Homework 4 (due on 12/10>

Retrieving DNA sequence / GenBank

題目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.

Ans:NCBI blast中查到此段sequence為tobacco(煙草)中的一段gene。
請看完整的查詢結果(the whole imformation) andthe whole gene sequence
其translate之後之 protein為lipid transferase(完整的資料)。 其sequence為:MEIAGKIACFVVLCMVVAAPCAEAITCGQVTSNLAPCLAYLRNT GPLGRCCGGVKALVNSARTTEDRQIACTCLKSAAGAISGINLGKA
AGLPSTCGVNIPY KISPSTDCSKVQ

題目2. How many nucleotide and protein sequence of Lycopersicon esculentum were know?
Please find its class II small heat shock protein mRNA, complete cds.

Ans:NCBITaxonomy 中查到:Lycopersicon esculentum tomato(番茄)
know sequence:nucleotide共:817個,protein1092個。(until 1997/12/8)
請看完整的 查詢結果.
接著在上述之查詢結果同一頁下方可以Entrez查所有的proteins,再以key word"heat shock protein"限制查詢,得24個proteins,顯示出來之後可以找到所要的
class II small heat shock protein 而在其DBSOURCE中U72396可link至 此protein之mRNA
其完整的cds如下:

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"