生物信息学作业实验.doc

1、 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_0002

2、30、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_000230 3.1.1 GenBank 格式 及主要字段含义 LOCUS（ 序列名称 ） NM_000230 3444 bp mRNA linear PRI 03-NOV-2013 DEFINITION（ 序列的简单说明 ）

3、 Homo sapiens leptin (LEP), mRNA. ACCESSION（ 序列编号 ） NM_000230 VERSION（ 序列版本号 ） NM_000230.2 GI:169790920 KEYWORDS（ 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 sapiens 3 学名和分类学位置 ） Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Euther

4、ia; 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 disease JOURNAL（相关文献刊物杂志名或递交序列的作者单位）

5、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: Leptin might play an important role in Legg-Calve-Perthes disease pathogenesis. REFERENCE 2 (bases 1 to 3444) AUTHORS Fourati,M., Mnif,M., Kharrat,N., Charfi,N., Kammoun,M., Fendri,N., Sessi,S., Abid,M

6、., Rebai,A. and Fakhfakh,F. TITLE（相关文献题目） Association between Leptin gene polymorphisms and plasma leptin level in three consanguineous families with obesity JOURNAL Gene 527 (1), 75-81 (2013) PUBMED 23751306 REMARK GeneRIF: Two functional variants in the regulatory region of the LEP gene are associ

7、ated with plasma leptin level as a quantitative trait. 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-di

8、abetic ankylosing spondylitis patients undergoing TNF-alpha antagonist therapy 4 JOURNAL Clin. Exp. Rheumatol. 31 (4), 538-545 (2013) PUBMED 23711190 REMARK GeneRIF: In non-diabetic patients with ankylosing spondylitis on treatment with infliximab leptin and visfatin serum levels do not correlate wi

9、th 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 leptin JOURNAL Minerva Endocrinol. 38 (2), 203-210 (2013) PUBMED 23732375 REMARK GeneRIF: we briefly discuss the role o

10、f two major adipocytokines adiponectin and leptin in the aging process and age-related diseases-REVIEW Review article REFERENCE 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 lepti

11、n and adiponectin and its relation to insulin resistance JOURNAL Neuro Endocrinol. Lett. 34 (3), 229-235 (2013) PUBMED 23685422 REMARK GeneRIF: Adiponectin is sensitive to maximal exercise when realised after intense training and that six months heavy cycling training dont affect adiponectin concent

12、rations, but decreases the synthesis of leptin and homostasis and improves aerobic capacity. REFERENCE 6 (bases 1 to 3444) 5 AUTHORS 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 ass

13、ignment of the human obese gene JOURNAL J. Biol. Chem. 270 (46), 27728-27733 (1995) PUBMED 7499240 REFERENCE 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

14、-specific expression and regional differences in the adipose tissue JOURNAL Diabetes 44 (7), 855-858 (1995) PUBMED 7789654 REFERENCE 8 (bases 1 to 3444) AUTHORS Zhang,Y., Proenca,R., Maffei,M., Barone,M., Leopold,L. and Friedman,J.M. TITLE Positional cloning of the mouse obese gene and its human hom

15、ologue JOURNAL Nature 372 (6505), 425-432 (1994) PUBMED 7984236 REMARK Erratum:Nature 1995 Mar 30;374(6521):479 REFERENCE 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 mutation JOURNAL Genomics 11 (4), 1054-1062 (1

16、991) PUBMED 1686014 REFERENCE 10 (bases 1 to 3444) 6 AUTHORS Groot,P.H., Scholte,H.R. and Hulsmann,W.C. TITLE Fatty acid activation: specificity, localization, and function JOURNAL Adv. Lipid Res. 14, 75-126 (1976) PUBMED 3952 COMMENT（ 关于 REVIEWED REFSEQ: This record has been curated by NCBI staff.

17、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 white adipocytes,

18、and which plays a major role in the regulation of body weight. This protein, which acts through the leptin receptor, functions as part of a signaling pathway that can inhibit food intake and/or regulate energy expenditure to maintain constancy of the adipose mass. This protein also has several endoc

19、rine functions, and is involved in the regulation of immune and inflammatory responses, hematopoiesis, angiogenesis and wound healing. Mutations in this gene and/or its regulatory regions cause severe obesity, and morbid obesity with hypogonadism. This gene has also been linked to type 2 diabetes me

20、llitus development. provided by RefSeq, Jul 2008. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the 7 transcript record were based on transcript alignments.

21、Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. #Evidence-Data-START# Transcript exon combination : U43653.1, BC060830.1 ECO:0000332 RNAseq introns : single sample supports all

22、introns ERS025081, ERS025084 ECO:0000348 #Evidence-Data-END# COMPLETENESS: full length. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-309 DA762132.1 1-309 310-1807 U43653.1 309-1806 1808-3383 AC018635.10 34398-35973 3384-3444 BU752306.1 1-61 c FEATURES（序列特征表起始） Location/Qualifiers sourc

23、e 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=“L

24、EPD; 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 obesit

25、y homolog); leptin (obesity homolog, 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=“MI

26、M:164160“ /translation=“MHWGTLCGFLWLWPYLFYVQAVPIQKVQDDTKTLIKTIVTRIND ISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLE NLRDLLHVLAFSKSCHLPWASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQ LDLSPGC“ sig_peptide 58.120 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /inference=“COORDINATES: ab initio predicti

27、on:SignalP:4.0“ mat_peptide 121.558 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /product=“leptin“ STS 172.254 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /standard_name=“LEP-3“ /db_xref=“UniSTS:253879“ exon 202.3427 /gene=“LEP“ 10 /gene_synonym=“LEPD; OB; OBS“ /inference=“alignment:Splign:1.39.8“ STS 59

28、4.843 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /standard_name=“STS-U43653“ /db_xref=“UniSTS:35281“ STS 594.699 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /standard_name=“OBS“ /db_xref=“UniSTS:35280“ STS 703.898 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /standard_name=“RH70631“ /db_xref=“UniSTS:78152“ STS 3193.3281 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ /standard_name=“D8S2279“ /db_xref=“UniSTS:473907“ polyA_signal 3405.3410 /gene=“LEP“ /gene_synonym=“LEPD; OB; OBS“ polyA_site 3427