Subject: Re: New merges
..
I've attached a file with the 18 cDNAs that indicate gene merges should
take place. 2 of the 18 are possible chimeric clones, and should probably
not be merged. A few of the cases are merges of 3 genes. I gather you
have already merged some of these. Let me know if something looks wrong.
For all but one of these I took the full-length cDNA sequence, did blastn
searches against na_gadfly.dros.RELEASE1 and na_geno.dros.RELEASE1 at
FlyBLAST. In one case, I did a local blastn against
na_gadfly.dros.RELEASE2 and na_geno.dros.RELEASE2.
Cheers,
Sima
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LD27988=CG3101
<up>By BLAST 908-2649 of the 3045bp  BcDNA:LD27988  matches CG3101 and
is on AE003447.1, 1-916 of LD27988 matches CG3102 and is on AE003448.1; this
says CG3101 and CG3102 should be merged.</up>
SD05444=Tim9b
<up>By BLAST 606-1484 of the 1582bp  BcDNA:SD05444  matches CG12788 and is
on AE003512.1, 1-508 of SD05444 matches Tim9b(CG17767) and is on AE003512.1;
this says Tim9b(CG17767) and CG12788 should be merged.</up>
GH24627=CG8572
<up>By BLAST 897-2090 of the 2652bp  BcDNA:GH24627  matches CG8576 and
is on AE003559.1, 1-901 matches CG8572 and is on AE003559.1; this says that
CG8572 and CG8576 should be merged.</up>
GH20492=CG18020
<up>By BLAST 1941-3823 of the 3974bp  BcDNA:GH20492  matches CG18021 and
is on AE003462.1, 1-1794 matches CG18020 and is on AE003462.1; this says that
CG18020 and CG18021 should be merged.</up>
GH21518=CG4000? \!Possible chimeric clone!
<up>By BLAST 562-1539 of the 1557bp  BcDNA:GH21518  matches CG4000 and
is on AE003731.1, 1-380 matches CG13841 and is on AE003740.1; this says that
CG4000 and CG13841 should perhaps be merged. However, because these are so
far apart in the genome (92E8-92F5 versus 94C1-94D3), this may be a case of a
chimeric clone rather than a merged gene</up>.
LD29969=CG18787
<up>By BLAST 186-1070 of the 1386bp  cDNA:LD29969  matches CG18789 and
is on AE003634.2, 1-982 matches CG18787 and is on AE003634.2; this says that
CG18787 and CG18789 should be merged.</up>
GH03013=CG3550
<up>By BLAST 1-988 of the 2553bp  BcDNA:GH03013  matches CG3550 and is
on AE003458.1, 987-2219 matches CG11605 and is on AE003458.1; this says that
CG3550 and CG11605 should be merged.</up>
LP01670=Lcp1? \!Possible chimeric clone!
<up>By BLAST 582-1507 of the 2080bp  BcDNA:LP01670  matches CG6044 and is
on AE003457.1, 1-532 matches Lcp1(CG11650) and is on AE003837.1; this says that
CG6044 and Lcp1 should perhaps be merged. However, because these are so
far apart in the genome (58D2-58E8 versus 44B8-44C6), this may be a case of a
chimeric clone rather than a merged gene</up>.
LD47466=dlp
<up>By BLAST 820-3093 of the 3762bp  BcDNA:LD47466  matches dlp(CG5031)
and is on AE003533.1, 1-766 matches CG17703 and is on AE003534.1; this says
that dlp(CG5031) and CG17703 should be merged.</up>
LD40565=CG7102
<up>By BLAST 887-1985 of 2089bp  BcDNA:LD40565  matches CG7102 and is on
AE003619.1, and 1-890 matches CG17973 and is on AE003619.1; this says that
CG7102 and CG17973 should be merged.</up>
GH11472=CG5544
<up>By BLAST 834-2268 of the 2289bp  BcDNA:GH11472  matches CG5544 and is
on AE003799.1, and 1-799 matches CG16859 and is on AE003799.1; this says that
CG5544 and CG16859 should be merged.</up>
LD39166=Hs6st
<up>By BLAST 725-1825 of the 2656bp  BcDNA:LD39166  matches CG4451 and is
on AE003728.1, 1-754 matches Hs6st(CG18533) and is on AE003728.1, 1821-1957
matches CG17188 and is on AE003728.1; this says that Hs6st and CG4451 and
CG17188 should be merged.</up>
SD07650=CG9510
<up>By BLAST 1232-2772 of the 2797bp  BcDNA:SD07650  matches CG9510 and
is on AE003623.1, 1-809 matches CG9515 and is on AE003623.1; this says that
CG9510 and CG9515 should be merged.</up>
GH15471=Myosin-heavy-chain-like
<up>By BLAST 1183-6127 of the 6223bp  BcDNA:GH15471  matches
Myosin-heavy-chain-like(CG10218) and is on AE003711.1, 1-1094 matches CG10224
and is on AE003711.1; this says that Myosin-heavy-chain-like(CG10218) and
CG10224 should be merged.</up>
GH13229=CG9584
<up>By BLAST 976-2691 of the 2764bp  BcDNA:GH13229  matches CG9585 and
is on AE003623.1, 1-780 matches CG9584 and is on AE003623.1, 762-986 matches
CG18566 and is on AE003623.1; this says that CG9584 and CG9585 and CG18566
should be merged.</up>
LD47625=CG14954
<up>By BLAST 641-1528 of the 2347bp  BcDNA:LD47625  matches CG16745 and
is on AE003476.1, 274-651 matches CG14954 and is on AE003477.1; this says that
CG14954 and CG16745 should be merged.</up>
SD03168=CG10439
<up>By BLAST 816-2753 of the 3307bp  BcDNA:SD03168  matches CG13435
and is on AE003791.1, 1-831 matches CG10439 and is on AE003791.1; this says
that CG10439 and CG13435 should be merged.</up>
LD29569=CG12790
<up>By BLAST 1665-3028 of the 3601bp  cDNA:LD29569  matches CG12790 and
is on AE003475.1, 1-1106 matches CG13797 and is on AE003474.1,
1093-1668 matches CG16763 and is on AE003475.1; this says that CG12790
and CG13797 and CG16763 should be merged.</up>
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