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NIG-RNAi Strains Detail
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Stock Detail (Last Update: November 2007_FlyBase version FB2007_11)
 Stock ID 5399R-2 
 Symbol CG5399  Full Name CG5399 
 CG No CG5399  Old CG No CG5399 
 Synonyms CG5399 
 Accession No (Link to NCBI) NM_142224.1 
 Inserted Chr. ll 
 Insertional Mutation  lethal 
 Phenotype induced by Act5C-GAL4 at 28 degrees viable 
 Map Viewer
 Reference
[Please submit your publication] 		Umetsu D, Dunst S, Dahmann C.
An RNA interference screen for genes required to shape the anteroposterior compartment boundary in Drosophila identifies the Eph receptor.
PLoS One (2014) 9(12) e114340 [ PubMed ID = 25473846 ] [ RRC reference ]  
 Comment  
 Sequence (Last Update: July 10, 2007_NCBI RefSeq Release 24)
 Primer Seq. 5' 
aaggcctacatggccggaccgACGCCACAATCCTGCGCCCAA 
 Primer Seq. 3' 
aatctagaggtaccCTGGCACGGCAATCCAACTGA 
 Predicted Fragment Size 
500 
 IR fragment full Seq 
0001 ACGCCACAAT CCTGCGCCCA AGCCACCGGC ATTAGTTTTA ACCAGACCGC TTTTAGTGGT 
0061 CAGTGGGTCG AGTTGGCCCG CAATCCCGCC TCAAATGTCT CCTGCATTTC CCTTAACGTG 
0121 GCTTTCTGGA ACAACAACAA TTACATGCTG GTCAATGTCA GCCATTCAAG CAATGTCGCC 
0181 TCCACTTTGG TGGACGTCTA TGAAACTGCG AATATCACGC TGGTGGAGAA CAACCTCAGC 
0241 GGATACAATG TCACCCTGGT GAATGGCCAG AAGCAGGAGT ACGTCTTCGT GAAGTTGCTT 
0301 AGCTTTGTGA ACTCCACCTA TCTGGTTGGA TGCACCTACA CCAATGCTAC CAACACATCA 
0361 ACCAGTGCTG GTTTTATTCT GGGTAGGTCC ACCTATACTC CGGAAGGCGT AAGGATTGCC 
0421 AACAATGATG CCTCCGTGTC CTTCAGCAAT TTCCAGAACA ACACCTACGG CAATGTCACT 
0481 CAGTTGGATT GCCGTGCCAG  
 in silico PCR Fragment 
0001 ACGCCACAAT CCTGCGCCCA AGCCACCGGC ATTAGTTTTA ACCAGACCGC TTTTAGTGGT 
0061 CAGTGGGTCG AGTTGGCCCG CAATCCCGCC TCAAATGTCT CCTGCATTTC CCTTAACGTG 
0121 GCTTTCTGGA ACAACAACAA TTACATGCTG GTCAATGTCA GCCATTCAAG CAATGTCGCC 
0181 TCCACTTTGG TGGACGTCTA TGAAACTGCG AATATCACGC TGGTGGAGAA CAACCTCAGC 
0241 GGATACAATG TCACCCTGGT GAATGGCCAG AAGCAGGAGT ACGTCTTCGT GAAGTTGCTT 
0301 AGCTTTGTGA ACTCCACCTA TCTGGTTGGA TGCACCTACA CCAATGCTAC CAACACATCA 
0361 ACCAGTGCTG GTTTTATTCT GGGTAGGTCC ACCTATACTC CGGAAGGCGT AAGGATTGCC 
0421 AACAATGATG CCTCCGTGTC CTTCAGCAAT TTCCAGAACA ACACCTACGG CAATGTCACT 
0481 CAGTTGGATT GCCGTGCCAG  
 Assemble Data 

5399R-2.IR_full       1   ACGCCACAATCCTGCGCCCAAGCCACCGGCATTAGTTTTAACCAGACCGCTTTTAGTGGT 60
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     1   ACGCCACAATCCTGCGCCCAAGCCACCGGCATTAGTTTTAACCAGACCGCTTTTAGTGGT 60


5399R-2.IR_full       61  CAGTGGGTCGAGTTGGCCCGCAATCCCGCCTCAAATGTCTCCTGCATTTCCCTTAACGTG 120
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     61  CAGTGGGTCGAGTTGGCCCGCAATCCCGCCTCAAATGTCTCCTGCATTTCCCTTAACGTG 120


5399R-2.IR_full       121 GCTTTCTGGAACAACAACAATTACATGCTGGTCAATGTCAGCCATTCAAGCAATGTCGCC 180
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     121 GCTTTCTGGAACAACAACAATTACATGCTGGTCAATGTCAGCCATTCAAGCAATGTCGCC 180


5399R-2.IR_full       181 TCCACTTTGGTGGACGTCTATGAAACTGCGAATATCACGCTGGTGGAGAACAACCTCAGC 240
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     181 TCCACTTTGGTGGACGTCTATGAAACTGCGAATATCACGCTGGTGGAGAACAACCTCAGC 240


5399R-2.IR_full       241 GGATACAATGTCACCCTGGTGAATGGCCAGAAGCAGGAGTACGTCTTCGTGAAGTTGCTT 300
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     241 GGATACAATGTCACCCTGGTGAATGGCCAGAAGCAGGAGTACGTCTTCGTGAAGTTGCTT 300


5399R-2.IR_full       301 AGCTTTGTGAACTCCACCTATCTGGTTGGATGCACCTACACCAATGCTACCAACACATCA 360
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     301 AGCTTTGTGAACTCCACCTATCTGGTTGGATGCACCTACACCAATGCTACCAACACATCA 360


5399R-2.IR_full       361 ACCAGTGCTGGTTTTATTCTGGGTAGGTCCACCTATACTCCGGAAGGCGTAAGGATTGCC 420
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     361 ACCAGTGCTGGTTTTATTCTGGGTAGGTCCACCTATACTCCGGAAGGCGTAAGGATTGCC 420


5399R-2.IR_full       421 AACAATGATGCCTCCGTGTCCTTCAGCAATTTCCAGAACAACACCTACGGCAATGTCACT 480
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5399R-2.in silico     421 AACAATGATGCCTCCGTGTCCTTCAGCAATTTCCAGAACAACACCTACGGCAATGTCACT 480


5399R-2.IR_full       481 CAGTTGGATTGCCGTGCCAG 500
                          ||||||||||||||||||||
5399R-2.in silico     481 CAGTTGGATTGCCGTGCCAG 500



 
 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   482  0  0  0  NM_142224.1  CG5399-RA (CG5399), mRNA 
0.62   3  3  2  4  NM_133004.1  CG8211-RA (CG8211), mRNA 
0   0  2  4  2  NM_166937.1  CG2841-RA, transcript variant A (ptr), mRNA 
0   0  2  4  2  NM_080022.2  CG2841-RB, transcript variant B (ptr), mRNA 
0   0  2  4  2  NM_166938.1  CG2841-RC, transcript variant C (ptr), mRNA 
0   0  2  4  2  NM_057961.4  CG3771-RA (a6), mRNA 
0   0  2  2  5  NM_137155.2  CG10228-RA (Pcf11), mRNA 
0   0  2  2  3  NM_131991.2  CG3252-RA (CG3252), mRNA 
0   0  1  4  10  NM_079282.1  CG3322-RA (LanB2), mRNA 
0   0  1  4  5  NM_130605.3  CG3806-RA, transcript variant A (eIF2B-epsilon), mRNA 
0   0  1  4  5  NM_206606.1  CG3806-RB, transcript variant B (eIF2B-epsilon), mRNA 
0   0  1  3  3  NM_078878.2  CG10123-RA (Top3alpha), mRNA 
0   0  1  3  3  NM_001032400.1  CG9850-RB, transcript variant B (CG9850), mRNA 
0   0  1  3  3  NM_137983.3  CG9850-RA, transcript variant A (CG9850), mRNA 
0   0  1  3  3  NM_058124.2  CG5772-RA (Sur), mRNA 
0   0  1  3  3  NM_142755.1  CG5732-RA (CG5732), mRNA 
0   0  1  2  3  NM_135964.2  CG17912-RA (CG17912), mRNA 
0   0  1  2  2  NM_057391.3  CG1977-RA (alpha-Spec), mRNA 
0   0  1  2  2  NM_132956.1  CG9086-RA (CG9086), mRNA 
0   0  0  6  8  NM_001043082.1  CG11798-RC, transcript variant C (chn), mRNA 
0   0  0  6  8  NM_206119.1  CG11798-RB, transcript variant B (chn), mRNA 
0   0  0  6  8  NM_137169.3  CG11798-RA, transcript variant A (chn), mRNA 
0   0  0  6  4  NM_137084.2  CG8241-RA (CG8241), mRNA 
0   0  0  6  4  NM_080118.2  CG2075-RA (aly), mRNA 
0   0  0  5  3  NM_206265.1  CG12008-RC, transcript variant C (kst), mRNA 
0   0  0  5  2  NM_079275.2  CG4463-RA (Hsp23), mRNA 
0   0  0  5  2  NM_001043081.1  CG11798-RD, transcript variant D (chn), mRNA 
0   0  0  4  9  NM_134500.2  CG14224-RA (CG14224), mRNA 
0   0  0  4  6  NM_141090.2  CG7158-RA (CG7158), mRNA 
0   0  0  4  6  NM_080302.2  CG3109-RA (mRpL16), mRNA 

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