HOMEWORK#5

Retrieving DNA sequence / GenBank

* due on 5/14

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

AATTAATTCTCTCAATCAAATCCAATTTTCTCCCTATAAAAACCCTAAGGTCCTATA

GTGTTCTATATCCAACACTAGCTCCTACTCCCTAAAGCATTTATTATATCTTCCCCT

AGCTAGATACTTCATTCCACAAATAGTTTGCAGCTTTTTCTTTTCCTCTAAAACAAT

GGAAATAGCTGGGAAAATTGCATGCTTTGTGGTATTGTGCATGGTGGTAGCTGCACC

CTGCGCAGAAGCCATAACCTGTGGCCAGGTTACGTCGAATTTGGCACCTTGTCTTGC

TTATCTTAGAAACACGGGGCCTCTGGGACGTTGTTGCGGTGGCGTTAAGGCTCTGGT

GAATTCTGCAAGGACCACAGAAGATCGTCAAATTGCATGCACTTGCCTGAAATCAGC

TGCAGGTGCTATTTCTGGAATCAATTTGGGCAAAGCTGCTGGTCTCCCTAGTACTTG

TGGTGTCAATATTCCTTACAAGATCAGCCCTTCCACTGACTGCTCCAAGTACCTCAC

TTTTTTTCTCTCTCATGCTATTCTTATCCTTATATTCTATCTGCTTCATTTTCGCTT

ATCTTTTAAATTTTTTATTCGGAATCTTTATACCA

Please help him to identify the gene and its protein sequence.

Data searched from NCBI BLAST Search:

pir||S22168 lipid transfer protein - common tobacco gi|19883 (X62395)

lipid transferase [Nicotiana tabacum]

Length = 114

Plus Strand HSPs:

Query:

170MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLAYLRNTGPLGRCCGGVKALVNS 349

MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLAYLRNTGPLGRCCGGVKALVNS

Sbjct:

1MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLAYLRNTGPLGRCCGGVKALVNS 60

Query:

350ARTTEDRQIACTCLKSAAGAISGINLGKAAGLPSTCGVNIPYKISPSTDCSK 505

ARTTEDRQIACTCLKSAAGAISGINLGKAAGLPSTCGVNIPYKISPSTDCSK

Sbjct:

61ARTTEDRQIACTCLKSAAGAISGINLGKAAGLPSTCGVNIPYKISPSTDCSK 112

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

know?

Nucleotide (742) Protein (1019)

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

1773290 ---------------------------------------------------

Definition Lycopersicon esculentum class II small heat shock protein Le-

HSP17.6 mRNA, complete cds.

GenBank Name: LEU72396, Accession: U72396

NCBI Seq ID: 1773290

Updated Jan 13, 1997

Citation REF [1]

D.K. Kadyrzhanova, K.E. Vlachonasios, P. Ververidis & D.R.

Dilley (1996). A heat-treatment chilling tolerance related

cDNA from tomato fruit encoding a small heat-shock protein

class II. Unpublished

Citation REF [2]

Data Submission: D.K. Kadyrzhanova, K.E. Vlachonasios, P.

Ververidis & D.R. Dilley (1996).

Created Oct 23, 1996

Updated Jan 14, 1997

Coding region Comments: heat treatment/chilling 1773290: 108..584

tolerance related protein from

tomato fruit.

Sequence 738 nt, linear rna

1 tacggctgcg agaagacgac agaaggggac tgcaattaca aatcaaacca

51 aaattgacaa atttcacgca caaaatcaca atatccaaaa atttctcaat

101 actgaaaatg gatttgaggt tgttgggtat cgataacaca ccactcttcc

151 acactctcca ccatatgatg gaagctgccg gtgaagattc cgacaagtct

201 gtcaatgcac catcaaggaa ctatgttcgt gatgctaagg ccatggctgc

251 tacaccagcg gatgtgaagg agtatcctaa ttcgtatgtt tttgttgtgg

301 atatgccagg gttgaaatct ggagatatca aagtgcaggt ggaagaagac

351 aatgtgctgt tgattagtgg tgaaaggaag agggaagaag agaaagaagg

401 tgcaaagttt attaggatgg agagaagggt tgggaaattc atgaggaagt

451 ttagtctgcc agagaatgcg aatactgatg caatttctgc agtttgtcaa

501 gatggagttc tgactgttac tgttcagaaa ttgcctcctc ctgagccaaa

551 gaaacccaaa acaattgagg tgaaagttgc ttgaagttat ggactctgtt

601 ttgatggttt gtggtatgat gtagtagaaa taaagttgta ggagtagtga

651 acttttcctt tcatctttct gctatgtttt cacgtctgtt tgaatgttac

701 aatagccatg ggtattgttt gttttgatgc caaaaaaa