Difference between revisions of "Phosphatase GeneID SpurP124"

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SpurP124 locates in short contig and its sequence is incomplete.
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SpurP124, SpurP125, SpurP126, Spur200 are partially identical in protein sequence. To find out whether they are encoded by different genes:
 
SpurP124, SpurP125, SpurP126, Spur200 are partially identical in protein sequence. To find out whether they are encoded by different genes:
  
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1. BLAT the three sequences. SpurP124 is encoded by Scaffold67922; SpurP125 is encoded by Scaffold20002; SpurP126 is encoded by Scaffold86115; SpurP200 is encoded by Scaffold52488.
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BLAT the four sequences. SpurP124 is encoded by Scaffold67922 + Scaffold86115/Scaffold20002; SpurP125 is encoded by Scaffold86115/Scaffold20002; SpurP126 is encoded by Scaffold86115; SpurP200 is encoded by Scaffold52488.
  
 
Below are BLAT results:
 
Below are BLAT results:
  
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ACTIONS      QUERY          SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
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ACTIONS      QUERY          SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN  
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browser details SpurP124        925    1  309  448 100.0%  Scaffold67922  +-      2510      5486  2977
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browser details SpurP124        925    1  309  448 100.0%  Scaffold67922  +-      2510      5486  2977  
  
 
browser details SpurP124        913    1  309  448  99.4%  Scaffold52488  ++    158719    162171  3453
 
browser details SpurP124        913    1  309  448  99.4%  Scaffold52488  ++    158719    162171  3453
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browser details SpurP126        302    95  197  601  99.1%  Scaffold33476  ++        582      1307    726
 
browser details SpurP126        302    95  197  601  99.1%  Scaffold33476  ++        582      1307    726
  
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browser details SpurP200        931    1  311  311 100.0%  Scaffold52488  ++    158719    162177  3459
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browser details SpurP200        931    1  311  311 100.0%  Scaffold52488  ++    158719    162177  3459 *
  
 
browser details SpurP200        919    1  311  311  99.4%  Scaffold67922  +-      2504      5486  2983
 
browser details SpurP200        919    1  311  311  99.4%  Scaffold67922  +-      2504      5486  2983
  
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2. Then, we obtained the genomic sequences and BLAT them.
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2. To find out whether Scaffold86115 and Scaffold20002 are identical, BLAT Scaffold86115: 132767-134498. They have slight differences:
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ACTIONS      QUERY          SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
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browser details strPur2_dna    1732    1  1732  1732 100.0%  Scaffold86115  +    132767    134498  1732
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browser details strPur2_dna    1710    1  1732  1732  99.2%  Scaffold20002  -      4103      5826  1724

Latest revision as of 19:37, 6 October 2015

SpurP124 locates in short contig and its sequence is incomplete.

SpurP124, SpurP125, SpurP126, Spur200 are partially identical in protein sequence. To find out whether they are encoded by different genes:

BLAT the four sequences. SpurP124 is encoded by Scaffold67922 + Scaffold86115/Scaffold20002; SpurP125 is encoded by Scaffold86115/Scaffold20002; SpurP126 is encoded by Scaffold86115; SpurP200 is encoded by Scaffold52488.

Below are BLAT results:

ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN

browser details SpurP124 925 1 309 448 100.0% Scaffold67922 +- 2510 5486 2977

browser details SpurP124 913 1 309 448 99.4% Scaffold52488 ++ 158719 162171 3453

browser details SpurP124 412 311 448 448 100.0% Scaffold86115 +- 132767 134495 1729

browser details SpurP124 412 311 448 448 100.0% Scaffold20002 ++ 4106 5826 1721

browser details SpurP125 415 1 139 139 100.0% Scaffold86115 +- 132767 134498 1732

browser details SpurP125 415 1 139 139 100.0% Scaffold20002 ++ 4103 5826 1724

browser details SpurP126 1752 10 601 601 99.8% Scaffold86115 +- 132767 227975 95209

browser details SpurP126 415 463 601 601 100.0% Scaffold20002 ++ 4103 5826 1724

browser details SpurP126 302 95 197 601 99.1% Scaffold33476 ++ 582 1307 726

browser details SpurP200 931 1 311 311 100.0% Scaffold52488 ++ 158719 162177 3459 *

browser details SpurP200 919 1 311 311 99.4% Scaffold67922 +- 2504 5486 2983

2. To find out whether Scaffold86115 and Scaffold20002 are identical, BLAT Scaffold86115: 132767-134498. They have slight differences:

ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN

browser details strPur2_dna 1732 1 1732 1732 100.0% Scaffold86115 + 132767 134498 1732

browser details strPur2_dna 1710 1 1732 1732 99.2% Scaffold20002 - 4103 5826 1724

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