Difference between revisions of "Phosphatase GeneID SpurP030"
(Created page with "SpurP030 is identical to part of SpurP030 in protein sequence. To find whether they are encoded by the same gene: 1. BLAT the two protein sequences of SpurP030 and SpurP031 ...") |
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ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN | ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN | ||
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browser details SpurP030 1130 1 377 377 100.0% Scaffold35563 +- 8548 10360 1813 | browser details SpurP030 1130 1 377 377 100.0% Scaffold35563 +- 8548 10360 1813 | ||
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browser details SpurP030 1130 1 377 377 100.0% Scaffold14519 ++ 131552 133364 1813 | browser details SpurP030 1130 1 377 377 100.0% Scaffold14519 ++ 131552 133364 1813 | ||
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browser details SpurP031 1581 1 529 529 100.0% Scaffold14519 ++ 102754 133364 30611 | browser details SpurP031 1581 1 529 529 100.0% Scaffold14519 ++ 102754 133364 30611 | ||
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browser details SpurP031 1130 153 529 529 100.0% Scaffold35563 +- 8548 10360 1813 | browser details SpurP031 1130 153 529 529 100.0% Scaffold35563 +- 8548 10360 1813 | ||
Latest revision as of 21:05, 29 September 2015
SpurP030 is identical to part of SpurP030 in protein sequence. To find whether they are encoded by the same gene:
1. BLAT the two protein sequences of SpurP030 and SpurP031
ACTIONS QUERY SCORE START END QSIZE IDENTITY CHRO STRAND START END SPAN
browser details SpurP030 1130 1 377 377 100.0% Scaffold35563 +- 8548 10360 1813
browser details SpurP030 1130 1 377 377 100.0% Scaffold14519 ++ 131552 133364 1813
browser details SpurP031 1581 1 529 529 100.0% Scaffold14519 ++ 102754 133364 30611
browser details SpurP031 1130 153 529 529 100.0% Scaffold35563 +- 8548 10360 1813
2. Get the genomic sequences aligned to SpurP030 and compare them by BL2SEQ: they are identical.
3. Further, BLAT the region of the shorter scaffold Scaffold35563:3506-10451, bounded by repeats. The sequence is 99.6% identical to the region of Scaffold14519. I also BLATed the region downstream Scaffold35563:12978-17572 (the region 10452-12977 has repeats), which only matches to Scaffold35563.
In sum, SpurP030 and SpurP030 are either gene originated by recent duplication or they are artifacts due to gene assembly.
