Subject: nc5 report, third installment
Hi Aubrey and Gillian,
Here is another installment of P insertions. Let me know if you
have any questions about them.
cheers,
sima
>l(2)05642=Uba1
p_name l(2)05642
name CG1782
gene Uba1
ct_name CT5340
relation inside
r_orientation \+
inside_intron 0
inside_exon 1
dist5 22
dist3 5018
<up>maps at nt 22 of gene in same orientation as gene; EP(2)2375 maps 544bp
downstream in same gene</up>
>l(2)05643=Rpt1
p_name l(2)05643
name CG1341
gene Rpt1
ct_name CT3016
relation inside
r_orientation \+
inside_intron 0
inside_exon 1
dist5 8
dist3 1389
<up>l(2)05643 and EP(2)2153 inserted at same nucleotide, 8nt downstream of Rpt1
gene, a gene nested in an intron of CG17985; insertion in same orientation as
gene</up>
>l(2)05714=CG8886
p_name l(2)05714
name CG3792
gene
ct_name CT12669
relation behind
r_orientation \+
inside_intron 0
inside_exon 0
dist5 6081
dist3 7323
p_name l(2)05714
name CG8891
gene
ct_name CT25526
relation front
r_orientation \-
inside_intron 0
inside_exon 0
dist5 8023
dist3 7320
CG8886|FBan0008886|CT25498|FBan0008886  last_updated:000321 
Length = 940
Score = 178 bits (90), Expect = 3e-45
Identities = 90/90 (100%), Positives = 90/90 (100%)
Query 1 gcgccgagtaaccgtcattactagacgccagccagctggagagctccggatatttctccc 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 290 gcgccgagtaaccgtcattactagacgccagccagctggagagctccggatatttctccc 231
Query 61 actctgtgcgatagcgttggtggtacagtc 90
||||||||||||||||||||||||||||||
Sbjct 230 actctgtgcgatagcgttggtggtacagtc 201
<up>not near any annotation by Guochun (not sure why); but by BLAST, inserted in
opposite orientation at bp 208 of CG8886 (in LD03394.5')</up>
>l(2)05836=CG7392=WD-40-family-member
p_name l(2)05836
name CG7392
gene WD-40-family-member
ct_name CT22741
relation inside
r_orientation \+
inside_intron 1
inside_exon 0
dist5 359
dist3 7378
<up>l(2)05836 and EP(2)2514 are 1bp away from each other in intron of CG7392;
l(2)05836 inserted in same orientation as gene, 53bp downstream of end of
first exon</up>
>l(2)05847=CG8732
p_name l(2)05847
name CG8732
gene CG8732
ct_name CT25221
relation inside
r_orientation \+
inside_intron 1
inside_exon 0
dist5 3089
dist3 12768
<up>l(2)05847 inserted in intron of CG8732, in same orientation as gene, 473bp
downstream of end of first exon; EP(2)2365 also inserted 286bp downstream of
l(2)05847 in same intron; plasmid rescue flanking sequence probably needs
trimming since only bp56-368 match genomic sequence (or polymorphic between
strains)</up>
>l(2)06225=CG6105
p_name l(2)06225
name CG6105
gene
ct_name CT19171
relation inside
r_orientation \-
inside_intron 2
inside_exon 0
dist5 692
dist3 782
<up>inserted in opposite orientation in second intron of CG6105</up>
>l(2)06270=CG8846=Phas1?
p_name l(2)06270
name CG8846
gene Phas1
ct_name CT9265
relation behind
r_orientation \+
inside_intron 0
inside_exon 0
dist5 20
dist3 1163
<up>l(2)06270 in hotspot for insertion: EP(2)2244 at 3396566, EP(2)1010,
l(2)k00609 (but complemented), EP(2)2266, EP(2)2085, EP(2)2255, EP(2)2429,
EP(2)2350, l(2)k13506 (but complemented), l(2)06270 at 3396689, EP(2)0818,
EP(2)2550, and l(2)k07736 at 3396696 (all within 130bp); l(2)06270 only 20bp
upstream of Phas 1 start in same orientation as gene</up>
>l(2)06496=CG9893
p_name l(2)06496
name CG9893
gene CG9893
ct_name CT27878
relation inside
r_orientation \+
inside_intron 0
inside_exon 1
dist5 18
dist3 622
<up>l(2)06496 inserted in same orientation as gene 18bp downstream of start of
CG9893 transcription and in LD16285.5'</up>
>l(2)06655=?
<up>no computed analysis but BLASTing against All fly sequence: 3' sequence
indicates inserted at 110608 minus orientation of AE003804.1, not near any
annotation; 5' says inserted at 112619 in minus orientation of AE003804.1;
polymorphism in strain or multiple inserts</up>
3' sequence:
Score = 326 (48.9 bits), Expect = 4.2e-08, P = 4.2e-08
Identities = 70/76 (92%), Positives = 70/76 (92%), Strand = Minus / Plus
Query: 76 GCGCCTTAGACCGCTCGGCCACGCTACCATGTCGTAGATTATGTCAAACGCACATGAAGA 17
|||||||||||||||||||||||||||||||| |||||||||||||||||| || ||||
Sbjct: 110533 GCGCCTTAGACCGCTCGGCCACGCTACCATGTTGTAGATTATGTCAAACGCTCAACAAGA 11059
2
Query: 16 CACAAGGCTAGGAAGC 1
|| ||||||||||||
Sbjct: 110593 GACGAGGCTAGGAAGC 110608
5' sequence:
Score = 411 (61.7 bits), Expect = 6.1e-12, P = 6.1e-12
Identities = 83/84 (98%), Positives = 83/84 (98%), Strand = Minus / Plus
Query: 84 GGCGACCCTTTTGCCAGTACGCTTGTTGCCAGTTTCAAGTGTTTTTGTTGCACGTTGACA 25
||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 112612 GGCGACCCTTTTGCCGGTACGCTTGTTGCCAGTTTCAAGTGTTTTTGTTGCACGTTGACA 11267
1
Query: 24 GTCCGTTAAAGGTGACACAGGCGC 1
||||||||||||||||||||||||
Sbjct: 112672 GTCCGTTAAAGGTGACACAGGCGC 112695
>l(2)06708 inserted in repeat in genome
>l(2)06850=grh
<up>no computed analysis; BLASTN against All shows l(2)06850 inserted in minus
orientation at 250845 of AE003801.1, in intron of grh in same orientation as
gene; also in intron of LP11035.5'; may be polymorphism because no match from
122 to 249 of flanking sequence to genomic sequence</up>
gadfly| SEG:AE003801 |gb|AE003801.1|Drosophila melanogaster genomic scaffold
142000013386047 section 11 of 52, complete sequence.|AE003801.1
 GI:7302679 
Length = 272,650
Minus Strand HSPs:
Score = 902 (135.3 bits), Expect = 9.1e-56, Sum P(2) = 9.1e-56
Identities = 186/192 (96%), Positives = 186/192 (96%), Strand = Minus / Plus
Query: 441 CGAATTCCCCCAAAGGGAAGTGGNTCGATGTGTGACTGCGATGGTGCTATGTAGCGAGCT 382
CGAA TC C CAAAGG AAGTGG TCGATGTGTGACTGCGATGGTGCTATGTAGCGAGCT
Sbjct: 250407 CGAACTCGCGCAAAGG-AAGTGGTTCGATGTGTGACTGCGATGGTGCTATGTAGCGAGCT 25046
5
Query: 381 CTGTGCGGGAGCGAGAGCACCATCCAAATCACGTACGCACACATACGATCGTATAACAGC 322
CTGTGCGGGAGCGAGAGCACCAT CAAATCACGTACGCACACATACGATCGTATAACAGC
Sbjct: 250466 CTGTGCGGGAGCGAGAGCACCATACAAATCACGTACGCACACATACGATCGTATAACAGC 25052
5
Query: 321 GTGCGAGCGTATAACAGTTGACCGTGCAGTGGCAGCAGCAAAGGCTCATTGTTGTTGTTG 262
GTGCGAGCGTATAACAGTTGACCGTGCAGTGGCAGCAGCAAAGGCTCATTGTTGTTGTTG
Sbjct: 250526 GTGCGAGCGTATAACAGTTGACCGTGCAGTGGCAGCAGCAAAGGCTCATTGTTGTTGTTG 25058
5
Query: 261 CTCGCGTACATA 250
CTCGCGTACATA
Sbjct: 250586 CTCGCGTACATA 250597
Score = 600 (90.0 bits), Expect = 9.1e-56, Sum P(2) = 9.1e-56
Identities = 120/120 (100%), Positives = 120/120 (100%), Strand = Minus / Plus
Query: 121 ACGCTGATTCGTATTGGCTGCAGCCACTAATACTCATTGCTCACTCACACCAGCAATTGA 62
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 250726 ACGCTGATTCGTATTGGCTGCAGCCACTAATACTCATTGCTCACTCACACCAGCAATTGA 25078
5
Query: 61 CAGACCAATTGCAGGTCTGTTAGACAACAGCAGCGGCAGCAACAACTACATCGCCCAGCA 2
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 250786 CAGACCAATTGCAGGTCTGTTAGACAACAGCAGCGGCAGCAACAACTACATCGCCCAGCA 25084
5
>l(2)06949=CG8151?
p_name l(2)06949
name CG8151
gene CG8151
ct_name CT24236
relation behind
r_orientation \-
inside_intron 0
inside_exon 0
dist5 35
dist3 2283
<up>l(2)06949 inserted 35bp upstream of CG8151 in opposite orientation of gene</up>
>l(2)07129=CG10941=mm?
p_name l(2)07129
name CG10941
gene mm
ct_name CT30649
relation behind
r_orientation \+
inside_intron 0
inside_exon 0
dist5 61
dist3 96016
<up>l(2)07129 inserted just 61bp upstream of start of mm; hotspot since same
insertion position as l(2)k07110 (but complemented) and l(2)k04222b (but
complemented)</up>
>l(2)07806=?
<up>no computed analysis but BLASTN against All indicated inserted in reverse
orientation relative to AE003452.1 around 193215, not near any annotations</up>
gadfly| SEG:AE003452 |gb|AE003452.1|Drosophila melanogaster genomic scaffold
 GI:7291191 
Length = 305,505
Minus Strand HSPs:
Score = 1299 (194.9 bits), Expect = 4.7e-52, P = 4.7e-52
Identities = 267/276 (96%), Positives = 267/276 (96%), Strand = Minus / Plus
Query: 277 TTGGCAAATTCTTGGTTATAGCACTTCTATAACTTGCATTTCAAATATCTTAAGAGATAG 218
|| ||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||
Sbjct: 192940 TTTGCAAATTCTTGGTTATAGCACTTCTTTAACTTGCATTTCAAATATCATAAGAGATAG 19299
9
Query: 217 CTAATTAAGTCTTAGCCCAACTTTTTAAGCCAAGCTTGGAAGCTCCCGCTCTCTTCCAAG 158
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193000 CTAATTAAGTCTTAGCCCAACTTTTTAAGCCAAGCTTGGAAGCTCCCGCTCTCTTCCAAG 19305
9
Query: 157 CTTTTTTCGCGCTCTTTGTGGAGCGCGGCTTTTGGTGGCTCGCCTGGCAATGCAATTCAG 98
|||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Sbjct: 193060 CTTTTTTCGCGCTCTTTGTGGAGCGCGGCTTTTGGTAGCTCGCCTGGCAATGCAATTCAG 19311
9
Query: 97 TTGCCAAACCAAACGCGATCGGCTAACAACCTCGTACCGCTCGCTCGCAGCTTTAGCTTT 38
||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193120 TTGCCAAACAAAACGCGATCGGCTAACAACCTCGTACCGCTCGCTCGCAGCTTTAGCTTT 19317
9
Query: 37 ACCGTTACGCCAGTGATTGAGCACTACTATATACCA 2
|||||||| |||||||||||||||||| |||| | |
Sbjct: 193180 ACCGTTACACCAGTGATTGAGCACTACAATATCCGA 193215
>l(2)07837=?
p_name l(2)07837
name CG3245
gene PpN58A
ct_name CT10905
relation behind
r_orientation \+
inside_intron 0
inside_exon 0
dist5 5491
dist3 6551
<up>l(2)07837 5.5kb upstream of PpN58A, in same orientation, but not near any
other gene</up>
>l(2)08014=?
<up>no computed analysis for l(2)08014 but BLASTN of All indicates insertion in
positive orientation at 186016 of AE003626.1; CG4539 starts at 186414 so
~400bp upstream in same orientation as gene</up>
gadfly| SEG:AE003626 |gb|AE003626.1|Drosophila melanogaster genomic scaffold
142000013386055 section 19 of 63, complete sequence.|AE003626.1
 GI:7297545 
Length = 265,236
Plus Strand HSPs:
Score = 1502 (225.4 bits), Expect = 3.2e-61, P = 3.2e-61
Identities = 330/354 (93%), Positives = 330/354 (93%), Strand = Plus / Plus
Query: 1 GCGCCAAGTCGAGAATTTGTTCCTTCAGTCTCGTCATCTGTTTCATCATTTGAGGCATAA 60
GCGCCAAGTCGAGAATTTGTTCCTTCAGTCTCGTCATCTGTTTCATCATTTGAGGCATAA
Sbjct: 185960 GCGCCAAGTCGAGAATTTGTTCCTTCAGTCTCGTCATCTGTTTCATCATTTGAGGCATAA 18601
9
Query: 61 CACTCTTCCATTTAAGCACTTTAATTCACTTGATGTAAAACTATTTACGAAGAGCACACA 120
CACTCTTCCATTTAAGCACTTTAATTCACTTGAT TAAAACTATTTACGAAGAGCACACA
Sbjct: 186020 CACTCTTCCATTTAAGCACTTTAATTCACTTGATATAAAACTATTTACGAAGAGCACACA 18607
9
Query: 121 ACTTACCATTTCGACTCTTGAAATAAAATGAACGAGTTTCGTCATTGCACGTGGAAGGAA 180
ACTTACCATTTCGA TCTTGAAATAAAATGAACGAGTTTCGTCAT GCACGTGGAAGGAA
Sbjct: 186080 ACTTACCATTTCGAGTCTTGAAATAAAATGAACGAGTTTCGTCATCGCACGTGGAAGGAA 18613
9
Query: 181 AAATTCTGTGAAAAGATGGCGGCCAACTATCGATGTCTCTGAATGCAACCATGGTAGTAT 240
AAATTCTGTGAAAAGATGGCGGCCAACTATCGATGTCTCTGAATGCAACCATGGTAGTAT
Sbjct: 186140 AAATTCTGTGAAAAGATGGCGGCCAACTATCGATGTCTCTGAATGCAACCATGGTAGTAT 18619
9
Query: 241 CGTATCGGAAAAATTGTTTGGTTTTTGCCTGATATATATTGTATAAGAATGTG-AATAAA 299
CGTATCGGAAAAATTGTTTGGTTTTTGCCTGATATATATTGTATAAGAATGTG AATAA
Sbjct: 186200 CGTATCGGAAAAATTGTTTGGTTTTTGCCTGATATATATTGTATAAGAATGTGCAATAAT 18625
9
Query: 300 TGATATT-CC-ATTTAAT--T-TTC-ATTAAATCATTCATAAAATACTTAATATA 348
T A T CC A T AAT T TTC ATT AAT TTCAT AAAT TT ATA A
Sbjct: 186260 TAACTTAACCGAATAAATGATATTCCATTTAATT-TTCATTAAATCATTCATAAA 186313
>l(2)08307 line has insertion that maps to CG3971 (on III)
p_name l(2)08307
name CG3971
gene CG3971
ct_name CT13185
relation inside
r_orientation \+
inside_intron 1
inside_exon 0
dist5 296
dist3 11219
<up>l(2)08307 inserted in same orientation as CG3971 in first intron about 120bp
downstream of end of first exon; element maps to 33A but gene maps to 73B;
multiple insert strain or needs to be resequenced?; l(3)02281 and l(3)neo21
also appear to have insertions in this intron, as well as a number of 3rd
chromosome EP lines</up>
>l(2)08492=CG1952
p_name l(2)08492
name CG1952
gene CG1952
ct_name CT6120
relation inside
r_orientation \+
inside_intron 0
inside_exon 2
dist5 685
dist3 3063
<up>l(2)08492 in second exon of CG1952, in same orientation as gene</up>
>l(2)08717=CG15095
p_name l(2)08717
name CG15095
gene CG15095
ct_name CT34970
relation inside
r_orientation \-
inside_intron 1
inside_exon 0
dist5 1790
dist3 3335
<up>l(2)08717 in opposite orientation of gene in first long intron about 1.3kb
downstream of end of first exon</up>