Difference between revisions of "Phosphatase GeneID SpurP124"

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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:
  
−
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.
+
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:
  
−
ACTIONS      QUERY          SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
+
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        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
Line 24: Line 24:
 
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
  
−
browser details SpurP200        931    1  311  311 100.0%  Scaffold52488  ++    158719    162177  3459
+
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
  
−
2. Then, we obtained the genomic sequences and BLAT them.
+
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

Revision as of 23:56, 29 September 2015

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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