生物信息学作业实验3(20页).doc

-生物信息学作业实验3开课学院及实验室：生命科学学院 计机楼407 2013年 11 月 15 日 学 院生命科学学院年级、专业、班生物工程10姓名学号10142000实验课程名称生物信息学成绩实验项目名称实验三 序列分析与比较指 导 教 师一、实验目的1、 掌握已知或未知序列接受号的核酸序列检索的基本步骤；2、 掌握使用BioEdit软件进行核酸序列的基本分析；3熟悉基于核酸序列比对分析的真核基因结构分析（内含子/外显子分析）；4、了解基因的电子表达谱分析。二、实验内容1、归纳对人瘦素 (leptin) 的核酸序列分析的结果，列出主要的分析结果；2、总结核酸序列分析的基本步骤，相互对比结果，指出应注意的事项。三、实验步骤3.1、人瘦素 (leptin) 的核酸序列分析Homo sapiens leptin (LEP), mRNAFASTA GraphicsGo to:LOCUS NM_000230 3444 bp mRNA linear PRI 03-NOV-2013DEFINITION Homo sapiens leptin (LEP), mRNA.ACCESSION NM_000230VERSION NM_000230.2 GI:169790920KEYWORDS RefSeq.SOURCE Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo.REFERENCE 1 (bases 1 to 3444) AUTHORS Lee,J.H., Zhou,L., Kwon,K.S., Lee,D., Park,B.H. and Kim,J.R. TITLE Role of leptin in Legg-Calve-Perthes disease JOURNAL J. Orthop. Res. 31 (10), 1605-1610 (2013) PUBMED 23832827 REMARK 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., Rebai,A. and Fakhfakh,F. TITLE 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 associated 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-diabetic ankylosing spondylitis patients undergoing TNF-alpha antagonist therapy 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 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 leptin JOURNAL Minerva Endocrinol. 38 (2), 203-210 (2013) PUBMED 23732375 REMARK GeneRIF: we briefly discuss the role of two major adipocytokines adiponectin and leptin in the aging process and age-related diseases-REVIEW Review 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 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 don't affect adiponectin concentrations, but decreases the synthesis of leptin and homostasis and improves aerobic capacity.REFERENCE 6 (bases 1 to 3444) 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 assignment of the human obese gene JOURNAL 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 and regional differences in the adipose tissue JOURNAL Diabetes 44 (7), 855-858 (1995) PUBMED 7789654REFERENCE 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 homologue JOURNAL Nature 372 (6505), 425-432 (1994) PUBMED 7984236 REMARK 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 mutation JOURNAL Genomics 11 (4), 1054-1062 (1991) PUBMED 1686014REFERENCE 10 (bases 1 to 3444) 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 3952COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from , , and . 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, 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 endocrine 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 mellitus 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 transcript record were based on transcript alignments. 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 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 cFEATURES Location/Qualifiers source 1.3444 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="7" /map="7q31.3" gene 1.3444 /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" 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 (obesity homolog, mouse); obese, mouse, homolog of; obesity factor; obese protein" /codon_start=1 /product="leptin precursor" /protein_id="" /db_xref="GI:4557715" /db_xref="CCDS:" /db_xref="GeneID:3952" /db_xref="HGNC:6553" /db_xref="HPRD:01249" /db_xref="MIM:164160" /translation="MHWGTLCGFLWLWPYLFYVQAVPIQKVQDDTKTLIKTIVTRIND ISHTQSVSSKQKVTGLDFIPGLHPILTLSKMDQTLAVYQQILTSMPSRNVIQISNDLE NLRDLLHVLAFSKSCHLPWASGLETLDSLGGVLEASGYSTEVVALSRLQGSLQDMLWQ LDLSPGC" sig_peptide 58.120 /gene="LEP" /gene_synonym="LEPD; OB; OBS" /inference="COORDINATES: ab initio prediction: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" /gene_synonym="LEPD; OB; OBS" /inference="alignment:Splign:1.39.8" STS 594.843 /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 /gene="LEP" /gene_synonym="LEPD; OB; OBS"ORIGIN 1 gtaggaatcg cagcgccagc ggttgcaagg cccaagaagc ccatcctggg aaggaaaatg 61 cattggggaa ccctgtgcgg attcttgtgg ctttggccct atcttttcta tgtccaagct 121 gtgcccatcc aaaaagtcca agatgacacc aaaaccctca tcaagacaat tgtcaccagg 181 atcaatgaca tttcacacac gcagtcagtc tcctccaaac agaaagtcac cggtttggac 241 ttcattcctg ggctccaccc catcctgacc ttatccaaga tggaccagac actggcagtc 301 taccaacaga tcctcaccag tatgccttcc agaaacgtga tccaaatatc caacgacctg 361 gagaacctcc gggatcttct tcacgtgctg gccttctcta agagctgcca cttgccctgg 421 gccagtggcc tggagacctt ggacagcctg gggggtgtcc tggaagcttc aggctactcc 481 acagaggtgg tggccctgag caggctgcag gggtctctgc aggacatgct gtggcagctg 541 gacctcagcc ctgggtgctg aggccttgaa ggtcactctt cctgcaagga ctacgttaag 601 ggaaggaact ctggcttcca ggtatctcca ggattgaaga gcattgcatg gacacccctt 661 atccaggact ctgtcaattt ccctgactcc tctaagccac tcttccaaag gcataagacc 721 ctaagcctcc ttttgcttga aaccaaagat atatacacag gatcctattc tcaccaggaa 781 gggggtccac ccagcaaaga gtgggctgca tctgggattc ccaccaaggt cttcagccat 841 caacaagagt tgtcttgtcc cctcttgacc catctccccc tcactgaatg cctcaatgtg 901 accaggggtg atttcagaga gggcagaggg gtaggcagag cctttggatg accagaacaa 961 ggttccctct gagaattcca aggagttcca tgaagaccac atccacacac gcaggaactc 1021 ccagcaacac aagctggaag cacatgttta tttattctgc attttattct ggatggattt 1081 gaagcaaagc accagcttct ccaggctctt tggggtcagc cagggccagg ggtctccctg 1141 gagtgcagtt tccaatccca tagatgggtc tggctgagct gaacccattt tgagtgactc 1201 gagggttggg ttcatctgag caagagctgg caaaggtggc tctccagtta gttctctcgt 1261 aactggtttc atttctactg tgactgatgt tacatcacag tgtttgcaat ggtgttgccc 1321 tgagtggatc tccaaggacc aggttatttt aaaaagattt gttttgtcaa gtgtcatatg 1381 taggtgtctg cacccagggg tggggaatgt ttgggcagaa gggagaagga tctagaatgt 1441 gttttctgaa taacatttgt gtggtgggtt ctttggaagg agtgagatca ttttcttatc 1501 ttctgcaatt gcttaggatg tttttcatga aaatagctct ttcagggggg ttgtgaggcc 1561 tggccaggca ccccctggag agaagtttct ggccctggct gaccccaaag agcctggaga 1621 agctgatgct ttgcttcaaa tccatccaga ataaaacgca aagggctgaa agccatttgt 1681 tggggcagtg gtaagctctg gctttctccg actgctaggg agtggtcttt cctatcatgg 1741 agtgacggtc ccacactggt gactgcgatc ttcagagcag gggtccttgg tgtgaccctc 1801 tgaatggtcc agggttgatc acactctggg tttattacat ggcagtgttc ctatttgggg 1861 cttgcatgcc aaattgtagt tcttgtctga ttggctcacc caagcaaggc caaaattacc 1921 aaaaatcttg gggggttttt actccagtgg tgaagaaaac tcctttagca ggtggtcctg 1981 agacctgaca agcactgcta ggcgagtgcc aggactcccc aggccaggcc accaggatgg 2041 cccttcccac tggaggtcac attcaggaag atgaaagagg aggtttgggg tctgccacca 2101 tcctgctgct gtgtttttgc tatcacacag tgggtggtgg atctgtccaa ggaaacttga 2161 atcaaagcag ttaactttaa gactgagcac ctgcttcatg ctcagccctg actggtgcta 2221 taggctggag aagctcaccc aataaacatt aagattgagg cctgccctca gggatcttgc 2281 attcccagtg gtcaaaccgc actcacccat gtgccaaggt ggggtattta ccacagcagc 2341 tgaacagcca aatgcatggt gcagttgaca gcaggtggga aatggtatga gctgaggggg 2401 gccgtgccca ggggcccaca gggaaccctg cttgcacttt gtaacatgtt tacttttcag 2461 ggcatcttag cttctattat agccacatcc ctttgaaaca agataactga gaatttaaaa 2521 ataagaaaat acataagacc ataacagcca acaggtggca ggaccaggac tatagc