NIG-Fly - Fly Stocks of National Institute of Genetics -

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NIG-RNAi Strains Detail

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discarded

Stock Detail (Last Update: November 2007_FlyBase version FB2007_11)

Stock ID

8597R-1

Symbol

lark

Full Name

lark

CG No

CG8597

Old CG No

CG8597

Synonyms

LARK, Lark, CG8597, lark

Accession No (Link to NCBI)

NM_079233.4

Inserted Chr.

lll

Insertional Mutation

Phenotype induced by Act5C-GAL4 at 28 degrees

lethal

Map Viewer

Reference
[Please submit your publication]

Cho Y, Lai CM, Lin KY, Hsu HJ. A Targeted RNAi Screen Reveals Drosophila Female-Sterile Genes That Control the Size of Germline Stem Cell Niche During Development. G3 (Bethesda) (2018) 8(7) 2345-2354 [ PubMed ID = 29764959 ] [ RRC reference ]

Sundram V, Ng FS, Roberts MA, Millán C, Ewer J, Jackson FR. Cellular requirements for LARK in the Drosophila circadian system. J Biol Rhythms (2012) 27(3) 183-95 [ PubMed ID = 22653887 ] [ RRC reference ]

Comment

Sequence (Last Update: July 10, 2007_NCBI RefSeq Release 24)

Primer Seq. 5'

aaggcctacatggccggaccgCGTGGGAAATCTAACGGACAA

Primer Seq. 3'

aatctagaggtaccTCTGATAGCGACGCTCATACA

Predicted Fragment Size

IR fragment full Seq

0001 CGTGGGAAAT CTAACGGACA AGACGCGGGC GCCGGAGGTG CGGGAACTGT TTCAGAAATA 
0061 CGGCACCGTC GTCGAATGCG ACATTGTGCG CAACTATGGT TTTGTCCATC TGGACTGTGT 
0121 CGGTGATGTG CAGGACGCCA TTAAGGAGCT GAACGGTCGC GTTGTCGATG GCCAGCCGCT 
0181 CAAGGTTCAA GTGTCGACCA GTCGGGTCCG CCCCAAGCCG GGCATGGGCG ATCCGGAGCA 
0241 GTGCTATCGG TGCGGAAGAT CCGGGCATTG GTCGAAAGAG TGTCCGCGAC TGTACGGCAG 
0301 TgNCGGAgGC GGACGCGAgc cGCCATCGCC CCTCAGCGCC GGCGGCTACA GAGATCGCAT 
0361 GTACGGTCGT GACCCGTATC CGCCGCCACC ACCGNCGCCG CCGTTCCtgC GTGACCGCAT 
0421 CATGGATGGC TTTAGGGACT ATGACTACTA TGACCGCCGC TTCGAGNACT CACGCGATCT 
0481 GTATGAgNGT CGCTATCAGA

in silico PCR Fragment

0001 CGTGGGAAAT CTAACGGACA AGACGCGGGC GCCGGAGGTG CGGGAACTGT TTCAGAAATA 
0061 CGGCACCGTC GTCGAATGCG ACATTGTGCG CAACTATGGT TTTGTCCATC TGGACTGTGT 
0121 CGGTGATGTG CAGGACGCCA TTAAGGAGCT GAACGGTCGC GTTGTCGATG GCCAGCCGCT 
0181 CAAGGTTCAA GTGTCGACCA GTCGGGTCCG CCCCAAGCCG GGCATGGGCG ATCCGGAGCA 
0241 GTGCTATCGG TGCGGAAGAT CCGGGCATTG GTCGAAAGAG TGTCCGCGAC TGTACGGCAG 
0301 TGCCGGAGGC GGACGCGAGC CGCCATCGCC CCTCAGCGCC GGCGGCTACA GAGATCGCAT 
0361 GTACGGTCGT GACCCGTATC CGCCGCCACC ACCGCCGCCG CCGTTCCTGC GTGACCGCAT 
0421 CATGGATGGC TTTAGGGACT ATGACTACTA TGACCGCCGC TTCGAGGACT CACGCGATCT 
0481 GTATGAGCGT CGCTATCAGA

Assemble Data

<PRE>

8597R-1.IR_full       1   CGTGGGAAATCTAACGGACAAGACGCGGGCGCCGGAGGTGCGGGAACTGTTTCAGAAATA 60
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8597R-1.in silico     1   CGTGGGAAATCTAACGGACAAGACGCGGGCGCCGGAGGTGCGGGAACTGTTTCAGAAATA 60


8597R-1.IR_full       61  CGGCACCGTCGTCGAATGCGACATTGTGCGCAACTATGGTTTTGTCCATCTGGACTGTGT 120
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8597R-1.in silico     61  CGGCACCGTCGTCGAATGCGACATTGTGCGCAACTATGGTTTTGTCCATCTGGACTGTGT 120


8597R-1.IR_full       121 CGGTGATGTGCAGGACGCCATTAAGGAGCTGAACGGTCGCGTTGTCGATGGCCAGCCGCT 180
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8597R-1.in silico     121 CGGTGATGTGCAGGACGCCATTAAGGAGCTGAACGGTCGCGTTGTCGATGGCCAGCCGCT 180


8597R-1.IR_full       181 CAAGGTTCAAGTGTCGACCAGTCGGGTCCGCCCCAAGCCGGGCATGGGCGATCCGGAGCA 240
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8597R-1.in silico     181 CAAGGTTCAAGTGTCGACCAGTCGGGTCCGCCCCAAGCCGGGCATGGGCGATCCGGAGCA 240


8597R-1.IR_full       241 GTGCTATCGGTGCGGAAGATCCGGGCATTGGTCGAAAGAGTGTCCGCGACTGTACGGCAG 300
                          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8597R-1.in silico     241 GTGCTATCGGTGCGGAAGATCCGGGCATTGGTCGAAAGAGTGTCCGCGACTGTACGGCAG 300


8597R-1.IR_full       301 TG<span class="snp"><tt>N</tt></span>CGGAGGCGGACGCGAGCCGCCATCGCCCCTCAGCGCCGGCGGCTACAGAGATCGCAT 360
                          ||<span class="snp"><tt>&nbsp;</tt></span>|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
8597R-1.in silico     301 TG<span class="snp"><tt>C</tt></span>CGGAGGCGGACGCGAGCCGCCATCGCCCCTCAGCGCCGGCGGCTACAGAGATCGCAT 360


8597R-1.IR_full       361 GTACGGTCGTGACCCGTATCCGCCGCCACCACCG<span class="snp"><tt>N</tt></span>CGCCGCCGTTCCTGCGTGACCGCAT 420
                          ||||||||||||||||||||||||||||||||||<span class="snp"><tt>&nbsp;</tt></span>|||||||||||||||||||||||||
8597R-1.in silico     361 GTACGGTCGTGACCCGTATCCGCCGCCACCACCG<span class="snp"><tt>C</tt></span>CGCCGCCGTTCCTGCGTGACCGCAT 420


8597R-1.IR_full       421 CATGGATGGCTTTAGGGACTATGACTACTATGACCGCCGCTTCGAG<span class="snp"><tt>N</tt></span>ACTCACGCGATCT 480
                          ||||||||||||||||||||||||||||||||||||||||||||||<span class="snp"><tt>&nbsp;</tt></span>|||||||||||||
8597R-1.in silico     421 CATGGATGGCTTTAGGGACTATGACTACTATGACCGCCGCTTCGAG<span class="snp"><tt>G</tt></span>ACTCACGCGATCT 480


8597R-1.IR_full       481 GTATGAG<span class="snp"><tt>N</tt></span>GTCGCTATCAGA 500
                          |||||||<span class="snp"><tt>&nbsp;</tt></span>||||||||||||
8597R-1.in silico     481 GTATGAG<span class="snp"><tt>C</tt></span>GTCGCTATCAGA 500

</PRE>

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	24	16	NM_168203.2	CG8597-RC, transcript variant C (lark), mRNA
100	482	0	22	23	NM_168205.2	CG8597-RE, transcript variant E (lark), mRNA
100	482	0	22	23	NM_079233.4	CG8597-RA, transcript variant A (lark), mRNA
100	482	0	22	21	NM_168202.2	CG8597-RB, transcript variant B (lark), mRNA
100	482	0	18	10	NM_168204.2	CG8597-RD, transcript variant D (lark), mRNA
0.82	4	2	7	12	NM_135785.1	CG6043-RD, transcript variant D (CG6043), mRNA
0.82	4	2	7	10	NM_165035.1	CG6043-RB, transcript variant B (CG6043), mRNA
0.82	4	2	7	10	NM_165037.1	CG6043-RC, transcript variant C (CG6043), mRNA
0.82	4	2	7	10	NM_165034.1	CG6043-RA, transcript variant A (CG6043), mRNA
0.41	2	7	36	41	NM_143635.1	CG2150-RA (CG2150), mRNA
0.41	2	4	8	12	NM_079853.2	CG15532-RA, transcript variant A (hdc), mRNA
0.41	2	4	8	12	NM_176591.1	CG15532-RC, transcript variant C (hdc), mRNA
0.41	2	3	5	12	NM_130728.1	CG15240-RA (CG15240), mRNA
0.41	2	2	7	48	NM_142330.1	CG5225-RA (CG5225), mRNA
0.41	2	2	7	8	NM_141528.1	CG11693-RA (CG11693), mRNA
0.41	2	2	4	13	NM_135957.2	CG31738-RB, transcript variant B (CG31738), mRNA
0.41	2	2	4	9	NM_165168.1	CG31738-RA, transcript variant A (CG31738), mRNA
0.2	1	11	8	17	NM_206362.1	CG9425-RB, transcript variant B (CG9425), mRNA
0.2	1	11	8	17	NM_140468.2	CG9425-RA, transcript variant A (CG9425), mRNA
0.2	1	5	6	2	NM_132519.1	CG9369-RA (m), mRNA
0.2	1	4	6	12	NM_079713.2	CG6376-RA, transcript variant A (E2f), mRNA
0.2	1	4	6	10	NM_169962.1	CG6376-RC, transcript variant C (E2f), mRNA
0.2	1	4	6	10	NM_169961.1	CG6376-RB, transcript variant B (E2f), mRNA
0.2	1	3	4	13	NM_141694.1	CG8516-RA (CG8516), mRNA
0.2	1	3	3	15	NM_166897.1	CG11491-RC, transcript variant C (br), mRNA
0.2	1	3	3	15	NM_166896.1	CG11491-RB, transcript variant B (br), mRNA
0.2	1	3	3	8	NM_166105.1	CG8205-RC, transcript variant C (fus), mRNA
0.2	1	3	3	7	NM_166106.1	CG8205-RA, transcript variant A (fus), mRNA
0.2	1	2	6	14	NM_135633.2	CG4636-RA (SCAR), mRNA
0.2	1	2	5	13	NM_167735.1	CG32521-RB, transcript variant B (CG32521), mRNA

Pathways (updated: 2024/04/26)

KEGG Pathway

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