HOMEWORK#7

Retrieving DNA sequence / GenBank

 

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

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







 Answer:

<1>

Identify :

*gb|J02263|MLM124

Moloney murine sarcoma virus clone 124 (proviral), complete genome.

Length = 5833, Plus Strand HSPs: Score = 7183 (1984.8 bits), Expect = 0.0, P = 0.0 Identities = 1447/1460 (99%),

Positives = 1447/1460 (99%), Strand = Plus / Plus

*emb|V01185|REMSVX

Genome of murine sarcoma virus (strain 124).

Contains genes for the gag polyprotein, which is post- translationally cleaved into the core proteins p15, p12, p30 and p10, for an unknown protein (gene X), and the transforming g... Length = 5833

Plus Strand HSPs:

Score = 7165 (1979.8 bits), Expect = 0.0, P = 0.0 Identities = 1445/1460 (98%), Positives = 1445/1460 (98%),

Strand = Plus / Plus



Possible Function::

Moloney murine sarcoma virus(M-MuSV), was obtained from sarcomas induced in Balb/c mice after passage of high doses of Moloney murine leukemia virus(M-MuLV; Moloney, 1966). M-MuSV is capable of transformation of fibroblasts in vitro and induction of tumors in the animals, but is unable to replicate. From the stocks of M-MuSV, J. Ball and colleagues have isolated a strain of M-MuSV clone 124, which has an overabundance of the transforming virus to that of the helper M-MuSV (Ball et al., 1973). Retroviruses can serve as excellent eucaryotic vectors, and hence a detailed knowledge of the nucleotide sequence of pMSV-1L should be very beneficial for construction of appropriate plasmid vectors.

source : 1.......5833

misc_feature : 2.......590

CDS : 1042.......2658

CDS : 3875.......4999

misc_feature : 5245.......5833




<2>

*Lycopersicon esculentum


*Lycopersicon esculentum class II small heat shock protein Le-HSP17.6 mRNA, complete cds gi|1773290|gb|U72396|LEU72396 [1773290]