生物信息学作业实验2.docx
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生物信息学作业实验2.docx
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生物信息学作业实验2
广州大学学生实验报告
开课学院及实验室:
生命科学学院计机楼401基础12013年11月8日
学院
生命科学学院
年级、专业、班
生物工程10
姓名
学号
10
实验课程名称
生物信息学
成绩
实验项目名称
实验二核酸序列的检索
指导教师
一、实验目的
1、掌握核酸序列检索的操作方法;
2、熟悉GenBank数据库序列格式及其主要字段的含义;
3、了解EMBL数据库序列格式及其主要字段的含义;
4、熟悉GenBank数据库序列格式的FASTA序列格式显示与保存;
二、实验内容
1、在GenBank数据库中查询核酸序列NM_000230、下载(以两种格式保存:
GenBank与Fasta)、写出GenBank格式主要字段含义。
2、在EMBL数据库中查询核酸序列BC060830、下载(以两种格式保存:
completeentries与Fasta)、写出completeentries格式主要字段含义。
三、实验步骤
3.1、GenBank数据库中查询核酸序列NM_000230
3.1.1GenBank格式及主要字段含义
LOCUS(序列名称)NM_0002303444bpmRNAlinearPRI03-NOV-2013
DEFINITION(序列的简单说明)Homosapiensleptin(LEP),mRNA.
ACCESSION(序列编号)NM_000230
VERSION(序列版本号)NM_000230.2GI:
169790920
KEYWORDS(与序列相关的关键词)RefSeq.
SOURCE(序列来源的物种名)Homosapiens(human)
ORGANISM(序列来源的物种Homosapiens
学名和分类学位置)Eukaryota;Metazoa;Chordata;Craniata;Vertebrata;Euteleostomi;
Mammalia;Eutheria;Euarchontoglires;Primates;Haplorrhini;
Catarrhini;Hominidae;Homo.
REFERENCE(相关文献编号与递交序列的注册信息)1(bases1to3444)
AUTHORS(相关文献的作者或递交序列的作者)Lee,J.H.,Zhou,L.,Kwon,K.S.,Lee,D.,Park,B.H.andKim,J.R.
TITLE(相关文献题目)RoleofleptininLegg-Calve-Perthesdisease
JOURNAL(相关文献刊物杂志名或递交序列的作者单位)J.Orthop.Res.31(10),1605-1610(2013)
PUBMED(PUBMED中文献的编号)23832827
REMARK(相关文献注释)GeneRIF:
LeptinmightplayanimportantroleinLegg-Calve-Perthes
diseasepathogenesis.
REFERENCE2(bases1to3444)
AUTHORSFourati,M.,Mnif,M.,Kharrat,N.,Charfi,N.,Kammoun,M.,Fendri,N.,
Sessi,S.,Abid,M.,Rebai,A.andFakhfakh,F.
TITLE(相关文献题目)AssociationbetweenLeptingenepolymorphismsandplasmaleptin
levelinthreeconsanguineousfamilieswithobesity
JOURNALGene527
(1),75-81(2013)
PUBMED23751306
REMARKGeneRIF:
Twofunctionalvariantsintheregulatoryregionofthe
LEPgeneareassociatedwithplasmaleptinlevelasaquantitative
trait.
REFERENCE3(bases1to3444)
AUTHORSMiranda-Filloy,J.A.,Lopez-Mejias,R.,Genre,F.,Carnero-Lopez,B.,
Ochoa,R.,DiazdeTeran,T.,Gonzalez-Juanatey,C.,Blanco,R.,
Llorca,J.andGonzalez-Gay,M.A.
TITLELeptinandvisfatinserumlevelsinnon-diabeticankylosing
spondylitispatientsundergoingTNF-alphaantagonisttherapy
JOURNALClin.Exp.Rheumatol.31(4),538-545(2013)
PUBMED23711190
REMARKGeneRIF:
Innon-diabeticpatientswithankylosingspondylitison
treatmentwithinfliximableptinandvisfatinserumlevelsdonot
correlatewithdiseaseactivityorsystemicinflammation.
REFERENCE4(bases1to3444)
AUTHORSGulcelik,N.E.,Halil,M.,Ariogul,S.andUsman,A.
TITLEAdipocytokinesandaging:
adiponectinandleptin
JOURNALMinervaEndocrinol.38
(2),203-210(2013)
PUBMED23732375
REMARKGeneRIF:
webrieflydiscusstheroleoftwomajoradipocytokines
adiponectinandleptinintheagingprocessandage-related
diseases--{REVIEW}
Reviewarticle
REFERENCE5(bases1to3444)
AUTHORSLakhdar,N.,BenSaad,H.,Denguezli,M.,Zaouali,M.,Zbidi,A.,
Tabka,Z.andBouassida,A.
TITLEEffectsofintensecyclingtrainingonplasmaleptinand
adiponectinanditsrelationtoinsulinresistance
JOURNALNeuroEndocrinol.Lett.34(3),229-235(2013)
PUBMED23685422
REMARKGeneRIF:
Adiponectinissensitivetomaximalexercisewhenrealised
afterintensetrainingandthatsixmonthsheavycyclingtraining
don'taffectadiponectinconcentrations,butdecreasesthe
synthesisofleptinandhomostasisandimprovesaerobiccapacity.
REFERENCE6(bases1to3444)
AUTHORSIsse,N.,Ogawa,Y.,Tamura,N.,Masuzaki,H.,Mori,K.,Okazaki,T.,
Satoh,N.,Shigemoto,M.,Yoshimasa,Y.,Nishi,S.etal.
TITLEStructuralorganizationandchromosomalassignmentofthehuman
obesegene
JOURNALJ.Biol.Chem.270(46),27728-27733(1995)
PUBMED7499240
REFERENCE7(bases1to3444)
AUTHORSMasuzaki,H.,Ogawa,Y.,Isse,N.,Satoh,N.,Okazaki,T.,Shigemoto,M.,
Mori,K.,Tamura,N.,Hosoda,K.,Yoshimasa,Y.etal.
TITLEHumanobesegeneexpression.Adipocyte-specificexpressionand
regionaldifferencesintheadiposetissue
JOURNALDiabetes44(7),855-858(1995)
PUBMED7789654
REFERENCE8(bases1to3444)
AUTHORSZhang,Y.,Proenca,R.,Maffei,M.,Barone,M.,Leopold,L.and
Friedman,J.M.
TITLEPositionalcloningofthemouseobesegeneanditshumanhomologue
JOURNALNature372(6505),425-432(1994)
PUBMED7984236
REMARKErratum:
[Nature1995Mar30;374(6521):
479]
REFERENCE9(bases1to3444)
AUTHORSFriedman,J.M.,Leibel,R.L.,Siegel,D.S.,Walsh,J.andBahary,N.
TITLEMolecularmappingofthemouseobmutation
JOURNALGenomics11(4),1054-1062(1991)
PUBMED1686014
REFERENCE10(bases1to3444)
AUTHORSGroot,P.H.,Scholte,H.R.andHulsmann,W.C.
TITLEFattyacidactivation:
specificity,localization,andfunction
JOURNALAdv.LipidRes.14,75-126(1976)
PUBMED3952
COMMENT(关于REVIEWEDREFSEQ:
ThisrecordhasbeencuratedbyNCBIstaff.The
序列的referencesequencewasderivedfromDA762132.1,U43653.1,
注释AC018635.10andBU752306.1.
信息)ThissequenceisareferencestandardintheRefSeqGeneproject.
OnMar12,2008thissequenceversionreplacedgi:
4557714.
Summary:
Thisgeneencodesaproteinthatissecretedbywhite
adipocytes,andwhichplaysamajorroleintheregulationofbody
weight.Thisprotein,whichactsthroughtheleptinreceptor,
functionsaspartofasignalingpathwaythatcaninhibitfood
intakeand/orregulateenergyexpendituretomaintainconstancyof
theadiposemass.Thisproteinalsohasseveralendocrine
functions,andisinvolvedintheregulationofimmuneand
inflammatoryresponses,hematopoiesis,angiogenesisandwound
healing.Mutationsinthisgeneand/oritsregulatoryregionscause
severeobesity,andmorbidobesitywithhypogonadism.Thisgenehas
alsobeenlinkedtotype2diabetesmellitusdevelopment.[provided
byRefSeq,Jul2008].
SequenceNote:
ThisRefSeqrecordwascreatedfromtranscriptand
genomicsequencedatatomakethesequenceconsistentwiththe
referencegenomeassembly.Thegenomiccoordinatesusedforthe
transcriptrecordwerebasedontranscriptalignments.
PublicationNote:
ThisRefSeqrecordincludesasubsetofthe
publicationsthatareavailableforthisgene.PleaseseetheGene
recordtoaccessadditionalpublications.
##Evidence-Data-START##
Transcriptexoncombination:
:
U43653.1,BC060830.1[ECO:
0000332]
RNAseqintrons:
:
singlesamplesupportsallintrons
ERS025081,ERS025084[ECO:
0000348]
##Evidence-Data-END##
COMPLETENESS:
fulllength.
PRIMARYREFSEQ_SPANPRIMARY_IDENTIFIERPRIMARY_SPANCOMP
1-309DA762132.11-309
310-1807U43653.1309-1806
1808-3383AC018635.1034398-35973
3384-3444BU752306.11-61c
FEATURES(序列特征表起始)Location/Qualifiers
source1..3444
/organism="Homosapiens"
/mol_type="mRNA"
/db_xref="taxon:
9606"
/chromosome="7"
/map="7q31.3"
gene1..3444
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/note="leptin"
/db_xref="GeneID:
3952"
/db_xref="HGNC:
6553"
/db_xref="HPRD:
01249"
/db_xref="MIM:
164160"
exon1..29
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/inference="alignment:
Splign:
1.39.8"
STS7..611
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/db_xref="UniSTS:
481242"
exon30..201
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/inference="alignment:
Splign:
1.39.8"
CDS58..561
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/note="leptin(murineobesityhomolog);leptin(obesity
homolog,mouse);obese,mouse,homologof;obesityfactor;
obeseprotein"
/codon_start=1
/product="leptinprecursor"
/protein_id="NP_000221.1"
/db_xref="GI:
4557715"
/db_xref="CCDS:
CCDS5800.1"
/db_xref="GeneID:
3952"
/db_xref="HGNC:
6553"
/db_xref="HPRD:
01249"
/db_xref="MIM:
164160"
/translation="MHWGTLCGFLWLWPYLFYVQAVPIQKVQDDTKTLIKTIVTRIND
ISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLE
NLRDLLHVLAFSKSCHLPWASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQ
LDLSPGC"
sig_peptide58..120
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/inference="COORDINATES:
abinitioprediction:
SignalP:
4.0"
mat_peptide121..558
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/product="leptin"
STS172..254
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/standard_name="LEP-3"
/db_xref="UniSTS:
253879"
exon202..3427
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/inference="alignment:
Splign:
1.39.8"
STS594..843
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/standard_name="STS-U43653"
/db_xref="UniSTS:
35281"
STS594..699
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/standard_name="OBS"
/db_xref="UniSTS:
35280"
STS703..898
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/standard_name="RH70631"
/db_xref="UniSTS:
78152"
STS3193..3281
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
/standard_name="D8S2279"
/db_xref="UniSTS:
473907"
polyA_signal3405..3410
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
polyA_site3427
/gene="LEP"
/gene_synonym="LEPD;OB;OBS"
ORIGIN(序列)
1gtaggaatcgcagcgccagcggttgcaaggcccaagaagcccatcctgggaaggaaaatg
61cattggggaaccctgtgcggattcttgtggctttggccctatcttttctatgtccaagct
121gtgcccatccaaaaagtccaagatgacaccaaaaccctcatcaagacaattgtcaccagg
181atcaatgacatttcacacacgcagtcagtctcctccaaacagaaagtcaccggtttggac
241ttcattcctgggctccaccccatcctgaccttatccaagatggaccagacactggcagtc
301taccaacagatcctcaccagtatgccttccagaaacgtgatccaaatatccaacgacctg
361gagaacctccgggatcttcttcacgtgctggccttctctaagagctgccacttgccctgg
421gccagtggcctggagaccttggacagcctggggggtgtcctggaagcttcaggctactcc
481acagaggtggtggccctgagcaggctgcaggggtctctgcaggacatgctgtggcagctg
541gacctcagccctgggtgctgaggccttgaaggtcactcttcctgcaaggactacgttaag
601ggaaggaactctggcttccaggtatctccaggattgaagagcattgcatggacacccctt
661atccaggactctgtcaatttccctgactcctctaagccactcttccaaaggcataagacc
721ctaagcctccttttgcttgaaaccaaagatatatacacaggatcctattctcaccagga
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