Phosphatase GeneID SpurP030

From PhosphataseWiki
Revision as of 21:05, 29 September 2015 by Mark (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

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.

Retrieved from "http://phosphatome.net/wiki/index.php?title=Phosphatase_GeneID_SpurP030&oldid=3025"