Homework7

Question :

1. Sho-Hua cloned a gene in the lab. The part of DNA sequence is listed here:

1 tttgaaagac cccacccgta ggtggcaagc tagcttaagt aacgccactt tgcaaggcat

61 ggaaaaatac ataactgaga ataggaaagt tcagatcaag gtcaggaaca aagaaacagc

121 tgaataccaa acaggatatc tgtggtaagc ggttcctgcc ccggctcagg gccaagaaca

181 gatgagacag ctgagtgatg ggccaaacag gatatctgtg gtaagcagtt cctgccccgg

241 ctcggggcca agaacagatg gtccccagat gcggtccagc cctcagcagt ttctagtgaa

301 tcatcagatg tttccagggt gccccaagga cctgaaaatg accctgtacc ttatttgaac

361 taaccaatca gttcgcttct cgcttctgtt cgcgcgcttc cgctctccga gctcaataaa

421 agagcccaca acccctcact cggcgcgcca gtcttccgat agactgcgtc gcccgggtac

481 ccgtattccc aataaagcct cttgctgttt gcatccgaat cgtggtctcg ctgttccttg

541 ggagggtctc ctctgagtga ttgactaccc acgacggggg tctttcattt gggggctcgt

601 ccgggatttg gagacccctg cccagggacc accgacccac caccgggagg taagctggcc

661 agcaacttat ctgtgtctgt ccgattgtct agtgtctatg tttgatgtta tgcgcctgcg

721 tctgtactag ttagctaact agctctgtat ctggcggacc cgtggtggaa ctgacgagtt

781 ctgaacaccc ggccgcaacc ctgggagacg tcccagggac tttgggggcc gtttttgtgg

841 cccgacctga ggaagggagt cgatgtggaa tccgaccccg tcaggatatg tggttctggt

901 aggagacgag aacctaaaac agttcccgcc tccgtctgaa tttttgcttt cggtttggaa

961 ccgaagccgc gcgtcttgtc tgctgcagca tcgttctgtg ttgtctctgt ctgactgtgt

1021 ttctgtattt gtctgaaaat tagggccaga ctgttaccac tcccttaagt ttgaccttag

1081 gtcactggaa agatgtcgag cggatcgctc acaaccagtc ggtagatgtc aagaagagac

1141 gttgggttac cttctgctct gcagaatggc caacctttaa cgtcggatgg ccgcgagacg

1201 gcacctttaa ccgagacctc atcacccagg ttaagatcaa ggtcttttca cctggcccgc

1261 atggacaccc agaccaggtc ccctacatcg tgacctggga agccttggct tttgaccccc

1321 ctccctgggt caagcccttt gtacacccta agcctccgcc tcctcttcct ccatccgccc

1381 cgtctctccc ccttgaacct cctcgttcga ccccgcctcg atcctccctt tatccagccc

1441 tcactccttc tctaggcggg aattcgttag cttggtaagt gaccagctac agtcggaaac

1501 catcagcaag caggtatgta ctctccaggg tgggcctggc ttccccagtc aagactccag

1561 ggatttgagg gacgctgtgg gctcttctct tacatgtacc ttttgctagc ctcaaccctg

1621 actatcttcc aggtcattgt tccaacatgg ccctgtggat cgacaggatg caactcctgt

1681 cttgcattgc actaagtctt gcacttgtca caaacagtgc acctacttca agttctacaa

1741 agaaaacaca gctgcaactg gagcatttac tgctggattt acagatgatt ttgaatggaa

1801 ttaataatta caagaatccc aaactcaccc gcatgctcac atttaagttt tacatgccca

1861 agaaggccac agaactgaaa catctgcagt gtctagaaga agaactcaaa cctctggagg

1921 aagtgctaaa tttagctcaa agcaaaaact ttcacttaag gcctagggac ttaatcagca

1981 atatcaacgt aatagttctc gagctaaagg gatctgaaac aacattcatg tgtgaatatg

2041 ctgatgagac agccaccatt gtggaatttc tgaacagatg gattaccttt tgtcaaagca

2101 tcatctcaac actaacttga taattaagtg cttcccactt aaaacatatc aggatccgct

2161 gtggaatgtg tgtcagttag ggtgtggaaa gtccccaggc tccccagcag gcagaagtat

2221 gcaaagcatg catctcaatt agtcagcaac caggtgtgga aagtccccag gctccccagc

2281 aggcagaagt atgcaaagca tgcatctcaa ttagtcagca accatagtcc cgcccctaac

2341 tccgcccatc ccgcccctaa ctccgcccag ttccgcccat tctccgcccc atggctgact

2401 aatttttttt atttatgcag aggccgaggc cgcctcggcc tctgagctat tccagaagta

2461 gtgaggaggc ttttttggag gcctaggctt ttgcaaaaag cttgggctgc aggtcgaggc

2521 ggatctgatc aagagacagg atgaggatcg tttcgcatga ttgaacaaga tggattgcac

2581 gcaggttctc cggccgcttg ggtggagagg ctattcggct atgactgggc acaacagaca

2641 atcggctgct ctgatgccgc cgtgttccgg ctgtcagcgc aggggcgccc ggttcttttt

2701 gtcaagaccg acctgtccgg tgccctgaat gaactgcagg acgaggcagc gcggctatcg

2761 tggctggcca cgacgggcgt tccttgcgca gctgtgctcg acgttgtcac tgaagcggga

2821 agggactggc tgctattggg cgaagtgccg gggcaggatc tcctgtcatc tcaccttgct

2881 cctgccgaga aagtatccat catggctgat gcaatgcggc ggctgcatac gcttgatccg

Please help him to identify the gene and its possible function.

 

2. How many nucleotide and protein sequence of Lycopersicon esculentum were know?

Please find its class II small heat shock protein mRNA, complete cds.

Answer

1.We use the BLAST of NCBI to search the sequence. The program is setted to blastn and the database is setted to nr. we can find the message.

                                                                                       high score   small sum probability

                                                                                                            P(N)           N

gb|J02263|MLM124 Moloney murine sarcoma virus clone... 7183              0.0              1

emb|V01185|REMSVX Genome of murine sarcoma virus (st... 7165         0.0              1

gb|AF011892|AF011892 Moloney murine sarcoma virus gag-m... 5474      0.0              1

dbj|D88622|D88622 Bicistronic retroviral vector 4936                                0.0              3

gb|U00220|U00220 Human immunodeficiency virus type ... 4936               0.0              3

gb|M77239|SYNRRV Cloning vector pLXSH from Moloney ... 4936         0.0              3

gb|M63653|SYNMMLPLN6 Moloney murine leukemia virus retr... 4936   0.0              3

gb|M28246|SYNMMLPLN2 Moloney murine leukemia virus retr... 4936   0.0              3

gb|M28248|SYNMMLPLN4 Moloney murine leukemia virus retr... 4936   0.0              3

gb|M64754|SYNMOV2 Moloney murine leukemia virus retr... 4936           0.0              2

gb|M28245|SYNMMLPLN1 Moloney murine leukemia virus retr... 4936   0.0              3

gb|M28247|SYNMMLPLN3 Moloney murine leukemia virus retr... 4936   0.0              3

gb|M64753|SYNMOV1 Moloney murine leukemia virus retr... 4936           0.0              4

gb|AF033813|AF033813 Moloney murine sarcoma virus, comp... 4782        0.0              1

gb|J02266|MLMPROCG Moloney murine sarcoma virus (prov... 4397         0.0             2

gb|M96854|MMSAAX Moloney murine sarcoma virus gene ... 4038            0.0             3

emb|AJ224004|RVPSF1NBH Retroviral vector plasmid pSF1 (NB... 2471  0.0              8

gb|AF010170|AF010170 Plasmid pAMS with hybrid amphotrop... 2456       0.0              5

emb|AJ224005|RVPSF1PSN Retroviral vector plasmid pSF1 (PS... 2451      0.0              8

emb|V01541|REAMLV Abelson murine leukemia virus geno... 2420           0.0              6

gb|J02009|MLAPRO Abelson murine leukemia virus (pro... 2420                 0.0              6

gb|U93512|CVU93512 Cloning vector CA1, complete sequence 2385           0.0              5

emb|Z93724|ASZ93724 Murine retrovirus shuttle vector p... 2095                 0.0              8

emb|Z22761|REVPSFF Retroviral expression vector pSFF ... 1786                0.0              6

gb|J02255|MLMCG Moloney murine leukemia virus, com... 2447            5.1e-305          3

gb|AF033812|AF033812 Abelson murine leukemia virus, com... 2420       1.4e-301         3

dbj|AB003468|AB003468 Cloning vector pAP3neo DNA, comple... 2105 1.6e-294         2

gb|M99566|SYNSCOS sCos cloning vector SfiI containin... 2095              2.8e-294          2

gb|M99569|SYNPWE15 sCos cloning vector SfiI containin... 2095            2.9e-294          2

gb|M83237|SYNRSV5NEO cDNA expression vector RSV.5(neo). 2095  3.2e-294          2

gb|L36555|SYNTCRC Cloning vector murine T-cell recep... 2095             3.5e-294          2

gb|U02434|XXU02434 Cloning vector pSV2neo, complete s... 2095          3.6e-294          2

gb|AF047654|AF047654 Expression vector pSTAR, complete ... 2095        5.1e-294          2

gb|U02432|XXU02432 Cloning vector pMAMneo, complete s... 2095        5.3e-294          2

gb|U02430|XXU02430 Cloning vector pMAMneoBlue, comple... 2095      5.3e-294         2

gb|U02431|XXU02431 Cloning vector pMAMneo-CAT, comple... 2095   5.8e-294          2

gb|U02448|U02448 Cloning vector pMAMneo-LUC, comple... 2095          6.5e-294          2

gb|U13189|CVU13189 Cloning vector pYACneo, complete s... 2095         1.0e-293           2

gb|U89930|CVU89930 Cloning vector pTet-On, complete s... 2095            1.0e-293          2

gb|U89929|CVU89929 Cloning vector pTet-Off, complete ... 2095            1.0e-293          2

gb|U52109|CVU52109 Cloning vector pLK-neo DNA. 2095                     5.3e-292          2

gb|U19276|XXU19276 Cloning vector pGFP-1 green fluore... 2061           9.6e-290          2

gb|U55761|CVU55761 Cloning vector pEGFP-1, complete s... 2061         9.6e-290           2

gb|AF028239|AF028239 Mammalian expression vector pCMV-S... 2061 9.9e-290           2

gb|AF025668|AF025668 Epitope tagging vector pCMV-Tag 1,... 2061      1.0e-289         2

gb|U37573|XXU37573 Shuttle expression vector pBKCMV. 2061            1.0e-289          2

gb|U19277|XXU19277 Cloning vector pGFP-N3 green fluor... 2061          1.1e-289          2

gb|U19278|XXU19278 Cloning vector pGFP-C3 green fluor... 2061          1.1e-289         2 

gb|U57607|CVU57607 Cloning vector pEGFP-C3 with enhan... 2061        1.1e-289        2

gb|U36202|CVU36202 Cloning vector pS65T-C1, with gree... 2061           1.1e-289         2

gb|U36201|CVU36201 Cloning vector pRSGFP-C1, with gre... 2061         1.1e-289         2

gb|U19279|XXU19279 Cloning vector pGFP-N1 green fluor... 2061          1.1e-289         2

gb|U19280|XXU19280 Cloning vector pGFP-C1 green fluor... 2061           1.1e-289         2

gb|U57609|CVU57609 Cloning vector pEGFP-N3 with enhan... 2061         1.1e-289       2

gb|U55763|CVU55763 Cloning vector pEGFP-C1, complete ... 2061          1.1e-289        2

gb|U19282|XXU19282 Cloning vector pGFP-N2 green fluor... 2061           1.1e-289        2

gb|U19281|XXU19281 Cloning vector pGFP-C2 green fluor... 2061           1.1e-289        2

gb|U55762|CVU55762 Cloning vector pEGFP-N1, complete ... 2061         1.1e-289         2

gb|U57606|CVU57606 Cloning vector pEGFP-C2 with enhan... 2061         1.1e-289       2

gb|U57608|CVU57608 Cloning vector pEGFP-N2 with enhan... 2061         1.1e-289       2

gb|AF050498| Fusion trans-activator vector pFA-... 2061                             1.1e-289        2

gb|AF050500| Cloning vector pFA-cFos, complete ... 2061                          1.1e-289        2

gb|AF050499| Cloning vector pFA2-elk1, complete... 2061                         1.1e-289         2

gb|AF049616|AF049616 Cloning vector pFA2-CREB, complete... 2061     1.3e-289         2

gb|AF041247|AF041247 Expression vector pDual, complete ... 2061           1.3e-289         2

gb|AF060226|AF060226 Eukaryotic expression vector pCR3.... 2061           1.3e-289         2

gb|U90717|TRU90717 Transfection reporter vector pAV4p... 2105              5.8e-286         3

emb|X96612|EVPCMVPA1 Expression vector pCMVPA1 for prot... 2105 6.3e-286         3

emb|X96611|EVPCMVPA3 Expression vector pCMVPA3 for prot... 2105 6.3e-286         3

emb|X96610|EVPCMVPA2 Expression vector pCMVPA2 for prot... 2105 6.3e-286         3

emb|X65279|PWE15 pWE15 cosmid vector DNA 2095                              8.2e-282         3

emb|Z12112|PWE15A pWE15A cosmid vector DNA 2095                         8.3e-282         3

gb|U47120|CVU47120 Cloning vector pCI-neo, mammalian ... 1925           4.6e-281         2

gb|L07040|NE1EXPVECA pFNeo eukaryotic expression vector... 2095       7.4e-281         3

gb|AF043739|AF043739 Synthetic construct human telomera... 1925            7.5e-281         2

emb|AJ000156|ASAJ156 Artificial DNA. Bicistronic eukary... 1905            1.9e-279         2

gb|L07041|NE1EXPVECB pMHNeo eukaryotic expression vecto... 2095    7.1e-278         3

emb|X57540|CASBREML CAS-BR-E murine leukemia virus, vi... 1752    8.2e-263         3

gb|U94692|RMU94692 Rauscher murine leukemia virus, co... 1849             2.8e-260         4

emb|Y13893|MULV13893 Murine leukemia virus RNA for gag-... 1831     1.5e-256         4

emb|Z11128|REFMLVCGD Friend murine leukemia virus FB29 ... 1813    1.5e-256         4

gb|M93134|MLFCG Friend murine leukemia virus, comp... 1831                 8.4e-256         4

dbj|D88386|D88386 Friend murine leukemia virus compl... 1831                  4.8e-255         4

gb|M64448|MLEENVAB N-tropic ecotropic endogenous retr... 1481            2.6e-253         5

emb|X02794|REFMLVCG Friend murine leukemia virus (F-Mu... 1592       3.2e-241        4

gb|AF033811|AF033811 Moloney murine leukemia virus, com... 2447          1.3e-240        2

gb|K00021|MLFRO Friend spleen focus-forming virus ... 1445                      3.2e-235        6

gb|J02264|MLMLTR Moloney murine sarcoma virus unint... 2926                 2.7e-232        1

gb|K02712|MSVMUSV FBR murine osteosarcoma virus (pro... 894              8.5e-220        7

gb|M64447|MLEENVAA N-tropic ecotropic endogenous retr... 780               2.6e-218        7

emb|X03347|REMSVFBR FBR-murine osteosarcoma provirus g... 987          4.1e-217        6

gb|K02729|MLV4070A Mouse leukemia virus (amphotropic)... 1315              2.1e-208        7

gb|M64095|MLVBM5ECOL Murine leukemia virus gag protein,... 981          2.3e-205        7

emb|X14576|REMULVDU Murine leukemia virus defective Du... 1008         2.9e-205       6

gb|M54792|MLVTSBA1 Murine leukemia virus long termina... 2180             9.2e-199         3

gb|S77834|S77834 IL-2=interleukin-2 [human, lymphoc... 2367                      8.6e-186         1

emb|V00564|HSIL02 Human mRNA encoding interleukin-2 ... 2367              8.6e-186         1

emb|X01586|HSIL2R Human mRNA for interleukin 2 2358                          4.8e-185          1

gb|K03174|GIBIL2 Ape (gibbon) interleukin 2 mRNA. 2358                         4.8e-185          1

gb|S82692|S82692 interleukin-2 [human, placenta, te... 2358                          4.8e-185          1 　

we find the the score of Moloney murine sarcoma virus clone is hightest, so we select first item. Please press this to see what information is gotten.

we find some abstract:

The transformation protein of MolonNey murine sarcoma virus is a solute cytoplasma protein

Analysis of transforming gene products from Moloney murine sarcoma virus

Complete nucleotide sequence and organization of the Moloney murine sarcoma virus genome

2.We use TAXONOMY of NCBI, and  we type Lycopersicon esculentum to search. we find commond name of Lycopersicon esculentum is tomato.

We use Entrez to search its nucleotide and protein sequence.

The measgaes show: 1271 nucleotide sequences were found.

                                  1230 protein sequences were found.

We use Entrez of NCBI, and we type tilte word Lycopersicon esculentum and heat shock protein. We find 5 citations and find Lycopersicon esculentum class II small heat shock protein. Press this to show information.

Here we see cds:

CDS              108..584
                     /note="heat treatment/chilling tolerance related protein
                     from tomato fruit"
                     /codon_start=1
                     /product="class II small heat shock protein Le-HSP17.6"
                     /db_xref="PID:g1773291"
                     /translation="MDLRLLGIDNTPLFHTLHHMMEAAGEDSDKSVNAPSRNYVRDAK
                     AMAATPADVKEYPNSYVFVVDMPGLKSGDIKVQVEEDNVLLISGERKREEEKEGAKFI
                     RMERRVGKFMRKFSLPENANTDAISAVCQDGVLTVTVQKLPPPEPKKPKTIEVKVA"

Here we see the mRNA:

         1 augccgacgc ucuugugcug ucuuccccug acguuaaugu uuaguuuggu uuuaacuguu
       61  uaaagugcgu guuuuagugu uauagguuuu uaaaguguua ugacuuuuac cuaaacucca
      121 acaacccaua gcuauugugu ggugagaagg ugugagaggu gguauacuac cuucgacggc
      181 cacuucuaag gcuguucuga caguuacgug guaguuccuu gauacuugca cuacgauucc
      241 gguaccgacg auguggucgc cuacauucc ucauaggatt aagcauacaa aaacaacacc
      301 uauacggucc caacuuuaga ccucuauagu uucacgucca ccuucuucug uuacacgaca
      361 acuaaucacc acuuuccuuc ucccuucuuc ucuuucuucc acguuucaaa uaauccuacc
      421 ucucuuccca acccuuuaag uacuccuuca aaucagacgg ucucuuacgc uuaugacuac
      481 guuaaagacg ucaaacaguu cuaccucaag acugacaaug acaagucuuu aacggaggag
      541 gacucgguuu cuuuggguuu uguuaacucc acuuucaacg aacuucaaua ccugagacaa
      601 aacuaccaaa caccauacua caucaucuuu auuucaacau ccucaucacu ucaaaaggaa
      661 aguagaaaga cgauacaaaa gugcagacaa acuuacaaug uuaucgguac ccauaacaaa
      721 caaaacuacg guuuuuuu