生物信息上机作业Word文档格式.docx
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生物信息上机作业Word文档格式.docx
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复旦大学理论生物中心:
http:
//tlife.fudan,
天津大学生物信息中心:
上海生物信息技术研究中心:
//www.scbit.org/index.php
3、了解一些生物论坛中有关生物信息学的部分。
如:
生物秀、生物谷生物信息学
生物秀
生物谷
4、利用NCBI的Entrenz查询系统索文献和核酸或蛋白质序列。
(phyA)并对照所学复习各字段的含义。
PU4_plate12_D18PU4PrunuspersicacDNAsimilartoidenticaltophotoreceptorPHYA(PHYA)gene[Prunuspersica],mRNAsequence
GenBank:
DY649091.1
GenBankFASTA
IDENTIFIERSdbESTId:
37221463ESTname:
PU4_plate12_D18GenBankAcc:
DY649091GenBankgi:
89493297CLONEINFOSource:
HermanSilva(hsilva@unab.cl)Insertlength:
631DNAtype:
cDNAPRIMERSPCRforward:
GTAAAACGACGGCCAGTAGAPCRbackward:
TAGGAAACAGCTATGACCATSequencing:
M13FWD=GTAAAACGACGGCCAGTPolyATail:
UnknownSEQUENCECTCAGGCTTCGCGGTTCCTATTTATGAAGAATAAGGTCCGAATGATTGTTGACTGTTGTGCAAAACAGGTGAAGGTGCTTCAAGATGAGAAGCTTCCATTTGATCTCACATTGTGCGGTTCAACCCTAAGATCCCCACATAGTTGCCATTTACAATATATGAAGAATATGGAATCTATTGCATCTCTTGTTATGGCAGTAGTGGTTAACGAGGGGGATGATGAGGTAGCCAGTCCTGATTCTGTTCAGCCTCAAAAAAGAAAGAGACTTTGGGGTTTGGTAGTATGTCATAATACAAGTCCAAGATTTGTTCCTTTCCCTCTCAGGTATGCCTGTGAGTTTCTAGCTCAAGTATTTGCCATCCATGTCAATAAGGAAATAGAGTTGGAAGATCAGATGGTTGAGAAGAACATCCTGCGCACCCAAACGCTGTTGTGTGATATGTTGTTACGAGATGCACCCTTGGGTATTGTGTCACAGAGCCCTAATATTATGGATCTAGTGAAATGTGATGGAGCTGCCCTATTATACAAGAGCAAGATATGGAGACTTGGCATAACTCCAAGTGACTTCCAGCTTCATGACATAGCCTCGTGGCTCGCTGAGTACCATATGGATTCCACAGGTTTGAGEntryCreated:
Mar132006LastUpdated:
Mar132006COMMENTSConsortium:
ChileanFunctionalGenomicsinPrunuspersica.ThemembersofthisConsortiumareUniversityofChile,InstitutodeInvestigacionesAgropecuarias(INIA),AsociaciondeExportadores(ASOEX),FundacionparaelDesarrolloFruticola(FDF)andFundaconChile.ThisConsortiumwasformedaspartoftheChileanGenomeInitiativeandsupportedbyFDI-CORFO(FDIG02P1001)PUTATIVEIDAssignedbysubmitteridenticaltophotoreceptorPHYA(PHYA)gene[Prunuspersica]LIBRARYLibName:
LIBEST_019257PU4Organism:
PrunuspersicaCultivar:
O`HenryOrgan:
FruitTissuetype:
MesocarpLabhost:
DH10BE.coliVector:
pDNR-1rR.Site1:
XhoIR.Site2:
SmaISUBMITTERName:
HermanSilvaLab:
CenterofPlantBiotechnologyInstitution:
AndresBelloUniversityAddress:
Av.Republica217,837-0146Santiago,ChileTel:
56-2-6618648Fax:
56-2-6615832E-mail:
hsilva@unab.clCITATIONSTitle:
ESTssequencesisolatedfrompeachesAuthors:
Silva,H.,Loira,N.,Vizoso,P.,Latorre,M.,Baeza-Yates,R.,Cambiazo,V.,Campos-Vargas,R.,Gonzalez,M.,Orellana,A.,Retamales,J.,Meisel,L.Year:
2005Status:
Unpublished
5、中科院计算所智能信息处理重点上机室生物信息学:
6、找到编码人(zwintI)基因的核酸序列编号。
NM_001005413
二核酸及蛋白质序列的比对
一、上机内容
利用检索出的蛋白质和核酸序列进行序列比对并进行分子进化树分析。
二、作业
1、绘制分子进化树,并标明各个物种phyA蛋白之间的序列相似性。
2、根据你所学生物分类的知识,试解释该分子进化树的合理性
①拟南芥:
植物界种子植物门被子植物门双子叶植物纲十字花目十字花科鼠耳芥属(拟南芥属)
②大豆:
植物界种子植物门被子植物亚门双子叶植物纲豆目蝶形花科大豆属
③血红肉果兰:
植物界种子植物门被子植物亚门百合纲百合目兰科树兰亚科肉果兰属
④水稻:
植物界种子植物门被子植物亚门单子叶植物纲禾本目禾本科稻属
⑤玉米:
植物界种子植物门被子植物亚门单子叶植物纲禾本目禾本科玉米属
⑥高粱:
植物界种子植物门被子植物亚门单子叶植物纲禾本目禾本科高粱属
经过对比可得下列同源性关系
高粱
玉米
水稻
拟南芥
大豆
血红肉果兰
与前面的同源树对比基本相似,说明软件分析结果与实际相符
3、找出一条可能的保守序列(多条蛋白共同的氨基酸序列)。
最长的保守序列:
kliqpfgcllaldek
三核酸序列分析
1、使用DNAstar进行核酸基本信息分析
2、ORF分析
1、记录人(zwintI)基因序列的序列组成
2、记录人(zwintI)基因序列最长的ORF的起止区间。
使用Editseq软件进行查找ORF序列
LOCUSNM_0010054131546bpmRNAlinearPRI12-FEB-2014DEFINITIONHomosapiensZW10interactingkinetochoreprotein(ZWINT),transcriptvariant3,mRNA.ACCESSIONNM_001005413VERSIONNM_001005413.1GI:
53729319KEYWORDSRefSeq.SOURCEHomosapiens(human)ORGANISMHomosapiensEukaryota;
Metazoa;
Chordata;
Craniata;
Vertebrata;
Euteleostomi;
Mammalia;
Eutheria;
Euarchontoglires;
Primates;
Haplorrhini;
Catarrhini;
Hominidae;
Homo.REFERENCE1(bases1to1546)AUTHORSEndoH,IkedaK,UranoT,Horie-InoueKandInoueS.TITLETerf/TRIM17stimulatesdegradationofkinetochoreproteinZWINTandregulatescellproliferationJOURNALJ.Biochem.151
(2),139-144(2012)PUBMED22023800REMARKGeneRIF:
theE3ubiquitinligaseterfcausesproteindegradationofZWINTandnegativelyregulatescellproliferationREFERENCE2(bases1to1546)AUTHORSKasuboskiJM,BaderJR,VaughanPS,TauhataSB,WindingM,MorrisseyMA,JoyceMV,BoggessW,VosL,ChanGK,HinchcliffeEHandVaughanKT.TITLEZwint-1isanovelAuroraBsubstraterequiredfortheassemblyofadynein-bindingplatformonkinetochoresJOURNALMol.Biol.Cell22(18),3318-3330(2011)PUBMED21775627REMARKGeneRIF:
Thesestudiesidentifyzwint-1asanovelAurBsubstraterequiredforkinetochoreassemblyandforproperspindleassemblycheckpointsilencingatmetaphaseREFERENCE3(bases1to1546)AUTHORSVosLJ,FamulskiJKandChanGK.TITLEhZwint-1bridgestheinnerandouterkinetochore:
identificationofthekinetochorelocalizationdomainandthehZw10-interactiondomainJOURNALBiochem.J.436
(1),157-168(2011)PUBMED21345172REMARKGeneRIF:
hZwint-1bridgestheinnerandouterkinetochore:
identificationofthekinetochorelocalizationdomainandthehZw10-interactiondomainREFERENCE4(bases1to1546)AUTHORSParsaA,ChangYP,KellyRJ,CorrettiMC,RyanKA,RobinsonSW,GottliebSS,KardiaSL,ShuldinerARandLiggettSB.TITLEHypertrophy-associatedpolymorphismsascertainedinafoundercohortappliedtoheartfailureriskandmortalityJOURNALClinTranslSci4
(1),17-23(2011)PUBMED21348951REFERENCE5(bases1to1546)AUTHORSBrendleA,BrandtA,JohanssonR,EnquistK,HallmansG,HemminkiK,LennerPandForstiA.TITLESinglenucleotidepolymorphismsinchromosomalinstabilitygenesandriskandclinicaloutcomeofbreastcancer:
aSwedishprospectivecase-controlstudyJOURNALEur.J.Cancer45(3),435-442(2009)PUBMED19008095REMARKGeneRIF:
Observationalstudyofgene-diseaseassociation.(HuGENavigator)REFERENCE6(bases1to1546)AUTHORSWangH,HuX,DingX,DouZ,YangZ,ShawAW,TengM,ClevelandDW,GoldbergML,NiuLandYaoX.TITLEHumanZwint-1specifieslocalizationofZesteWhite10tokinetochoresandisessentialformitoticcheckpointsignalingJOURNALJ.Biol.Chem.279(52),54590-54598(2004)PUBMED15485811REMARKGeneRIF:
showthatZW10interactingprotein-1(Zwint-1)isrequiredandissufficientforkinetochorelocalizationofZesteWhite10(ZW10)inHeLacellsREFERENCE7(bases1to1546)AUTHORSObuseC,IwasakiO,KiyomitsuT,GoshimaG,ToyodaYandYanagidaM.TITLEAconservedMis12centromerecomplexislinkedtoheterochromaticHP1andouterkinetochoreproteinZwint-1JOURNALNat.CellBiol.6(11),1135-1141(2004)PUBMED15502821REFERENCE8(bases1to1546)AUTHORSMusioA,MarianiT,MontagnaC,ZambroniD,AscoliC,RiedTandVezzoniP.TITLERecapitulationoftheRobertssyndromecellularphenotypebyinhibitionofINCENP,ZWINT-1andZW10genesJOURNALGene331,33-40(2004)PUBMED15094189REFERENCE9(bases1to1546)AUTHORSVanHooserAA,OuspenskiII,GregsonHC,StarrDA,YenTJ,GoldbergML,YokomoriK,EarnshawWC,SullivanKFandBrinkleyBR.TITLESpecificationofkinetochore-formingchromatinbythehistoneH3variantCENP-AJOURNALJ.Cell.Sci.114(PT19),3529-3542(2001)PUBMED11682612REFERENCE10(bases1to1546)AUTHORSStarrDA,SafferyR,LiZ,SimpsonAE,ChooKH,YenTJandGoldbergML.TITLE
HZwint-1,anovelhumankinetochorecomponentthatinteractswithHZW10JOURNALJ.Cell.Sci.113(PT11),1939-1950(2000)PUBMED10806105
COMMENT
REVIEWEDREFSEQ:
ThisrecordhasbeencuratedbyNCBIstaff.ThereferencesequencewasderivedfromBG615304.1,BM724168.1,BC020979.1andBC016357.2.Summary:
Thisgeneencodesaproteinthatisclearlyinvolvedinkinetochorefunctionalthoughanexactroleisnotknown.ItinteractswithZW10,anotherkinetochoreprotein,possiblyregulatingtheassociationbetweenZW10andkinetochores.TheencodedproteinlocalizestoprophasekinetochoresbeforeZW10doesanditremainsdetectableonthekinetochoreuntillateanaphase.Ithasauniformdistributioninthecytoplasmofinterphasecells.Alternativelysplicedtranscriptvariantsencodingdifferentisoformshavebeenfoundforthisgene.[providedbyRefSeq,Jul2008].TranscriptVariant:
Thisvariant(3)lacksanalternatein-framesegmentcomparedtovariant1.Theresultingisoform(b)hasthesameN-andC-terminibutisshortercomparedtoisoforma.PublicationNote:
ThisRefSeqrecordincludesasubsetofthepublicationsthatareavailableforthisgene.PleaseseetheGenerecordtoaccessadditionalpublications.##Evidence-Data-START##Transcriptexoncombination:
:
BX448627.2,AL557130.3[ECO:
0000332]RNAseqintrons:
singlesamplesupportsallintronsERS025087,ERS025093[ECO:
0000348]##Evidence-Data-END##COMPLETENESS:
completeonthe3'
end.PRIMARYREFSEQ_SPANPRIMARY_IDENTIFIERPRIMARY_SPANCOMP1-5BG615304.11-56-46BM724168.19-4947-556BC020979.134-543557-1358BC020979.1685-14861359-1511BC020979.11487-16391512-1519BC016357.2957-9641520-1546
BC016357.21147-1173FEATURES
Location/Qualifiers
source1..1546/organism="
Homosapiens"
/mol_type="
mRNA"
/db_xref="
taxon:
9606"
/chromosome="
10"
/map="
10q21-q22"
gene1..1546/gene="
ZWINT"
/gene_synonym="
HZwint-1;
KNTC2AP;
ZWINT1"
/note="
ZW10interactingkinetochoreprotein"
GeneID:
11130"
HGNC:
13195"
HPRD:
18366"
MIM:
609177"
exon1..78/gene="
KNTC
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