生物信息学作业实验

1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 1 2013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：complete entries 与 Fasta）、写出 complete entries格式主要字段含义。2三、实验步骤3.1、GenBank 数据库中查询核酸序列 NM_0002303.1.1 GenBank 格式及主要字段含义LOCUS（序列名称） NM_000230 3444 bp mRNA linear PRI 03-NOV-2013DEFINITION（序列的简单说明） Homo sapiens leptin (LEP), mRNA.ACCESSION（序列编号） NM_000230VERSION（序列版本号） NM_000230.2 GI:169790920KEYWORDS（与序列相关的关键词）RefSeq.SOURCE（序列来源的物种名） Homo sapiens (human)ORGANISM（序列来源的物种 Homo sapiens3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 (bases 1 to 3444)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. and Kim,J.R.TITLE（相关文献题目） Role of leptin in Legg-Calve-Perthes diseaseJOURNAL（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） 23832827REMARK（相关文献注释） GeneRIF: Leptin might play an important role in Legg-Calve-Perthesdisease pathogenesis.REFERENCE 2 (bases 1 to 3444)AUTHORS Fourati,M., Mnif,M., Kharrat,N., Charfi,N., Kammoun,M., Fendri,N.,Sessi,S., Abid,M., Rebai,A. and Fakhfakh,F.TITLE（相关文献题目） Association between Leptin gene polymorphisms and plasma leptinlevel in three consanguineous families with obesityJOURNAL Gene 527 (1), 75-81 (2013)PUBMED 23751306REMARK GeneRIF: Two functional variants in the regulatory region of theLEP gene are associated with plasma leptin level as a quantitativetrait.REFERENCE 3 (bases 1 to 3444)AUTHORS Miranda-Filloy,J.A., Lopez-Mejias,R., Genre,F., Carnero-Lopez,B.,Ochoa,R., Diaz de Teran,T., Gonzalez-Juanatey,C., Blanco,R.,Llorca,J. and Gonzalez-Gay,M.A.TITLE Leptin and visfatin serum levels in non-diabetic ankylosingspondylitis patients undergoing TNF-alpha antagonist therapy4JOURNAL Clin. Exp. Rheumatol. 31 (4), 538-545 (2013)PUBMED 23711190REMARK GeneRIF: In non-diabetic patients with ankylosing spondylitis ontreatment with infliximab leptin and visfatin serum levels do notcorrelate with disease activity or systemic inflammation.REFERENCE 4 (bases 1 to 3444)AUTHORS Gulcelik,N.E., Halil,M., Ariogul,S. and Usman,A.TITLE Adipocytokines and aging: adiponectin and leptinJOURNAL Minerva Endocrinol. 38 (2), 203-210 (2013)PUBMED 23732375REMARK GeneRIF: we briefly discuss the role of two major adipocytokinesadiponectin and leptin in the aging process and age-relateddiseases-REVIEWReview articleREFERENCE 5 (bases 1 to 3444)AUTHORS Lakhdar,N., Ben Saad,H., Denguezli,M., Zaouali,M., Zbidi,A.,Tabka,Z. and Bouassida,A.TITLE Effects of intense cycling training on plasma leptin andadiponectin and its relation to insulin resistanceJOURNAL Neuro Endocrinol. Lett. 34 (3), 229-235 (2013)PUBMED 23685422REMARK GeneRIF: Adiponectin is sensitive to maximal exercise when realisedafter intense training and that six months heavy cycling trainingdont affect adiponectin concentrations, but decreases thesynthesis of leptin and homostasis and improves aerobic capacity.REFERENCE 6 (bases 1 to 3444)5AUTHORS Isse,N., Ogawa,Y., Tamura,N., Masuzaki,H., Mori,K., Okazaki,T.,Satoh,N., Shigemoto,M., Yoshimasa,Y., Nishi,S. et al.TITLE Structural organization and chromosomal assignment of the humanobese geneJOURNAL J. Biol. Chem. 270 (46), 27728-27733 (1995)PUBMED 7499240REFERENCE 7 (bases 1 to 3444)AUTHORS Masuzaki,H., Ogawa,Y., Isse,N., Satoh,N., Okazaki,T., Shigemoto,M.,Mori,K., Tamura,N., Hosoda,K., Yoshimasa,Y. et al.TITLE Human obese gene expression. Adipocyte-specific expression andregional differences in the adipose tissueJOURNAL Diabetes 44 (7), 855-858 (1995)PUBMED 7789654REFERENCE 8 (bases 1 to 3444)AUTHORS Zhang,Y., Proenca,R., Maffei,M., Barone,M., Leopold,L. andFriedman,J.M.TITLE Positional cloning of the mouse obese gene and its human homologueJOURNAL Nature 372 (6505), 425-432 (1994)PUBMED 7984236REMARK Erratum:Nature 1995 Mar 30;374(6521):479REFERENCE 9 (bases 1 to 3444)AUTHORS Friedman,J.M., Leibel,R.L., Siegel,D.S., Walsh,J. and Bahary,N.TITLE Molecular mapping of the mouse ob mutationJOURNAL Genomics 11 (4), 1054-1062 (1991)PUBMED 1686014REFERENCE 10 (bases 1 to 3444)6AUTHORS Groot,P.H., Scholte,H.R. and Hulsmann,W.C.TITLE Fatty acid activation: specificity, localization, and functionJOURNAL Adv. Lipid Res. 14, 75-126 (1976)PUBMED 3952COMMENT（关于 REVIEWED REFSEQ: This record has been curated by NCBI staff. The序列的 reference sequence was derived from DA762132.1, U43653.1,注释 AC018635.10 and BU752306.1.信息）This sequence is a reference standard in the RefSeqGene project.On Mar 12, 2008 this sequence version replaced gi:4557714.Summary: This gene encodes a protein that is secreted by whiteadipocytes, and which plays a major role in the regulation of bodyweight. This protein, which acts through the leptin receptor,functions as part of a signaling pathway that can inhibit foodintake and/or regulate energy expenditure to maintain constancy ofthe adipose mass. This protein also has several endocrinefunctions, and is involved in the regulation of immune andinflammatory responses, hematopoiesis, angiogenesis and woundhealing. Mutations in this gene and/or its regulatory regions causesevere obesity, and morbid obesity with hypogonadism. This gene hasalso been linked to type 2 diabetes mellitus development. providedby RefSeq, Jul 2008.Sequence Note: This RefSeq record was created from transcript andgenomic sequence data to make the sequence consistent with thereference genome assembly. The genomic coordinates used for the7transcript record were based on transcript alignments.Publication Note: This RefSeq record includes a subset of thepublications that are available for this gene. Please see the Generecord to access additional publications.#Evidence-Data-START#Transcript exon combination : U43653.1, BC060830.1 ECO:0000332RNAseq introns : single sample supports all intronsERS025081, ERS025084 ECO:0000348#Evidence-Data-END#COMPLETENESS: full length.PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP1-309 DA762132.1 1-309310-1807 U43653.1 309-18061808-3383 AC018635.10 34398-359733384-3444 BU752306.1 1-61 cFEATURES（序列特征表起始） Location/Qualifierssource 1.3444/organism=“Homo sapiens“/mol_type=“mRNA“/db_xref=“taxon:9606“/chromosome=“7“/map=“7q31.3“gene 1.3444/gene=“LEP“8/gene_synonym=“LEPD; OB; OBS“/note=“leptin“/db_xref=“GeneID:3952“/db_xref=“HGNC:6553“/db_xref=“HPRD:01249“/db_xref=“MIM:164160“exon 1.29/gene=“LEP“/gene_synonym=“LEPD; OB; OBS“/inference=“alignment:Splign:1.39.8“STS 7.611/gene=“LEP“/gene_synonym=“LEPD; OB; OBS“/db_xref=“UniSTS:481242“exon 30.201/gene=“LEP“/gene_synonym=“LEPD; OB; OBS“/inference=“alignment:Splign:1.39.8“CDS 58.561/gene=“LEP“/gene_synonym=“LEPD; OB; OBS“/note=“leptin (murine obesity homolog); leptin (obesityhomolog, mouse); obese, mouse, homolog of; obesity factor;obese protein“/codon_start=1/product=“leptin precursor“9/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=“MHWGTLCGFLWLWPYLFYVQAVPIQKVQDDTKTLIKTIVTRINDISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLENLRDLLHVLAFSKSCHLPWASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQLDLSPGC“sig_peptide 58.120/