Subject: Genuine duplication or assembly error?
Hi,
There appears to be what is either a genuine duplication or assembly error
in AE003634.2 (NCBI version dated 16 Sept \- we seem to still as a version
skew between NCBI and BDGP blast server so attempting to report coordinates
is a non-starter).
The duplication  spans:- 
1st copy:
=======
C-terminal part of CG5202 to N-terminal of CG31864.
immediately followed  by:- 
2nd  copy:- 
=======
C-terminal part of CG31864 to CG12264.
The sequence of the first copy is listed here so you can place it against
whichever scaffold you  use:- 
GAGATCTGGTTCGTACGCTTCGCCTTCAACGCCTGGCAAAAGATTCTGGCCTTGGGCAAT
CAACTGGGCACAACATTTGTCTGGGAATTGGACTGCAATGATCCCAATTTAACAAAGTGT
AGCCAGCTGGTTCATCCCAAAAGCAACTCCACCATCCGACAGACTTCCTTCTCCAAAGAC
GGTTCCATTTTAGTTTGCGTGTGCGACGACAGCACCGTGTGGCGATGGGATCGCGTCAAT
TAGGATGAGTGTTTCTAGGCTAAAAGAATTTTCCTTATCCTTCTAAATCCGATACCATAT
TTATGTAACCATAGTTATTTTCAGTGTAATGTTTACCTTCAATATTAAGTATGTTATTAT
GCGTAGCATTTATATACAATACTCATTGTATTGACAATTTATGTTAAATTATGTTAAATT
TTTTAACATTAACCAAGATATTTATTCTATTCTATTACTTTTTTAATGATCAAATAGCTT
CGCAAATATTATCATCTTATGTTGTGTGAATGGCGTGGGCTCTATCTTTAATGTTTATAT
TTTAACTAACTAACTTGTACACAATAAAAACTGTGAACACTAAAGATTAAAACCAATATT
TTTTTAAAGGGTTCTTCAAAAATAACGGTTTTTATCTCAAATGTATCTGGTATTTTCAGC
CGTTCTTTGAACGGTCACTCGAATCAGCTGCATTCATTTGTTTATATAGCAATTCGCAAA
CAGTTGGATTTTCCTGTTTAGTTGTTATTCCCATTACTAAAATGCTTACCGACAGAGTTC
TGGCCACCAAGGAGGCGCTAGTGGTGGCTCTGGGCGACAACTGGGAGCGTTACCGGGCCA
ACATGAAGAATTGGTTTCGGAGCCGTTGGACTAAGGAGGAATTCGATGCGGAGTCGCGGA
AAATCCTAACACCTGACAAACTGCACCTGCACAATCAGTTCCTGCTCGCCCTGCTCAACA
AGATCGACGCCTTTGCTCCCCTGGAGAATCCTCCGGCCGTCCAGACCAGCAGCAGTAGTG
GCAACCGAAGCAAACGGCGCAAAAGAAGTTCCCGCACCTTCGCCGAACGCCTTAATTTTG
AGCTCAGCGACGTCCTGGACTTTGTAGCCGAGGACAACATGCAAATCATTCGTCCGCCAA
CCACGATCGGTATTCCGTCGGACCAGCAACAGCAACAGCTTCAGTCGCAGCGGTACTGCG
CGCAGGAACTTTTCCTGCCCGACGCGGGATTCATTATGGGACGATTTCTGATCGGTGCCT
GGGAAATCGGACTTGTCTCCGTGGACGACAATGTCGCCGAGTACGTTGCCATGGCCGTGC
AAGTTCTGCTCAAGGATCTACTATCGGCAATCATCAAGAAACGAAAGCACTACAAGACCA
GCGGCGAGGGAAACTTTTACTACGATGTAGGTGCTCCGTTGCGTGATCCTTCGCTGCGCA
ACACCGTCACCCGGCAGAAGGTCGACGACACGCCGCTGGAACTGGACAAGGAACTGAATA
CGGCCAACTTTATGCGGCGACAGAACGACGATGTGACCTTCCTCTCCGCCTGCGAAGAAG
TGTAAGCTCCTGAATAATAATGAGATTTTCATGTGAAACACAAACTTAGGTTTTGTTTCT
TTCAGCCAACCCACCGAACGCACAGTAATCACCCTCAAGGACTGCCAACTGGCCTTACGG
GATCGCAACCTGATAGGCTCGCATGCCGTCTACTCTATAAACATGGAACGACTCAATATG
ATGATGCATTAGCTTATAAGTTCTAATTATTTTATTATATCAGCTTCTGTAAAAATATAT
ACATTATACGCTAGTGTACCATTAAGTGTTTGGTTCAGCAAAAATTCCGTGGAGGCGGTT
TGAATGGCAAGGCACCTGGTAGAAATTGATCCGCCTTGAATGCTTCGATTTCCTGCTCGT
TGAGATCCTCCATGCGACTGTAAACTGAGGACTGGATTTCGTTGGTCGGTTGAGCTTGCT
GCTGCTGCTGCTGCATCATTTGCTGTTGCTGTTGCATTTGAAATTGTTGTTGCTGCTGCT
GCATTTGTTGCTGTTGCATCTGCTGCTGCTGATGCATTTGTTGCTGTTGCATCTGTTGCT
GCTGCTGCATCTGTTGCTGCTGCTGCATCTGTTGTTGATTAGGGAATGCAGATGCTGCTG
CTTGAGCAAATAATCCGGAGGCAGCTGCCTGCTGCTGCTGTTGTAGTTGCTGAGAAGCCT
GAGTAAACATTCCGCCCATATTTTGGCTTGCGGCTTGGCCAAAGATTCCCGTCGACTGTG
GTTGCTGCTGCTGCTGTTGGAAACCACCGAAAGGATTAGGATTCACTGGCTGAGCTTGCA
CCTGAACCTGCGCCTGGGCGAAAATGTTGCCCCCTTGGAAAGCTTGTGCAGCAGGCTGCA
GCTGTTGCTGCTGTGGCTGTCCAAAGACACTTTGTGCACCTGTTGCCGCAGCTCCTACAC
CAAAAATGCTATTCCTTGCATTGGCATTGCTAATCGTTCCGCCGAAAATGCTATTGGTGT
TGCTGGCTTGGCTTGTGGCATTCCCAAATATATTTCCCGCACTCAGCGTGGGCTTTCCAA
AAATGGATGCAGATGTATTGGCGGCAGCCGGAGCTGCTGCAGCGAAGGGATTACTGGACT
GCTGAGGGGCAGCCGACACAGTGCCGCCCTCCGGCGTCTCGTGGATCTTGATCATCATTT
CCAGGACCTGCGGCGACATCTGAAGCATGGTCTTCATCTTGTTGTTAGCCTCTAGGACCT
CACGGTTAAACTGTTGGCTGAACTGTTCGAATTGGTTTTGTCGTTTGGCCTCGTAACACA
TGAACCGCACCTCCTCGAAGGATTGGTCCTGAATAAAGTTGGGGAAATTCGCTTTGTCCT
TAAAGGGTCCGTAGGCGGACAAAGGCCACATCTTGCCATTGAGGCTGGATTCCATGTCGG
CTTTGAGATATTGCCTAAAATAATTAAGTTATTAGTTCATCTGCATAGTTTTAATATCAA
TGTACTCACTTAACATCGAAATGCTCGTTGTTGCACTTTGCGCCATAGCGGCAGGAGCCT
TGTTGAAAGAACCGGCAGACAACCATATTTAAATTTGATTTTAATTTTTGCCTATTTCCT
ATATTTATTATTTCAAAACTGCTTCAACTTTTGTACTTTTGTTTATAATTGTCTTACTTT
GCGTATTGAGTATTCTTTGAGTATTTTATGGCTCACTGAGAAAAATATACCGTGCCTATG
CGCGCAATTTCGTGAATTCGTAACTTAAGTTCGCTGAATGATTAAGATAATTTTGTAAGC
AAACATATTTAAGATGAAAACTGGTTTTTGAAAATATAGTTCCTTGTAAATTATACATTA
AGTGCGAATATATCTGAAAAATATTGGTTTCTTGCACAGATGCTATTCATTTTTCATATG
TTCAAAGAAATTCAGAAACTTGCTTCTGCATAATCGAATCAGATAATTTTAAAGTGAATT
CCGGAGTCCTTTGGTATATCTCGTGCCGCCGAATACGGTCCCACTGATTGTGAAATCCGT
GATAACGAATTTTAACACCAGAATTTCTAGGATTCCATCAGAATGCAAAAAGTGCTGGGA
CGCATCCAGGCGCAGGTCCTCCGCTCCCGGGCGACGAATGCATTAGCCAATGTGGTTAGA
CACGAGGCCACCTCCTCCAGGACAGCGGCTAAACCAGCCGCCACATCCAAAGGTAAGCGG
ATCCTCCAAGATGCACAGTTACCGCTTACCAAAATCGTATTCGTTCGTAGAATTCCGGGA
GAGACAGGTGCGATTCAACATAAAGAACGAACAGACCGAGGGTAGACCACTTTACCTGGA
TGCCCAGGCCACCACTCCAATGGACCCACGTGTATTGGACGCTATGCTCCCCTATCTGAC
CAATTTCTACG
The first and second copy are identical except in a small central portion
(nts 1973-2137).
This central portion is very slightly  different:- 
Score = 825 (129.8 bits), Expect = 2.0e-30, P = 2.0e-30
Identities = 165/165 (100%), Positives = 165/165 (100%), Strand = Plus
/Plus
Query: 1 AGCTTGCTGCTGCTGCTGCTGCATCATTTGCTGTTGCTGTTGCATTTGAAATTGTTGTTG
60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 172919 AGCTTGCTGCTGCTGCTGCTGCATCATTTGCTGTTGCTGTTGCATTTGAAATTGTTGTTG
172978
Query: 61 CTGCTGCTGCATTTGTTGCTGTTGCATCTGCTGCTGCTGATGCATTTGTTGCTGTTGCAT
120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 172979 CTGCTGCTGCATTTGTTGCTGTTGCATCTGCTGCTGCTGATGCATTTGTTGCTGTTGCAT
173038
Query: 121 CTGTTGCTGCTGCTGCATCTGTTGCTGCTGCTGCATCTGTTGTTG 165
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 173039 CTGTTGCTGCTGCTGCATCTGTTGCTGCTGCTGCATCTGTTGTTG 173083
Score = 751 (118.7 bits), Expect = 4.3e-27, P = 4.3e-27
Identities = 157/161 (97%), Positives = 157/161 (97%), Strand = Plus / Plus
Query: 5 TGCTGCTGCTGCTGCTGCATCATTTGCTGTTGCTGTTGCATTTGAAATTGTTGTTGCTGC
64
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 176837 TGCTGCTGCTGCTGCTGCATCATTTGCTGTTGCTGTTGCATTTGAAATTGTTGTTGCTGC
176896
Query: 65 TGCTGCATTTGTTGCTGTTGCATCTGCTGCTGCTGATGCATTTGTTGCTGTTGCATCTGT
124
||| |||||||||| |||||||||||||||||||||||||||||||||||||||||||
Sbjct: 176897 TGC---ATTTGTTGCTATTGCATCTGCTGCTGCTGATGCATTTGTTGCTGTTGCATCTGT
176953
Query: 125 TGCTGCTGCTGCATCTGTTGCTGCTGCTGCATCTGTTGTTG 165
|||||||||||||||||||||||||||||||||||||||||
Sbjct: 176954 TGCTGCTGCTGCATCTGTTGCTGCTGCTGCATCTGTTGTTG 176994
This has the following  implications:- 
============================
1) CG31864 is a fusion between two known genes, CG12264 and CG5202.
Evidence for the genuineness of CG12264 and CG5202 is strong.
2) CG31865 and CG31866 are identical.
3) CG18787 and CG18789 are almost identical. The difference lies in near
the C-terminal end of the genes where the slight sequence difference
between the copies leads to CG18787 terminating first. I note that the
sequence viewer from BDGP names both these genes as CG18787: perhaps in the
current version of AE003634, both sequences are now identical? if this is
the case, it will be worth reviewing what evidence there is for this
duplication being there at all. It may well be artifactual.
Regards,
David Huen, Dept. of Genetics, Cambridge