HOMEWORK#4

Retrieving DNA sequence / GenBank

• due on 12/10

1. Sho-Hua 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.

This sequence belongs to the ltp1 gene for lipid transferase in Nicotiana tabacum. The sequence identity between the above one and residue 1178-1782 of N. tabacum ltp1 gene is 98%.

Protein sequence:
MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLAYLRNTGPLGRCCGG
VKALVNSARTTEDRQIACTCLKSAAGAISGINLGKAAGLPSTCGVNIPYKISPSTDCSKVQ

 

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

There are 814 genes and 1088 proteins with their sequences known in Lycopersicon esculentum.

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

1	tacggctgcg	agaagacgac	agaaggggac	tgcaattaca	aatcaaacca	aaattgacaa
61	atttcacgca	caaaatcaca	atatccaaaa	atttctcaat	actgaaaatg	gatttgaggt
121	tgttgggtat	cgataacaca	ccactcttcc	acactctcca	ccatatgatg	gaagctgccg
181	gtgaagattc	cgacaagtct	gtcaatgcac	catcaaggaa	ctatgttcgt	gatgctaagg
241	ccatggctgc	tacaccagcg	gatgtgaagg	agtatcctaa	ttcgtatgtt	tttgttgtgg
301	atatgccagg	gttgaaatct	ggagatatca	aagtgcaggt	ggaagaagac	aatgtgctgt
361	tgattagtgg	tgaaaggaag	agggaagaag	agaaagaagg	tgcaaagttt	attaggatgg
421	agagaagggt	tgggaaattc	atgaggaagt	ttagtctgcc	agagaatgcg	aatactgatg
481	caatttctgc	agtttgtcaa	gatggagttc	tgactgttac	tgttcagaaa	ttgcctcctc
541	ctgagccaaa	gaaacccaaa	acaattgagg	tgaaagttgc	ttgaagttat	ggactctgtt
601	ttgatggttt	gtggtatgat	gtagtagaaa	taaagttgta	ggagtagtga	acttttcctt
661	tcatctttct	gctatgtttt	cacgtctgtt	tgaatgttac	aatagccatg	ggtattgttt
721	gttttgatgc	caaaaaaa