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NIG-RNAi Strains Detail
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Stock Detail (Last Update: November 2007_FlyBase version FB2007_11)
 Stock ID 11942R-3 
 Symbol skpE  Full Name skpE 
 CG No CG11942  Old CG No CG11942 
 Synonyms CG11942, skpE 
 Accession No (Link to NCBI) NM_134515.1 
 Inserted Chr. lll 
 Insertional Mutation   
 Phenotype induced by Act5C-GAL4 at 28 degrees lethal 
 Map Viewer
 Reference
[Please submit your publication] 		Du J, Zhang J, Su Y, Liu M, Ospina JK, Yang S, Zhu AJ.
In vivo RNAi screen reveals neddylation genes as novel regulators of Hedgehog signaling.
PLoS One (2011) 6(9) e24168 [ PubMed ID = 21931660 ] [ RRC reference ]  
 Comment  
 Sequence (Last Update: July 10, 2007_NCBI RefSeq Release 24)
 Primer Seq. 5' 
aaggcctacatggccggaccgATGGTTACTCCCACCATCAAG 
 Primer Seq. 3' 
aatctagaggtaccATCCATGGGCCACAAAAACAG 
 Predicted Fragment Size 
498 
 IR fragment full Seq 
0001 ATGGTTACTC CCACCATCAA GCTTGAGTCC TCGGAAGGGG TGATCTTTCC GACGGAAGTC 
0061 CGAGTCGCCA TGGTCTCCGA AACCATCAAG ACCATGTTGG ATCACTTTGC CGTGCAGNAA 
0121 CGACGAGAAT GCCATCGTGC CCCTGCACTC GGTGAGCACG TTCACCCTGG GCAAGATTCT 
0181 AGCCTGGGCC AATCACCACA AGGACGATGA TGATCAGTCA ACGGAGGGTG AGGAGCTGAA 
0241 GCCACGTCGC CCATATGCCA TCTCCCCATG GGACGCCATC TTCTTGATGG TCAATTCAAC 
0301 CACCTTGCTC GAAATCATAC TGGCCGCCAA ACAACTGCAG ATCAAGGGCC TACTGGAACT 
0361 CACCTACAAT GTGGTGGCCA ATATGATTAG GGGCAAGACT CCCGAGGAGA TCCGCTTCAT 
0421 CTTCAACATT CCGGAAGACG TCTCGCCATC CGTGGACGGG GAGTTGAGAT GGAAAGACCT 
0481 GTTTTTGTGG CCCATGGAT 
 in silico PCR Fragment 
0001 ATGGTTACTC CCACCATCAA GCTTGAGTCC TCGGAAGGGG TGATCTTTCC GACGGAAGTC 
0061 CGAGTCGCCA TGGTCTCCGA AACCATCAAG ACCATGTTGG ATCACTTTGC CGTGCAG-AA 
0121 CGACGAGAAT GCCATCGTGC CCCTGCACTC GGTGAGCACG TTCACCCTGG GCAAGATTCT 
0181 AGCCTGGGCC AATCACCACA AGGACGATGA TGATCAGTCA ACGGAGGGTG AGGAGCTGAA 
0241 GCCACGTCGC CCATATGCCA TCTCCCCATG GGACGCCATC TTCTTGATGG TCAATTCAAC 
0301 CACCTTGCTC GAAATCATAC TGGCCGCCAA ACAACTGCAG ATCAAGGGCC TACTGGAACT 
0361 CACCTACAAT GTGGTGGCCA ATATGATTAG GGGCAAGACT CCCGAGGAGA TCCGCTTCAT 
0421 CTTCAACATT CCGGAAGACG TCTCGCCATC CGTGGACGGG GAGTTGAGAT GGAAAGACCT 
0481 GTTTTTGTGG CCCATGGAT 
 Assemble Data 

11942R-3.IR_full       1   ATGGTTACTCCCACCATCAAGCTTGAGTCCTCGGAAGGGGTGATCTTTCCGACGGAAGTC 60
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     1   ATGGTTACTCCCACCATCAAGCTTGAGTCCTCGGAAGGGGTGATCTTTCCGACGGAAGTC 60


11942R-3.IR_full       61  CGAGTCGCCATGGTCTCCGAAACCATCAAGACCATGTTGGATCACTTTGCCGTGCAGNAA 120
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||
11942R-3.in silico     61  CGAGTCGCCATGGTCTCCGAAACCATCAAGACCATGTTGGATCACTTTGCCGTGCAG-AA 120


11942R-3.IR_full       121 CGACGAGAATGCCATCGTGCCCCTGCACTCGGTGAGCACGTTCACCCTGGGCAAGATTCT 180
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     121 CGACGAGAATGCCATCGTGCCCCTGCACTCGGTGAGCACGTTCACCCTGGGCAAGATTCT 180


11942R-3.IR_full       181 AGCCTGGGCCAATCACCACAAGGACGATGATGATCAGTCAACGGAGGGTGAGGAGCTGAA 240
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     181 AGCCTGGGCCAATCACCACAAGGACGATGATGATCAGTCAACGGAGGGTGAGGAGCTGAA 240


11942R-3.IR_full       241 GCCACGTCGCCCATATGCCATCTCCCCATGGGACGCCATCTTCTTGATGGTCAATTCAAC 300
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     241 GCCACGTCGCCCATATGCCATCTCCCCATGGGACGCCATCTTCTTGATGGTCAATTCAAC 300


11942R-3.IR_full       301 CACCTTGCTCGAAATCATACTGGCCGCCAAACAACTGCAGATCAAGGGCCTACTGGAACT 360
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     301 CACCTTGCTCGAAATCATACTGGCCGCCAAACAACTGCAGATCAAGGGCCTACTGGAACT 360


11942R-3.IR_full       361 CACCTACAATGTGGTGGCCAATATGATTAGGGGCAAGACTCCCGAGGAGATCCGCTTCAT 420
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     361 CACCTACAATGTGGTGGCCAATATGATTAGGGGCAAGACTCCCGAGGAGATCCGCTTCAT 420


11942R-3.IR_full       421 CTTCAACATTCCGGAAGACGTCTCGCCATCCGTGGACGGGGAGTTGAGATGGAAAGACCT 480
                           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
11942R-3.in silico     421 CTTCAACATTCCGGAAGACGTCTCGCCATCCGTGGACGGGGAGTTGAGATGGAAAGACCT 480


11942R-3.IR_full       481 GTTTTTGTGGCCCATGGAT 499
                           |||||||||||||||||||
11942R-3.in silico     481 GTTTTTGTGGCCCATGGAT 499



 
 Off-target information (Last Update: November 4, 2007_NCBI RefSeq Release 26)
 Off-target search result

cv : coefficient of variation

(0 mm hits / total siRNA count)

mm : mismatch
cv 0mm 1mm 2mm 3mm target transcript off target name
100   480  0  0  2  NM_134515.1  CG11942-RA (skpE), mRNA 
7.08   34  59  61  50  NM_134514.1  CG11941-RA (skpC), mRNA 
5.83   28  61  39  66  NM_134513.2  CG12700-RA (skpD), mRNA 
1.45   7  2  5  2  NM_079238.2  CG8532-RB, transcript variant B (lqf), mRNA 
1.45   7  2  5  2  NM_168221.2  CG8532-RC, transcript variant C (lqf), mRNA 
1.45   7  2  5  2  NM_168219.1  CG8532-RA, transcript variant A (lqf), mRNA 
1.45   7  2  5  2  NM_168220.1  CG8532-RD, transcript variant D (lqf), mRNA 
1.45   7  2  5  2  NM_206291.1  CG8532-RE, transcript variant E (lqf), mRNA 
0.62   3  2  2  5  NM_206693.1  CG1522-RF, transcript variant F (cac), mRNA 
0.62   3  2  2  5  NM_001014732.1  CG1522-RJ, transcript variant J (cac), mRNA 
0.62   3  2  2  5  NM_001014735.1  CG1522-RG, transcript variant G (cac), mRNA 
0.62   3  2  2  5  NM_206695.1  CG1522-RD, transcript variant D (cac), mRNA 
0.62   3  2  2  5  NM_206694.1  CG1522-RE, transcript variant E (cac), mRNA 
0.62   3  2  2  5  NM_001014733.1  CG1522-RI, transcript variant I (cac), mRNA 
0.62   3  2  2  5  NM_001014734.1  CG1522-RH, transcript variant H (cac), mRNA 
0.62   3  2  2  5  NM_078578.2  CG1522-RA, transcript variant A (cac), mRNA 
0.62   3  2  2  5  NM_206696.1  CG1522-RC, transcript variant C (cac), mRNA 
0.62   3  2  2  5  NM_206697.1  CG1522-RB, transcript variant B (cac), mRNA 
0   0  2  4  5  NM_001043021.1  CG17800-PAT (Dscam), mRNA 
0   0  2  4  3  NM_001043014.1  CG17800-PAL (Dscam), mRNA 
0   0  2  4  3  NM_001043063.1  CG17800-PAI (Dscam), mRNA 
0   0  2  4  3  NM_001043048.1  CG17800-PAH (Dscam), mRNA 
0   0  2  4  3  NM_001043064.1  CG17800-PAE (Dscam), mRNA 
0   0  2  4  3  NM_001043061.1  CG17800-PAD (Dscam), mRNA 
0   0  2  4  3  NM_001043036.1  CG17800-PAA (Dscam), mRNA 
0   0  2  4  3  NM_001043052.1  CG17800-RZ, transcript variant Z (Dscam), mRNA 
0   0  2  4  3  NM_001043056.1  CG17800-RW, transcript variant W (Dscam), mRNA 
0   0  2  4  3  NM_206047.1  CG17800-RE, transcript variant E (Dscam), mRNA 
0   0  2  4  3  NM_001043018.1  CG17800-RV, transcript variant V (Dscam), mRNA 
0   0  2  4  3  NM_001043054.1  CG17800-RS, transcript variant S (Dscam), mRNA 

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