PhyA基因序列分析-生物信息学论文.docx

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| Arabidopsis thaliana phytochrome A (PHYA) gene, partial cds
GACTTTGAGCCGGTGAAGCCTTACGAAGTCCCCATGACAGCTGCTGGTGCCTTACAATCATACAAGCTCG
CTGCCAAAGCAATCACTAGGCTGCAATCTTTACCCAGCGGGAGTATGGAAAGGCTTTGTGATACAATGGT
TCAAGAGGTTTTTGAACTCACGGGGTATGACAGGGTGATGGCTTATAAGTTTCATGAAGATGATCACGGT
GAGGTTGTCTCCGAGGTTACAAAACCTGGGCTGGAGCCTTATCTTGGGCTGCATTATCCTGCCACCGACA
TCCCTCAAGCAGCCCGTTTTCTGTTTATGAAGAACAAGGTCCGGATGATAGTTGATTGCAATGCAAAACA
TGCTAGGGTGCTTCAAGACGAAAAGCTTTCCTTTGACCTTACCTGGTGTGGCTCCACCCTTAGAGCACCG
CACAGCTGCCATTTGCAGTACATGGCCAACATGGATTCAATTGCATCTCTGGTTATGGCGGTTGTAGTTA
ACGAGGAAGATGGAGAAGGGGATGCTCCTGATGCTACTACACAGCCTCAAAAGAGAAAGAGACTATGGGG
TTTAGTGGTTTGTCACAATACGACTCCGAGGTTTGTTCCATTTCCTCTCAGGTATGCCTGTGAGTTTCTA
GCTCAAGTGTTTGCCATACACGTCAATAAGGAGGTGGAACTCGATAACCAGATGGTGGAGAAGAACATTN
TGCGCACGCAGACACTCTTGTGCGATATGCTGATGCGTGATGCTCCACTGGGTATTGTGTCGCAAAGCCC
CAACATAATGGACCTTGTGAAATGTGATGGAGCAGCTCTCTTGTATAAAGACAAGATATGGAAACTGGGA
ACAACTCCAAGTGAGTTCCACCTGCAGGAGATAGCTTCATGGTTGTGTGAATACCACATGGATTTAACGG
GTTTGAGCACTGATAGTTTGCATGACGCCGGGTTTCCTAGGGCTCTATCTCTCGGGGATTCGGTATGTGG
GATGGCAGCTGTGAGGATATCATCGAAAGACATGATTTTCTGGTTCCGTTCTCATACCGCTGGTGAAGTG
AGATGGGGAGGTGCGAAGCATGATCCAGATGATAGGGATGATGCAAGGAGAATGCACCCAACGTCATCGT
TCAAGGCTTTCCTTGAAGTGGTCAAGACAAGGAGTTTACCTTGGAAGGACTATGAGATGGATGCCATACA
CTCCTTGCAACTTATTTTGAGGAATGCTTTCAAGGATAGTGAAACTACTGATGTGAATACAAAGGTCATT
TACTCGAAGCCAAATGATCTCAAAATTGATGGTATACAAGAACTAGAAGCTGTGACCAGTGAGATGGTTC
GTTTAATTGAGACTGCTACGGTGCCAATATTGGCGGTTGATTCTGATGGACTGGTTAATGGTTGGAACAC
GAAAATCGCTGAGCTGACTGGTCTTTCGGTTGATGAAGCAATCGGGAAGCATTTCCTCACACTTGTTGAA
GATTCTTCAGTGGAAATCGTTAAAAGGATGCTAGAGAACGCATTAGAAGGTAAACTCTCTTCCTAAGTTA
TGCTGAGTTTGCTAAGAATCTTCCAACTAGATTTCACTATTCAAGTTCCAGTTGAGTATCGTGGTCGAAG
AAACTTGATGCAATGTGTTGTTTTTGGTTCTTAATGATGGAATTTTGTTTTCCAATTTTATCAAACACTG
AAGCCGAGTCTATAACTTCACTTGCTTATCTATGCAGGAACTGAGGAGCAGAATGTCCAGTTTGAGATCA
AGACACATCTGTCCAGGGCTGATGCTGGGCCAATAAGTTTAGTTGTAAATGCATGCGCAAGTAGAGATCT
CCATGAAAACGTGGTTGGGGTGTGTTTTGTAGCCCATGATCTTACTGGCCAGAAGACTGTGATGGACAAG
TTTACGCGGATTGAAGGTGATTACAAGGCAATCATCCAA

protein_id="ACN56799.1"

蛋白质序列：
>gi|224576212|gb|ACN56799.1| phytochrome A [Arabidopsis thaliana]
DFEPVKPYEVPMTAAGALQSYKLAAKAITRLQSLPSGSMERLCDTMVQEVFELTGYDRVMAYKFHEDDHG
EVVSEVTKPGLEPYLGLHYPATDIPQAARFLFMKNKVRMIVDCNAKHARVLQDEKLSFDLTWCGSTLRAP
HSCHLQYMANMDSIASLVMAVVVNEEDGEGDAPDATTQPQKRKRLWGLVVCHNTTPRFVPFPLRYACEFL
AQVFAIHVNKEVELDNQMVEKNIXRTQTLLCDMLMRDAPLGIVSQSPNIMDLVKCDGAALLYKDKIWKLG
TTPSEFHLQEIASWLCEYHMDLTGLSTDSLHDAGFPRALSLGDSVCGMAAVRISSKDMIFWFRSHTAGEV
RWGGAKHDPDDRDDARRMHPTSSFKAFLEVVKTRSLPWKDYEMDAIHSLQLILRNAFKDSETTDVNTKVI
YSKPNDLKIDGIQELEAVTSEMVRLIETATVPILAVDSDGLVNGWNTKIAELTGLSVDEAIGKHFLTLVE
DSSVEIVKRMLENALEGTEEQNVQFEIKTHLSRADAGPISLVVNACASRDLHENVVGVCFVAHDLTGQKT
VMDKFTRIEGDYKAIIQ
文献资料：Brassicaceae 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 OTHER
Percentage: 32% A; 23% C; 32% G; 14% T; 0%OTHER
Molecular 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 S
1 ACTACTCGAG AAGCAGCGAC AGAGGCGTTA GCCCGCTCAG CAGACTGGCA GTTCTCTACC
61 GACAAAAAAG AGGTAGGAGG CACAGTAATG ATACAGGCGT AGCAGGAGGG
C S
1 CCCTCCTGCT ACGCCTGTAT CATTACTGTG CCTCCTACCT CTTTTTTGTC GGTAGAGAAC
61 TGCCAGTCTG CTGAGCGGGC TAACGCCTCT GTCGCTGCTT CTCGAGTAGT
R C S
1 TGATGAGCTC TTCGTCGCTG TCTCCGCAAT CGGGCGAGTC GTCTGACCGT CAAGAGATGG
61 CTGTTTTTTC TCCATCCTCC GTGTCATTAC TATGTCCGCA TCGTCCTCCC
D DNA S
1 GGGAGGACGA TGCGGACATA GTAATGACAC GGAGGATGGA GAAAAAACAG CCATCTCTTG
CCCTCCTGCT ACGCCTGTAT CATTACTGTG CCTCCTACCT CTTTTTTGTC GGTAGAGAAC
61 ACGGTCAGAC GACTCGCCCG ATTGCGGAGA CAGCGACGAA GAGCTCATCA
TGCCAGTCTG CTGAGCGGGC TAACGCCTCT GTCGCTGCTT CTCGAGTAGT
RNA S
1 GGGAGGACGA UGCGGACAUA GUAAUGACAC GGAGGAUGGA GAAAAAACAG CCAUCUCUUG
61 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 US
Methylation: dam-No dcm-No
Screened with 117 enzymes, 5 sites found
Ecl136II 1 GAG/CTC
103
EcoICRI 1 GAG/CTC
103
SacI 1 GAGCT/C
105
SapI 1 GCTCTTCN/
93
SstI 1 GAGCT/C
105
List by Site Order
93 SapI 103 Ecl136II 105 SstI 105 SacI
103 EcoICRI

Non Cut Enzymes
AatII Acc65I AccIII AclI AflII AgeI
AhaIII Alw44I AlwNI ApaBI ApaI ApaLI
AscI Asp718I AsuII AvrII BalI BamHI
BbeI BbvII BclI BglI BglII Bpu1102I
Bsc91I BsiI BsmI Bsp1407I BspHI BspMI
BspMII BssHII BstD102I BstEII BstXI Bsu36I
ClaI Csp45I CspI CvnI DraI DraIII
DrdI EagI Eam1105I Eco31I Eco47III Eco52I
Eco56I Eco57I Eco72I EcoNI EcoRI EcoRV
EheI EspI FseI HindIII HpaI I-PpoI
KpnI MfeI Mlu113I MluI MscI MstI
MstII NaeI NarI NcoI NdeI NheI
NotI NruI NsiI PacI PflMI PinAI
PmaCI PmeI PstI PvuI PvuII RleAI
SacII SalI SauI ScaI SciI SfiI
SgrAI SmaI SnaBI SpeI SphI SplI
SpoI SrfI SspI SstII StuI SunI
SwaI Tth111I VspI XbaI XcmI XhoI
XmaI XmaIII XmnI XorII
Restriction sites on US
1 GGGAGGACGATGCGGACATAGTAATGACACGGAGGATGGAGAAAAAACAGCCATCTCTTG

SacI
SstI
Ecl136II
SapI EcoICRI
61 ACGGTCAGACGACTCGCCCGATTGCGGAGACAGCGACGAAGAGCTCATCA
设计的引物及其综合评价：
2 GGAGGACGATGCGGACATA
Oligo: 5'-GGAGGACGATGCGGACATA-3'
Primer1: 19 bases
Composition 6 A; 3 C; 8 G; 2 T; 0 OTHER
Percentage: 31% A; 15% C; 42% G; 10% T; 0%OTHER
MW=5.99 kDa
Hybridization: D:D
Salt: 50 mM
Formamide: 0%
Mismatch: 0 bp
Thermo Tm = 62.0 Hybridization Tm = 52.1 GC+AT Tm = 60.0
Primer-US(1-110) complementarity.
First complementarity in continuous: 19 bp
5'-GGAGGACGATGCGGACATA-3' Primer
|||||||||||||||||||
3'-CCTCCTGCTACGCCTGTAT-5' (20) Strand -
No second possible complementarity
Max complementarity in discontinuous: 19 bp
5'-GGAGGACGATGCGGACATA-3' Primer
|||||||||||||||||||
3'-CCTCCTGCTACGCCTGTAT-5' (20) Strand -
105 AGCTCTTCGTCGCTGTCTCC
Oligo: 5'-AGCTCTTCGTCGCTGTCTCC-3'
Primer1: 20 bases
Composition 1 A; 8 C; 4 G; 7 T; 0 OTHER
Percentage: 5% A; 40% C; 20% G; 35% T; 0%OTHER
MW=6.07 kDa
Hybridization: D:D
Salt: 50 mM
Formamide: 0%
Mismatch: 0 bp
Thermo Tm = 62.2 Hybridization Tm = 54.5 GC+AT Tm = 64.0
Primer-US(1-110) complementarity.
First complementarity in continuous: 20 bp
5'-AGCTCTTCGTCGCTGTCTCC-3' Primer
||||||||||||||||||||
3'-TCGAGAAGCAGCGACAGAGG-5' (86) Strand +
No second possible complementarity
Max complementarity in discontinuous: 20 bp
5'-AGCTCTTCGTCGCTGTCTCC-3' Primer
||||||||||||||||||||
3'-TCGAGAAGCAGCGACAGAGG-5' (86) Strand +
同源新基因：
>gi|1892415|gb|AA255511.1|AA255511 zr85c04.r1 Soares_NhHMPu_S1 Homo sapiens cDNA clone IMAGE:682470 5', mRNA sequence
AGAGTGCGAGGGACAAAGCAAAGACAGACGATTGATGGTCAAAACCAGGAAAAGGAGTTTACTTCAGTAC
TTGACATAGTAATGGTTGTTCGGTGCTGCTGGCCTGCTTGTCTAATTTACGTCTTTAGTGGATTCCATAA
CTTTATTTATTTCCACTCTAGGATATCCTGTACCTTCACAACTCTTTAGAGGAGGTAAACAGTGCCCTAG
TGGGGTACCAGAGACAGAATGATCTTAAACTCGAGGGAATGAACGAGACAGTCAGTAATCTTACCCAGAG
AGTCAACCTGATAGAAAGCGATGTGGTTGCTATGAGCAAGGTAGAAAAGAAAGCAAACCTGTCCTTC
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 from phytochrome A and ndhF sequence data: tribes and trichomes revisited.
[2] 惠婕, 黄丛林, 吴忠义, 张秀海. 拟南芥光敏色素基因PHYA转化菊花的研究[J]. 江苏农业科学, 2011,(02)