Subject: Re: Suspect multiple cases, Exelixis lines
> Bob and Roger,
>
> We are trying to resolve discrepancies between previously existing
> FlyBase
> records and data from the massive August xml submission for the
> Exelixis
> lines.
...
> ============================================
>
> Category 3
>
> A little different \-- not flagged as multiples, but 2004 data sent
> to Bloomington suggest existence of additional insertion.  For these,
> a second insertion record was never created, and the recent submission
> confirms the existing record.  ... Do you have any more
> specific data?
>
> "Original line may have contained an additional insertion on arm."
> PBac{PB}CG9619c02710 FBti0041050 (76A3)
> Possible second insertion on 3R?
> 10971,"PB","c02710","c02710-3","3R",17786791,"minus","c02710-5","3L",19235486
,"minus"
There are two 3prime sequences for this line in Joe's database that map
to different arms and neither are to the same arm as the 5prime.
The following 3prime sequence maps to 3R in 93F14:
TTAATCAATTACACT
CGTTTTTGTTTTCACGTATTTATGGGAGGGCAAACGCGTTATAT
The other 3prime sequence maps to 2L-21F1:
TTAAATATTTGCAAG
TGAGGCAATTAGCCAGAATTAGCTTTCAAATAAATATAATATAAATATAT
AATATACAAATATAACATAAGCCATCCATATTTATTATACATTTTACACT
AGTCAAGTGCATTGAGTACTAATATAGTGAATTTACATAACAACCAGTGT
CATAGCGGCATAACCAGCACCACAGAGGCCCACCGATGCGACCTGGCAGT
AACGCAGCTCTTTGCAGATCCGGCGC
> PBac{PB}GRHRc03956    FBti0041118  (27A1)
> Possible second insertion on 3R?
> 11320,"PB","c03956","c03956-3","3R",5457779,"plus","c03956-5","2L",6706464,"m
inus"
There are two 3prime sequences in the database that map to different
sites and neither site is near the 5prime flank site.
The following sequence maps to SpdS on 3R:
TTAAGCTGTTGAGATTTTAAGGACT
AACCTACAATAGCCTAATCCCATATGTATCCTACATTGAAGGTCCCTAAA
TCATAGATTGTAGAAATCGAAAATTTTCCACTGGTTGTTCAAACACAAAT
TGCCCAGCCAGCATTTTCGGACCCTTTGGTTTTCGTGTGTTTATTCTTGA
TCTGCACCAACAGCCTTATCGATGGAGTCATCTAGGGCCAAAAACGACAG
ACAGAATACTGATAGCAAGTCAGCTCGTCTTTCAGGTTTGAGTTCCTCCA
GTCGAACATTGGGTACACTTGCGC
The other 3prime sequence maps in CG15443 on 2L:
ttatttCAGGTCAATGGTGGTAATCTGAGCCC
GGAATCGATGGATAAACATATTCAGTGGCACCCAGGAACCCGATTTTTCA
TATGTGAATTTATTTTTATACTGGCAAAGAAGTTCGGCGAGGAGATTCAT
TTCCTTTTTGTGCCTTTTTAATTTAATTTTTCTATGATTTCCACGGAAAA
AGTCCAGTGCTCCTTCTGTCCAAAATTATTCACCACTAGCTAGGCGAAAA
TGTGAAAAAACTATACGAAGATAAATGTTTGTTTTTCCAAAGAAATTTAT
TTCAATTTTATATTCTTCAACAGGTAAAGGATATCGATATCCGATAAGAA
TTTTCCCATCAAAACTTGGGCTGACCACCACAGGGCGACCCTTGCAAGTT
TGCGTTTATCTCAGCTGTTAAATATGGTAAACACACCTTAGTTTCAAAAA
TCATCATTTTGATAAATAATTTGAATTTCGAACATCGATAATAAATCGAT
TTAGCATATGGCCCAAAGAATAGGGTGCCCAGTGTACTGTGCACAATGTG
AAGTTTAGCTTATTATTATTTTGAATTGTTCATCAAGGCAATCGCATTAA
CTTTCAATTAATTGGGATGTAT
> PBac{PB}deflc06100  FBti0041269 (67C5)
> Possible second insertion on 4?
> 17746,"PB","c06100","c06100-3","3L",9681120,"plus","c06100-5","4",1050811,"pl
us"
There are three 5prime sequences in the database.  Two of these map to
the same site as the 3prime flank and one maps to CG11076 on the 4th
chromosome
1) The following sequence maps to defl on 3L:
TTAAGGAAGCTCTCGTTGAAAGTGCTCACGCGGGTGCCGGTCAGGTGAGAC
ATGGTTACAGGTTTCCTCACTCACATTTATCGCAGATAAATCGTGTTTAT
TGAGGTTTTCATTAGCCAAACGACACAAAAACAAACCGGCTGCAAATGCT
TCTTCTTGCTAATTTGTCGTTCGTAGGAAACTCCGG
2) The following sequence maps to CG11076 in 102F5:
ttaa
atcctatctagcTTTCGTAGTTCCTGtgatc
3) The following sequence maps to the same site in defl as \#1
TTAAGGAAGCTCTCGTTGAAAGTGCTCACGCGGGTGCCGGTCAGGTGAGACA
TGGTTACAGGTTTCCTCACTCACATTTATCGCAGATAAATCGTGTTTATT
GAGGTTTTCATTAGCCAAACGACACAAAAACAAACCGGCTGCAAATGCTT
CTTCTTGCTAATTTGTCGTTCGTAGGAAACTCCGGTATCATTGCAGCGAT
AGCTGGTCACTTAACAGTACAAAAACGATTGAATCCAAAGTCTATAATGT
CAATTCTTAAGAAGTGTTTATTAAGATC
...Bob
\--
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Robert W. Levis, Ph.D.
Carnegie Institution of Washington
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