HOMEWORK 3

 

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1. Please find the genes for the protein that you showed the structures in homework 2.
   Answer:
   

           caaaagctcgtgccggaacccggcacgaatcatcatcaaccaattcgcaccgatcgatcg
           atcgatccagcaactagatcaacagtactagctaggaagcatggcccgtgcacagttggt
           gttggtcgccctggtggcagctctgctcctcgccgccccgcacgccgccgtggccatcac
           ctgcggccaggtcaactccgccgtcgggccctgcctgacctacgcccgcggcggcgccgg
           gccgtcggcggcctgctgcagcggcgtgaggagcctttttgctgcagcaagcacgaccgc
           agaccggcgcaccgcctgcaactgcctcaagaacgcggcccgcggcatcaaggggctcaa
           cgccggcaacgccgccagcatcccctccaagtgcggcgtcagcgtcccctacaccatcag
           cgcttccatcgattgctccagggtgagctgagccatcgatcagagacggatcatatatat
           acagcagcgcgccggttgccacctagtagattttgcctgggtcgatgtgtggagccgaat
           tatgtatccagtactagtagtatcatatctgtattctggaataaaagatgagctagctaa
           ggtttcgatcaatcaccatgcatccatggttgatcggcccggtcacgctagctagctttc
           ttcttcttgtgtgttcgtttcgtacgttttgctccttttcgaggggtacgtgtaccagag
           agagctagagattctacatgcatgtactgcaactccttgtactacgtgcttgttttggat
           tattacacataaaaaaaaa

2. Which organism do these genes come from? How many sequences of DNA and Protein have been known for this organism?
   Answer: a. Oryza sativa (Rice) b. DNA sequence: 69340 c. protein: 2255
3. How many BLAST hits you can get if you use the gene you found for this protein as the query sequence to search against non-redundant GenBank + EMBL + DDBJ + PDB sequence database? Please also show 10 sequences that produce significant alignments ( you just need to show their names and ID numbers ).
   Answer: I got 69 BLAST hits!

   Name	ID number
   O.sativa mRNA for lipid transfer protein	Y08691
   Oryza sativa lipid transfer protein LPT III mRNA	AF017360
   O.sativa mRNA for lipid transfer protein, a15	X83435
   Oryza sativa lipid transfer protein LPT IV mRNA	AF017361
   Rice mRNA EN4	D29994
   Oryza sativa lipid transfer protein precursor (LTP2) mRNA	U31766
   O.sativa mRNA for lipid transfer protein, b1	X83434
   O.sativa lipid transfer protein gene	Z23271
   Oryza sativa lipid transfer protein mRNA	AF017358
   Rice mRNA for Phospholipid transfer protein	D10955