PhyA基因序列分析,生物信息学论文

1、PhyA基因序列分析前言：phyA基因是编码拟南芥（arabidopsis）phyA（光敏色素A）基因，光敏色素是植物体本身合成的一种调节生长发育的色蛋白，由蛋白质及生色团两部分组成。植物光敏色素作为光受体,感知环境条件,进行能量转换。深入挖掘光敏色素基因作用的分子机理,便于提升其在作物遗传改良中应用的有效性。在生物学中起着重要作用。因此，用生物信息学的方法和软件对phyA基因进行分析是很有必要的。编码拟南芥（arabidopsis）phyA（光敏色素A）基因，它的GI: 224576211. Unigene号：EU915082 基因序列：gi|224576211|gb|EU915082.1|

2、 Arabidopsis thaliana phytochrome A (PHYA) gene, partial cdsGACTTTGAGCCGGTGAAGCCTTACGAAGTCCCCATGACAGCTGCTGGTGCCTTACAATCATACAAGCTCGCTGCCAAAGCAATCACTAGGCTGCAATCTTTACCCAGCGGGAGTATGGAAAGGCTTTGTGATACAATGGTTCAAGAGGTTTTTGAACTCACGGGGTATGACAGGGTGATGGCTTATAAGTTTCATGAAGATGATCACGGTGAGGTTGTCTCCGAGGTTACAAAACCTGGG

3、CTGGAGCCTTATCTTGGGCTGCATTATCCTGCCACCGACATCCCTCAAGCAGCCCGTTTTCTGTTTATGAAGAACAAGGTCCGGATGATAGTTGATTGCAATGCAAAACATGCTAGGGTGCTTCAAGACGAAAAGCTTTCCTTTGACCTTACCTGGTGTGGCTCCACCCTTAGAGCACCGCACAGCTGCCATTTGCAGTACATGGCCAACATGGATTCAATTGCATCTCTGGTTATGGCGGTTGTAGTTAACGAGGAAGATGGAGAAGGGGATGCTCCTGATGCTACTACACAGCCTCAA

4、AAGAGAAAGAGACTATGGGGTTTAGTGGTTTGTCACAATACGACTCCGAGGTTTGTTCCATTTCCTCTCAGGTATGCCTGTGAGTTTCTAGCTCAAGTGTTTGCCATACACGTCAATAAGGAGGTGGAACTCGATAACCAGATGGTGGAGAAGAACATTNTGCGCACGCAGACACTCTTGTGCGATATGCTGATGCGTGATGCTCCACTGGGTATTGTGTCGCAAAGCCCCAACATAATGGACCTTGTGAAATGTGATGGAGCAGCTCTCTTGTATAAAGACAAGATATGGAAACTGGGA

5、ACAACTCCAAGTGAGTTCCACCTGCAGGAGATAGCTTCATGGTTGTGTGAATACCACATGGATTTAACGGGTTTGAGCACTGATAGTTTGCATGACGCCGGGTTTCCTAGGGCTCTATCTCTCGGGGATTCGGTATGTGGGATGGCAGCTGTGAGGATATCATCGAAAGACATGATTTTCTGGTTCCGTTCTCATACCGCTGGTGAAGTGAGATGGGGAGGTGCGAAGCATGATCCAGATGATAGGGATGATGCAAGGAGAATGCACCCAACGTCATCGTTCAAGGCTTTCCTTGAAGTG

6、GTCAAGACAAGGAGTTTACCTTGGAAGGACTATGAGATGGATGCCATACACTCCTTGCAACTTATTTTGAGGAATGCTTTCAAGGATAGTGAAACTACTGATGTGAATACAAAGGTCATTTACTCGAAGCCAAATGATCTCAAAATTGATGGTATACAAGAACTAGAAGCTGTGACCAGTGAGATGGTTCGTTTAATTGAGACTGCTACGGTGCCAATATTGGCGGTTGATTCTGATGGACTGGTTAATGGTTGGAACACGAAAATCGCTGAGCTGACTGGTCTTTCGGTTGATGAAGCA

7、ATCGGGAAGCATTTCCTCACACTTGTTGAAGATTCTTCAGTGGAAATCGTTAAAAGGATGCTAGAGAACGCATTAGAAGGTAAACTCTCTTCCTAAGTTATGCTGAGTTTGCTAAGAATCTTCCAACTAGATTTCACTATTCAAGTTCCAGTTGAGTATCGTGGTCGAAGAAACTTGATGCAATGTGTTGTTTTTGGTTCTTAATGATGGAATTTTGTTTTCCAATTTTATCAAACACTGAAGCCGAGTCTATAACTTCACTTGCTTATCTATGCAGGAACTGAGGAGCAGAATGTCCAG

8、TTTGAGATCAAGACACATCTGTCCAGGGCTGATGCTGGGCCAATAAGTTTAGTTGTAAATGCATGCGCAAGTAGAGATCTCCATGAAAACGTGGTTGGGGTGTGTTTTGTAGCCCATGATCTTACTGGCCAGAAGACTGTGATGGACAAGTTTACGCGGATTGAAGGTGATTACAAGGCAATCATCCAAprotein_id= HYPERLINK /protein/224576212 ACN56799.1蛋白质序列：gi|224576212|gb|ACN56799.1| phytochrome A Arabidopsis

9、thalianaDFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRVMAYKFHEDDHGEVVSEVTKPGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCNAKHARVLQDEKLSFDLTWCGSTLRAPHSCHLQYMANMDSIASLVMAVVVNEEDGEGDAPDATTQPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFLAQVFAIHVNKEVELDNQMVEKNIXRTQTLLCDMLMRDAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLGTTPSEFHLQEIA

10、SWLCEYHMDLTGLSTDSLHDAGFPRALSLGDSVCGMAAVRISSKDMIFWFRSHTAGEVRWGGAKHDPDDRDDARRMHPTSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDSETTDVNTKVIYSKPNDLKIDGIQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHFLTLVEDSSVEIVKRMLENALEGTEEQNVQFEIKTHLSRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKTVMDKFTRIEGDYKAIIQ 文献资料：Brassicac

11、eae phylogeny inferred from phytochrome A and ndhF sequence data: tribes and trichomes revisited.它的分子质量、碱基组成：Composition 35 A; 25 C; 35 G; 15 T; 0 OTHERPercentage: 32% A; 23% C; 32% G; 14% T; 0%OTHERMolecular Weight (kDa): ssDNA: 34.26 dsDNA: 67.8互补序列、反向序列、反向互补序列、DNA双链序列和RNA序列：R S1 ACTACTCGAG AAGCAG

12、CGAC AGAGGCGTTA GCCCGCTCAG CAGACTGGCA GTTCTCTACC61 GACAAAAAAG AGGTAGGAGG CACAGTAATG ATACAGGCGT AGCAGGAGGGC S1 CCCTCCTGCT ACGCCTGTAT CATTACTGTG CCTCCTACCT CTTTTTTGTC GGTAGAGAAC61 TGCCAGTCTG CTGAGCGGGC TAACGCCTCT GTCGCTGCTT CTCGAGTAGTR C S1 TGATGAGCTC TTCGTCGCTG TCTCCGCAAT CGGGCGAGTC GTCTGACCGT CAAGAG

13、ATGG61 CTGTTTTTTC TCCATCCTCC GTGTCATTAC TATGTCCGCA TCGTCCTCCCD DNA S1 GGGAGGACGA TGCGGACATA GTAATGACAC GGAGGATGGA GAAAAAACAG CCATCTCTTG CCCTCCTGCT ACGCCTGTAT CATTACTGTG CCTCCTACCT CTTTTTTGTC GGTAGAGAAC61 ACGGTCAGAC GACTCGCCCG ATTGCGGAGA CAGCGACGAA GAGCTCATCA TGCCAGTCTG CTGAGCGGGC TAACGCCTCT GTCGCTGC

14、TT CTCGAGTAGTRNA S1 GGGAGGACGA UGCGGACAUA GUAAUGACAC GGAGGAUGGA GAAAAAACAG CCAUCUCUUG61 ACGGUCAGAC GACUCGCCCG AUUGCGGAGA CAGCGACGAA GAGCUCAUCA限制性酶切位点分析结果（酶及识别位点）：Restriction analysis on USMethylation: dam-No dcm-NoScreened with 117 enzymes, 5 sites foundEcl136II 1 GAG/CTC 103 EcoICRI 1 GAG/CTC 103 S

15、acI 1 GAGCT/C 105 SapI 1 GCTCTTCN/ 93 SstI 1 GAGCT/C 105 List by Site Order93 SapI 103 Ecl136II 105 SstI 105 SacI103 EcoICRI Non Cut EnzymesAatII Acc65I AccIII AclI AflII AgeIAhaIII Alw44I AlwNI ApaBI ApaI ApaLIAscI Asp718I AsuII AvrII BalI BamHIBbeI BbvII BclI BglI BglII Bpu1102IBsc91I BsiI BsmI Bs

16、p1407I BspHI BspMIBspMII BssHII BstD102I BstEII BstXI Bsu36IClaI Csp45I CspI CvnI DraI DraIIIDrdI EagI Eam1105I Eco31I Eco47III Eco52IEco56I Eco57I Eco72I EcoNI EcoRI EcoRVEheI EspI FseI HindIII HpaI I-PpoIKpnI MfeI Mlu113I MluI MscI MstIMstII NaeI NarI NcoI NdeI NheINotI NruI NsiI PacI PflMI PinAIP

17、maCI PmeI PstI PvuI PvuII RleAISacII SalI SauI ScaI SciI SfiISgrAI SmaI SnaBI SpeI SphI SplISpoI SrfI SspI SstII StuI SunISwaI Tth111I VspI XbaI XcmI XhoIXmaI XmaIII XmnI XorII Restriction sites on US1 GGGAGGACGATGCGGACATAGTAATGACACGGAGGATGGAGAAAAAACAGCCATCTCTTG SacI SstI Ecl136II SapI EcoICRI61 ACG

18、GTCAGACGACTCGCCCGATTGCGGAGACAGCGACGAAGAGCTCATCA设计的引物及其综合评价：2 GGAGGACGATGCGGACATAOligo: 5-GGAGGACGATGCGGACATA-3Primer1: 19 basesComposition 6 A; 3 C; 8 G; 2 T; 0 OTHERPercentage: 31% A; 15% C; 42% G; 10% T; 0%OTHERMW=5.99 kDaHybridization: D:DSalt: 50 mMFormamide: 0%Mismatch: 0 bpThermo Tm = 62.0 Hyb

19、ridization Tm = 52.1 GC+AT Tm = 60.0Primer-US(1-110) complementarity.First complementarity in continuous: 19 bp5-GGAGGACGATGCGGACATA-3 Primer |3-CCTCCTGCTACGCCTGTAT-5 (20) Strand -No second possible complementarityMax complementarity in discontinuous: 19 bp5-GGAGGACGATGCGGACATA-3 Primer |3-CCTCCTGCT

20、ACGCCTGTAT-5 (20) Strand -105 AGCTCTTCGTCGCTGTCTCCOligo: 5-AGCTCTTCGTCGCTGTCTCC-3Primer1: 20 basesComposition 1 A; 8 C; 4 G; 7 T; 0 OTHERPercentage: 5% A; 40% C; 20% G; 35% T; 0%OTHERMW=6.07 kDaHybridization: D:DSalt: 50 mMFormamide: 0%Mismatch: 0 bpThermo Tm = 62.2 Hybridization Tm = 54.5 GC+AT Tm

21、= 64.0Primer-US(1-110) complementarity.First complementarity in continuous: 20 bp5-AGCTCTTCGTCGCTGTCTCC-3 Primer |3-TCGAGAAGCAGCGACAGAGG-5 (86) Strand +No second possible complementarityMax complementarity in discontinuous: 20 bp5-AGCTCTTCGTCGCTGTCTCC-3 Primer |3-TCGAGAAGCAGCGACAGAGG-5 (86) Strand +

22、同源新基因：gi|1892415|gb|AA255511.1|AA255511 zr85c04.r1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:682470 5, mRNA sequenceAGAGTGCGAGGGACAAAGCAAAGACAGACGATTGATGGTCAAAACCAGGAAAAGGAGTTTACTTCAGTACTTGACATAGTAATGGTTGTTCGGTGCTGCTGGCCTGCTTGTCTAATTTACGTCTTTAGTGGATTCCATAACTTTATTTATTTCCACTCTAGGATATCCTGTACCTTCAC

23、AACTCTTTAGAGGAGGTAAACAGTGCCCTAGTGGGGTACCAGAGACAGAATGATCTTAAACTCGAGGGAATGAACGAGACAGTCAGTAATCTTACCCAGAGAGTCAACCTGATAGAAAGCGATGTGGTTGCTATGAGCAAGGTAGAAAAGAAAGCAAACCTGTCCTTC进化树的分析：以上各植物都属被子植物门。sorghum propinquum（高粱），zea mays（玉米），oat（燕麦）三种植物都是禾本科单子叶，但sorghum propinquum（高粱），zea mays（玉米）都是C4植物，而oat（燕麦）是C3植物。potato（马铃薯）管花目茄科茄属植物和arabidopsis thaliana（拟南芥）是白花菜目十字花科植物拟南芥属；cyrtosia septentrionalis（血红肉果兰）属于兰科植物肉果兰属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：GLHYPATDIPQAARFLFMKNKVRMI参考文献：1 Brassicaceae phylogeny inferred fr