Homework 3


  1. Please find the genes for the protein that you showed the structures in homework 2.
    1 cgccgaccgc cagaccacct gcgcctgcct caagcagcag accagcgcca tgggcggcct
 61 gaggnccgac ctcgtcgncg gcatcccctc caagtgcgac gtcaacatcc cctacggcat
121 cagcccttcc accgactgct ccagggtgca ctgatgagcg gatcaacgtc gacaagtgat
181 gcgacaatan taaaggngag atcgatccat cgatctccaa nctctnattt cgcgggttgc
241 tatgtacatg cgaccgttgg tttaatggtc gagcttagaa atantataat gcatnnntng
301 ttcctttngt ttgtgnttaa ttntcttgnt ttaacntgat tgtanatttn anaagtttan
361 gntaantntt ga

 
  1. Which organism do these genes come from? How many sequences of DNA and Protein have been known for this organism?
Organism : Oryza sativa
DNA sequences : 74032
Protein sequences : 2347
  1. 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 ).
BLAST hits : 37 
10 Sequences :

1. dbj|D10955|RIC323PTP  Rice mRNA for Phospholipid transfer protein
     Query: 1   cgccgaccgccagaccacctgcgcctgcctcaagcagcagaccagcgccatgggcggcct 60
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
     Sbjct: 1   cgccgaccgccagaccacctgcgcctgcctcaagcagcagaccagcgccatgggcggcct 60
     Query: 61  gaggnccgacctcgtcgncggcatcccctccaagtgcgacgtcaacatcccctacggcat 120
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
     Sbjct: 61  gaggnccgacctcgtcgncggcatcccctccaagtgcgacgtcaacatcccctacggcat 120
     Query: 121 cagcccttccaccgactgctccagggtgcactgatgagcggatcaacgtcgacaagtgat 180
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
     Sbjct: 121 cagcccttccaccgactgctccagggtgcactgatgagcggatcaacgtcgacaagtgat 180
     Query: 181 gcgacaatantaaaggngagatcgatccatcgatctccaanctctnatttcgcgggttgc 240
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
     Sbjct: 181 gcgacaatantaaaggngagatcgatccatcgatctccaanctctnatttcgcgggttgc 240
     Query: 241 tatgtacatgcgaccgttggtttaatggtcgagcttagaaatantataatgcatnnntng 300
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
     Sbjct: 241 tatgtacatgcgaccgttggtttaatggtcgagcttagaaatantataatgcatnnntng 300
     Query: 301 ttcctttngtttgtgnttaattntcttgntttaacntgattgtanatttnanaagtttan 360
                ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
     Sbjct: 301 ttcctttngtttgtgnttaattntcttgntttaacntgattgtanatttnanaagtttan 360
     Query: 361 gntaantnttga 372
                ||||||||||||
     Sbjct: 361 gntaantnttga 372

2. gb|AF051369|AF051369 Oryza sativa lipid transfer protein mRNA, complete cds
     Query: 1   cgccgaccgccagaccacctgcgcctgcctcaagcagcagaccagcgccatgggcggcct 60
                ||||||||||||||||||||||||||||||||||||||||||||  ||||||||| | ||
     Sbjct: 244 cgccgaccgccagaccacctgcgcctgcctcaagcagcagaccaaggccatgggccggct 303
     Query: 61  gaggnccgacctcgtcgncggcatcccctccaagtgcgacgtcaacatcccctacggcat 120
                |||| |||||| ||||| ||||||||||||||||||||  ||||||||||||||||  ||
     Sbjct: 304 gaggcccgaccacgtcgccggcatcccctccaagtgcggggtcaacatcccctacgctat 363
     Query: 121 cagcccttccaccgactgctccagggtgcactgatgagcggatcaacgtcgacaagtgat 180
                |||||||||||||||||||||||||||||||   |||| ||||||||||   ||||||||
     Sbjct: 364 cagcccttccaccgactgctccagggtgcac---tgagtggatcaacgt---caagtgat 417
     Query: 181 gcgacaatantaaaggngagatcgatccatcgatct 216
                || |||||| ||| || ||||| |||||||||||||
     Sbjct: 418 gccacaataataatggagagatggatccatcgatct 453
 

3. gb|J04176|MZEPLTP Maize phospholipid transfer protein mRNA, complete cds. of clone
           9C2.
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| ||||||||||  ||||||| | |||||||||||||
     Sbjct: 391 gcatcccctccaagtgcggcgtcagcatcccctacaccatcagcacctccaccgactgct 450
     Query: 141 ccagggtgcactga 154
                |||||||| |||||
     Sbjct: 451 ccagggtgaactga 464

4. emb|X71668|SVLTP2 S.vulgare ltp2 gene
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| ||||||||||  ||||||| | |||||||||||||
     Sbjct: 905 gcatcccctccaagtgcggcgtcagcatcccctacaccatcagcacctccaccgactgct 964
     Query: 141 ccagggtg 148
                ||||||||
     Sbjct: 965 ccagggtg 972

5. gb|U66105|ZMU66105 Zea mays phospholipid transfer protein mRNA, complete cds
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| ||||||||||  ||||||| | |||||||||||||
     Sbjct: 363 gcatcccctccaagtgcggcgtcagcatcccctacaccatcagcacctccaccgactgct 422
     Query: 141 ccagggtg 148
                ||||||||
     Sbjct: 423 ccagggtg 430

6. emb|Z23271|OSLPTPRA O.sativa lipid transfer protein gene, complete CDS
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| ||||||||||  ||||||||| |||| ||||||||
     Sbjct: 641 gcatcccctccaagtgcggcgtcagcatcccctacaccatcagcccctccatcgactgct 700
     Query: 141 ccagg 145
                |||||
     Sbjct: 701 ccagg 705

7. gb|M57249|MZEPLTPA Maize phospholipid transfer protein mRNA, 3' end.
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| ||||||||||  ||||||| | |||||||||||||
     Sbjct: 204 gcatcccctccaagtgcggcgtcagcatcccctacaccatcagcacctccaccgactgct 263
     Query: 141 ccagg 145
                |||||
     Sbjct: 264 ccagg 268

8. emb|X71669|SVTLP1R S.vulgare ltp1 mRNA
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| | ||||||||  ||||||| | |||||||||||||
     Sbjct: 234 gcatcccctccaagtgcggcgtcagcgtcccctacaccatcagcacctccaccgactgct 293
     Query: 141 ccagggtg 148
                ||||||||
     Sbjct: 294 ccagggtg 301

9. emb|X83434|OSLTPB1 O.sativa mRNA for lipid transfer protein, b1
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| ||||||||||  ||||||||| |||| ||||||||
     Sbjct: 271 gcatcccctccaagtgcggcgtcagcatcccctacaccatcagcccctccatcgactgct 330
     Query: 141 ccag 144
                ||||
     Sbjct: 331 ccag 334

10. emb|X83435|OSLTPA15 O.sativa mRNA for lipid transfer protein, a15
     Query: 81  gcatcccctccaagtgcgacgtcaacatcccctacggcatcagcccttccaccgactgct 140
                |||||||||||||||||| ||||| | ||||||||  ||||||| |||||| ||||||||
     Sbjct: 353 gcatcccctccaagtgcggcgtcagcgtcccctacaccatcagcgcttccatcgactgct 412
     Query: 141 ccagggtg 148
                ||||||||
     Sbjct: 413 ccagggtg 420
 


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