStructureGenomeBooksCancerChromosomesConserved Domains3D DomainsGeneGenome Project LI IC7 UOLLCI88 as a national resour

4、ce for biology information. NCBI creates abases, conducts research in Dnal biology, develops software nalyzing genome data, and ites biomedical inforrnation - all for understanding of molecular Assembly Archive Clusters of orthologous groupsprocesses affecting human health and disease. Ivlon. Coffee

5、 Break, Genes & Disease, NCBI Handbook Electronic PCR在出现了检索结果界面（下图）后，直接点击红箭头所指的AY047586就可以 看到基因的相关信息。2 NCBIHi for |16151096PubMedNuoleotideProteinNucleotideMy NCBIElAll Database?©enomeStru ctureFMCTaxonomyBooks：Search | NucleotideAbout EntrezEn trez NucleotideHelp | FAQEntrez ToolsCheck seq

6、uence revision historyLimitsPreview/lndexDisplay I SummaryAll：1bacteria: 0| Clear i gave SearchDetails习Show120 xllSendtoHistury | ClipbuandmRNA： 1 加陶：0 jaShow only records from; CoreKluclEcitidE (1), EST (o)丿 G5S (o). fWhat's this?lF LJVY047586 Reportssapiens calreticulin (CALK) mRlTA, complete

7、cdsgi|1615W96|gb|AY047586.1|1615W96Links这里需要指岀一下，在显示基因的页面右侧有一个Link,点击后出现一个小菜单，里面 是与该基因相关的链接，很有用的。NCBlJNucleotideMyNCBIAll DatabasesPubMedNucleMide2Genome販创 rePMCSearch I Nucleotidejdfor(16161096Go ClearLimitsvr l丫)Preview/lndex History Clipboard DetailsDisplay I SummaryHl Show|20| Send toT axonomu B

8、wksLinks 1About EntrezEntrez NucleotideHelp | FAQbacteria: 0mRNA: 1RefSeq: 0Show only records from: CorehJucleotide (1), EST (o), GSG (o).WFEntrezToolsChecksequencerevision history厂 1: AY04方務 ReportsHomo sapiens calreticulin (CALS) mRNA, complete cds gi|16151096|gb|AY047586.1|16151096iks点击AY047586后出

9、现的界面如下:% NCBIve5.Nucleotide(Sian Ini IReqisterlPubMcdNucleotideProteinCcnomeStructjrePMCT dzonomyOMIMBqoIoSearch | NucleotidedforlGo| Clear |LimitsPreview/iridexHistoryClipboardDetailsDisplay |GenBank 1 Show 15Send to 二J Hide:厂 Sequence 厂 Les set featuresRange: fiom leginto |end厂 Reverse completrien

10、ted stiand Features: jjJRefresh厂 1: AY047586. Reports Homo sapiens calZgi：16151096)LinksFE?arire?s SequenceLOCUSDEFIMITIONAY0475861402 bp niRNA linear PRI 15-OCT-2001Homo SGpiena calreticulin (CALR) mRNA, coirplete cds ACCESSIONVERSIONKEYWORDSSOURCEORGANISMAY047586AY047586.1 GI:16151096Homo sapiens

11、(human)Homo s&piensREFERENCEAUTHORSTITLEJOURNALFEATURESEuKaryota; Metazoa; Chordata; craniaca; vertenraca; Euceieostomi; Marrtrralia; Eutheria; Euarchontoglires; Priirates; Haplorrhini; Catarrhini; Horninidae; Horno1 (bases 1 to 1402)Liuz J , Pengz X , Yuan；J and Qiangz BDirect SubmissionSubxrii

12、tted (O6-JUL-2OO1) Department of Biochewistry, Institute of Bcnic Medical Science； Chinese Academy of Medical Sciences, S Dong Dan San Tiao, Beijing 100005, PR ChinaLocation/Qualifierssource11402/orcanisxti=frHorno sapiensrr/rno l_type=rririPI>IA,r最下面就是核酸序列（ORIGIN后面）mat netitideEDEEDEEDKEEDEEEDyP

13、GQRKDEL"54593/gene=rrCALRrr/ product= rrvas ostat inrr/note= rrderived from calreticulin. post-translational cleavagerrORIGIN16112118124130136142148154160166172178184190196110211081114112Q1126113211381ctgccggagg tatccgtgcc tcaaggagca agtcagattt ataaaggttt ctttcagcaa tcgactgtgg acggagactc aggttc

14、atgt gcaaggatga aggtgaagat tgccacccaa ccaagatcga ctgaccctga ccccagtgat cagattacaa ccagtatcta ctggcaccat gcaacgagac aggagcagag aggacaagga aagatgagga cagggctgga ctgtgagactgtcgttttaa gctgctgctc gtttctggac tggcattccaaaggccag gggcggctat agaatacaac catcttcaac tgagttt.aca tgacaacagc gaagaraaag tgarcccaca t

15、gctaagaag tcagaacccr gggcacrrgg tgcctatgatgtggggcgta gcttaaggag ggatgatgag ggaagatgtc ctgaggcctg cgagaacttLagggcccgcg ggcctcctcg ggagacgggt gttctcagtt caggatgcac acgctggtgg gtgaagctgt ateatgtttg tacaagggca cacctgtaca caggtggagt gatcctgatg gactccaagc cccgaggact gagtacaagg arccacccag aactttggcg ttcctc

16、atca acaaaggcag gaggaagaag gacaaagatg cccggccagg agcgctcctg cacgttgccgcc gcctggccgt ggacttcccg ccggcaagtt gcttttatgc tgcagttcac ttcct aat ag* gt c c c gac at agaacgtgct cactgaXtgt ccggct c c 11 etteaaaacc ctgaggactg gggatgaaga gtgagtggaa aaattgacaa tgctgggcct ccaacgatga cagagaaaca acaagaaacg aggatga

17、gga ccaaggacga ccgcagagctf olloLiing ccctcggccc cgccgagrcct etggategraa ctacggtgac tctgtcggcc gg七gaaacat ttt crgaccag ctgtggccct gatcaacaag gcggccagac ggaagaegat ggaagact-gg ggacaagccc gatggaegga gccccggcag ccccgagt-at- gg盘ccccugg ggcavaeget aatgaaggac caaagaggag ggatgaggag getgtagaga tgccgcgccagcca

18、tgctgc grccgtctact tecaaacaca gaggagaaag agtttegage gagcagaaca acagacatgc ggcaccaaga gacatccgtt aacacctatg tgggacttcc gat-gage ggg gagcatat.cc gagt-gggaac at-cgacaacc t-ct-cccgat-c caggtcaagt gaggagtttg aaacaggacg gaggaggcag gacaaggagg ggcctgcctc aat. aat g 匚c 匸Disclaimer! Write to the Help DeskNCBI

19、INLMINIH如果你只想获得序列（例如去设计PCR引物的时候），那就可以选择FASTA,这样 就得到了FASTA格式的序列文件，没有其他数字和格式的干扰。2 NCBINucleotideProteinGenorrii?5NucleotidePubMedStructurePMCTaxonomyOMMBooksSearch I Nucleotidez forGo ClearDisplayGenBankLimitsPreview/lndexShow(53|SendtoClipboardDetailsHistoryqueuee Lesser featuresGenBankRange： iGenBan

20、k(Full) 些里XMLReverse complemented strand Features: +1 Refreshn： aLOCUS DEF INI! ACCESS VERSIOKTinySeq XMLASN.1XMLGraphGl ListBriefNummaryto |endsapiens calr.gi:161510961402 bp mPNA linear PRI 15-OCT-2001 Lens calreticulin. (CALR) kiPMAz coraplete cds.1 GI:16151096LinksKEYWORDSSOURCEORGANISMHoino sap

21、iens (huinan.)Hcoto日api已n日Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;这就是FASTA格式的序列:Search | NucleotideGo | Clmar |LimitsPreview/lndexHistoryClipboardD已怕ilsDisplay FAST.AFRange： frotti beginShow f531 Send to to |沁'厂Revetse cotttpkmented strandRefresh厂 1: AY047刃6 Reports Homo

22、 sapiens calr.gi:16151096Links>gi|16151096|gb|AY047586.1| Homo sapiens calreticulin (CALRJ wRNA complete cds CTGCCGGAGGGTCGTTTTUAGGGCCCGCGCGTTGCCGCCCCCTCGGCCCGCCATGCTGCTATCCGTGCCGCTGCTGCTCGGCCTCCTCGGCCTGGCCGTCGCCGTlGCCTGCCGTCTACTTCAAGGAGCAGTTTCTGGTlCGGAGACGGGTGGACTTCCCGCTGGATCGA1TCCAAACACAAGTCAGA

23、TTTTGGCAA1TTCGTTCTCAGTTCCGGCAAGTTCTACGGTCACGAGGAGAAAGATAAAGGTTTCCAGACAAGCCAGGATGCACGCTTTTATGCTCTGTCGGCCAGTTTCGAGCCTTTCAGCAACAAAGGCCAGACGCTGGTGGTGC1GTTCACGGTGAA1CATGAGCAGAACATCGACTGTGGGGGCGGCTATGTGAAGCTGTTTCCTAATAGTTTGGACCAGACAGACATGCACGGAGACTCAGAATACAACATCATGTTTGGTCCCGACATCTGTGGCCCTGGCACCAAGAAGGTTCA

24、TGTCATCTTCAACTACAAGGGCAAGA1CGTGCTGATCAACAAGGAC1TCCGTTGCA1GG1TG1TG1GTTTAC1CACCTGTACACACTCATTGTGCGGCCAGACAACACCTATGAGGTGAAGATTGACAACAGCCAGGTGGAGTCCGGCTCCTTGGAAGACGATTGGGACTTCCTGCCACCCAAGAAGATAAxGGATCCTGATGCTTCAAAACC练习1:请在Entrez的蛋口质数据库中杳找,gi (NCBI GenBank ID)为13375618所登录的蛋白质的名称，并且回答该蛋白含 有什么样的特殊结构域(至少一个

25、)？如何查找基因序列？在Genbank中寻找目的基因2.根据已经获得的基因的相关信息进行查找如果只是知道基因的名字，怎么查序列呢？还是举例说明，比如我想做的基因名称是人 的VEGF基因，那么怎么在Genbank中找到它呢？在search后面的下拉框中选择Gene,然后在中间的文本框中输入基因名称 “VEGF”，点击GO.2 NCBINational Center for Biotechnology InformationNational library of MedicineNational InMUuks of IleiillhPubMed All DatabasesBLASTOMIMBoo

26、ksTaxBrowser StructureSearch |AII Databases (AlTbatabases V/eb Sitewl-HiProteinNucleoiideStructureGenomeBooksCancerChromosomes |EmlBOUCcinGr/d Domains D DomainsGenome Project gensat 閒JjGEO Profiles gGEO Datasets in®gBHomoloGene J Journals ISaffiMBMeSHNLM CatalogOMIAAbout N An introdi NCBIJ for

27、|VEGFoes NCBI dHot Spotsin 1988 as a national resource for biology information, NCBI creates abases, conducts research in cnal biology. develops sofhA'are lalyzing gencm© data, and ites biomedical information - sll for inderstanding of molecular ;affecting human health andIfliole Genome Ass

28、ociation (WGA) resource ecearcherc with accede to genotype and 1 phenotype information that will help the link between genes and disease Fot maxion, click here to see The the WGA Assembly Archive Clusters of orthologous groups Coffee Break. GoriGG & Disease, NCBI Handbook Electronic PCR Entraz H

29、ome Entrez Tools Gene expression omnibus (GEO)NCBIAll DatabusSearch | GeneEntrez GeneHomeAboutFAQHelpGene HandbookStatistics Downloads (FTP)Mailing ListsGeneRefSeqFeedbackHelp DeskCorrectionsAb cut GeneRIFsRelated SitesToo much!Entrez GenePubM«dProteinGmoe©Siruclu 4PMCMVNCBIISian im Reais沦

30、rlDo ofcOMIM三I for |VEGF| Go | Cl 阳r | Save SearchLimits Rreyjew/lnctex: History CliptioanJD 巳 l$Display SummaryAll： 698T Show|20 jjlSendtojCurrent On" 685 Gedes GErmE$: 659 SNP GgneView: 442*厂 1： VEGFA厂2:Items 1 20 of 698Page | Tof 35 NextLinksOfficial Symbol; VEGFA and Name; vascular endothel

31、ial growth factor AsapiensOther Alices: MOC70609. VEGF, VEGF-A, VPFOther Desigiitions: vascular permeability factorCliLomosoine: 6, Location: 6pl2RUM! 192240GeneW: 7422LinksPvtPDGf- and VEGF-receptor related Drosophila eianoaslerOthw Alixx： DmeLCG8222, CG8222, CT24332, DmVEGFR, PVR, VEGFR, VEGFR-A,

32、UGR1, Vegfr-b, Veg-c, stai Other Designations： PDGF and VEGF-receptor related CG8222-PA, isofrm A PDGF- and VEGF-receptor related CG2222 PB, isoform B, PDGF- and VEGF-receptor related CG8222-PC. isoform C; PDGF- and VEGF-receptor related CG8222PD, isofdrm D, PDGF- and VEGF-receptor related CG8222-PE

33、, isofbrm E; PDGF- and VEGF-receptor related CG8222-PF, isoform F CT TCCT 巾 nQT?C点击箭头所指的Limits,2 NCBIEntrez GeneAll DatabasesPubMedNucleo-tideProieinGenomeStructurePMCT axq岡 Cl却 |s釣e SearchI Search (Gene3) for |VEGFP LimitsPreview/lndexHistoryCIlpDosrilDetailsEntrez GeneHomeAboutFAQHelpGene Handbook

34、 Statistics Downloads(FTP)All: 698Current Only: 685厂,Genes Genomes' 659厂SNP GeneView: 442Display SummaryItems 1 - 20 of 6983 滥。討2（ 帥工）厂 1: VEGFAMailing ListsGeneRefSeqOfficial Symbol： VEGFA and Name: vascular endotheEal growth factor A Homo sapiens Orher.iases: MGC70609, VEGF, VEGF-A, VPFOther D

35、esignations: vascular permeability fectorChromosome; 6; Location; 6pl2NUM: 192240GenelD： 7422FeedbackHelp DeskCorrections About GeneRIFs厂 2: PvrPDGF- and VEGP-receptor related Drosophila melaogasterOther .AJiasos: DmEl_CG8222, CG8222, CT24332, DmVEGFR, PVK, VEGFR, VEGFR扎 VcOther Designations: PDGF-

36、and VEGF-receptc-r related CG8222-PA, isoform A, PDGF- and PB, isoform B; PDGF- and VEGF-receptor related CG8222PC, isofbrm C; PDGF and VEGFr isofbim D; PDGF- and VEGF-receptor related CG2222-PE, isofbrm E; PDGF and "7EGF-recep出现了如下界面Limits的意思其实就是高级检索，你可以在这里对检索词进行很多限制，这样能 大大精简查询结果。在Limits这个界面，先

37、选择查询的限定范围。人的VEGF基因，那就开始选择: 先选Gene name（基因名称）；然后再选择Limit by Taxonomy （生物分类限定） 中的Homo sapiens （人类），然后再点击“GO”E NCBIEntrez GeneAll DatabasesPubMedNucleotideProteinGenomePMCTaxonomy| Search | GeneZJ for |VEGFI Limits Preview/lndex History f Clipboard f DetailsEntrez GeneHemeAboutFAQHelpGene Handbook Stat

38、istics Downloads(FTP) To apply your query to all fields, leave this page uncharged. Eoclean epeetsr AND, OR, NOT must be in upper case. To limit your search to a specific field, select:Structure| Go Clear |Mailing ListsGeneRefS eqFeedbackHelp DeskCorrections About GeneREFsRelated sitesBLASTEntrez Ge

39、nomeGenome ProjectsExclihichiAll FieldsAll Fields ChromosomeCreation Date Data Discontinued Default map ：ocation Disease/Phenotype Domain Name EC；RN Number FilteriGene NameInferredKnownLimit by Taxonomy：in square brackets, e.g. aaatitle. y checking boxes below.r ModelLiinit by RefSeq Status:厂 Plasti

40、dsMitochondriar Predicted厂 Pseudogenes厂 ReSeqs厂NEWPlastridsPlastids厂 RefSeqsReviewed厂 Mammalia厂 Bostaurus厂 Cards fairiliaris厂 Pan troglodytes厂 Rattus ncrvegicus厂 Mon-mammalian vertebratesPtovicional“ Homo sapiensSus scrofa厂 Mus muscuiusL rr /; fol直接点击基因名称"VEGFA”就可以看到有关基因的信息了。需要指出的是，在Genbank中，基因

41、有很多别名（Aliases）,和Genbank中记录的 名称有可能不一致比如在这里，VEGFA是Genbank中记录的基因名称，而它还有很 多别名，比如MGC70609, VEGF （这就是我们要找的基因名称）,VEGF-A, VPF； 还有，在这里可以看到该基因在染色体上的位置2 NCBIEntrez GeneMvNCBISign In ReqisterAll DatabasesPubMedNucleotideProteinGenomePMC Search | GeneZJ for |VEGFSave SearchStru ctureTaxonomyBooksOMIMF LimitsYPre

42、view/lndexHistory 7 Clipboard DetailsField: Gene Name, Limits: Homo sapiensEntrez GeneDisplay I SummaryZJ Show 120 2j|SendtoHomeAb outFAQHelpGene Handbook Statistics Downloads (FTP)Mailing ListsGen巳2佑刚Current Only: 1Genes Genomes 1r 1： VEGFASNP GeneView: 1Official Symbol： VEGFA and Name： vascular en

43、dotheEal growth fhctor A Homo sapiens Other .Aliases: MGC70609, VEGF, VEGF-A, WFOther Designations: vascular permeability factorCluomosomt: 6; Location: 6pl2MHI： 192240GeneH): 7422Links下面就是点击VEGFA后出现的界面:下面就是点击VEGFA后出现的界面:2 NCBIEntrez Gene下面就是点击VEGFA后出现的界面:All DatabasesPubMedNucleotideP rote i nGenom

44、eStru cturePMC1SearchGeneVfor7422 mdnn(Limits/ 、 Preview/lndexHistory | Clipboard |DetailsDisplayFull Report2Show20 7Sort by RelevanceSend toAll：1Current Only; 1Z3rGenes Genomes: 1'SNP GeneView: 1 1: VEGFA vascular endothelial growth factor A Homo sapiens 4GenelD: 7422updated 14-May-200SSummary&

45、lt; ?Official Symbol VEGFAprovided by HGhJCOfficial Full Name vascular endothelial growth factor Aprovided by HGNCPrimary source HGNC: 12680Locus tag RP1-261G23.1See related Ensembl: ENSG00000112715; HPRD: 01889;MIM;192240Gene type protein codingRpfRpnGenomic regions. transceipts. and productsGo to

46、reference seQuence detailsNC.0000O6.JL043845931 »5"卜NP001020537>2<4precursorNP0033G7*4 iisoFo" b precursor CCDS407*lNP0 (HO 20538.2isoomCprecursorNP001020539*2isoomdprecursorNP00102892841QprecursorNP001020540<2eprecursorNP001020541<2isoorvAfprecursor43862202 i y再往下看，nJ以看至U

47、Genomic regions, transcripts, and products,这里显示 了该基因在基因组中的位置，以及转录本的生成情况就看见了目的基因的mRNA的链接(如NM_001025366.1)和蛋白质的链接 (如N P_001020537.2)UniSTSAceViewCCDSEvidence ViewerGDBHGMDHGNCHPRDKEGG ModelMaker PharmGKB Reactome Un iGene LinkOut Entrez Gene InfoNCBI Reference Sequences (RefSeq)RefSeqs maintained inde

48、pendently of An no tated GenomesThese reference sequences exist independently of genome builds ExplainnrRNA and Proteins)1.NMLJ3CH0253e&l->NP_00：LI2D5372 vascular endothelial growth factor isoform a precursor/Description Transcript Variant: This variant (1) represents the longest transcript a

49、nd 亡ncodes the longest isoform(6 also referred to as VEGF206). This variant initiates translation from four non-AUG (CUG) sites and also from a downstream in-frame AUGSource sequence(s) BC058855.BC06552乙CR614384,S85192<2(100135Location :230 - 2 13Blast Score:2S4Conserved Domains (1) summa"PD

50、GF; Platelet-deriued and vascular endo thwliwl grow th fartoKS (PDGFj VEGF) family domain; PDGF is -3 potent actiutor for cells of mesenchymal origin; PD«3F-A and PDGF-B forrvb AA and BB homodimers and A& heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogansis with a uniq

51、ue specificity for vascular endothelial(:色Ils; VEGF forms homodirners and exists in 4 different iofcrms; overalb the VEGF monomer resembles that of PDGF丿 but its Nterminal segmen t iw helical rat her than «ext ended; the cysteine knot motif is a common feature of this domainNMLJCH02536?：lf MP0C

52、I：L(2(5382 vascular endothelial growth factor AJsoform c ) precursorDescription Transcript Variant: This variant (3) uses an altern«ate in-frarne splice site in the 3' coding region compared to variant lj resulting in a shorter protein (isoform c,2.LOCUSDEFINITIONACCESSIONVERSIONKEYWORDS SO

53、URCEOR GM ISMREFERENCEa iTHPurs nc如果想找的基因是第一个序列即isoform a,就可以点击NM_001025366.1, 得到如下界面：2 NCBIw肾w左Nucleotide :PubMedNucleotideProieinCenomeStructureFMCT axonoSearch 1 NucleotidezlforT|lGi)j Clear |LimitsPreview/lndexHistory:GlipboatdDisplay | Gen BankT Showf5 jdlSendl° 二1Hide:厂 SequenceLesser featuresRange: from |beginto lend厂 Reverse comple±nented strand