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Technical Bulletin #502

Published siRNA Target Sequences

April 2003 - The significant increase in the rate of publication of siRNA target sequences has made it difficult to maintain a comprehensive list of these sequences. Therefore, we will no longer be updating this list. We apologize for any inconvenience this may cause.

The following siRNA target sequences have been used in published gene silencing experiments. The extent of silencing, which was assessed by various methods including immunodetection, Western blotting, and phenotypic analysis, varied among the targets. Please see the indicated references for experimental details.

Gene (Ref)

Accession #

Position from ATG

Gene Target
(Comments)

Cell Line Tested

siRNA Sequences*

Template Sequences**

ß-actin (1)

NM_001101

972-994

aatgaagatcaagatcattgc

Human HeLa

gamma-actin (1)

NM_001614

8-30

aagagatcgccgcgctggtca

Human HeLa
AIB1 (estrogen receptor coactivator) (22)     AAAGACUCCUUAGGACCGCUU
Ishikawa
View, Order
Apaf-1 (31)  
978-998
AATTGGTGCACTTTTACGTGA
IMR90E1
View, Order

ARC21 (1)

AF006086

181-203

aagaatgaagctgataggacc

Human HeLa
ATR interacting protein (4)
254-274
AAGGTCCACAGATTATTAGAT
Human HeLa
ATR interacting protein (4)
464-484
CTAGAGGAACAGAGAAGATCACA
Human HeLa
 
ATR interacting protein (4)
867-887
AAGAAGAGGCCCAGAAAAGCT
Human HeLa
Bcr-abl (32)    
AAGCAGAGUUCAAAAGCCCUU
TonB, K562, hematopoetic cells
Brc-abl (32)    
AAAGCAGAGUUCAAAAGCCCU
TonB, K562, hematopoetic cells
beta-tubulin- mouse neuronal (21) AF312873  
AAGACAGAGCCAAGUGGACUC
Mouse P19
View, Order
Bruton's tyrosine kinase (Btk) (33) NM_000061
1682-1700
AAUUGGUAAACGAUCAAGGAG
RBL-2H3, WEHI-231, NALM-6
View, Order
Bruton's tyrosine kinase (Btk) (33) NM_000061
895-913
AAGGGAAAGAAGGAGGUUUCA
RBL-2H3, WEHI-231, NALM-6
View, Order
Bruton's tyrosine kinase (Btk) (33) NM_000061
518-536
AAGAAGCUUAAAACCUGGGAG
RBL-2H3, WEHI-231, NALM-6
View, Order
Casein Kinase I epsilon and delta (CKI-epsilon and CKI-delta) (17)
 
520-538
AACUGGGGAAGAAGGGCAACC
HEK293
Caspase 1 (34)  
191-211
AAGGGGCACAGGCATGCCAAA
IMR90E1A
Caspase 2 (34)  
94-114
AAACAGCTGTTGTTGAGCGAA
IMR90E1A
hCdc2 (24)  
125-147
 
HeLa
   
Cdc14A (23)  
89-109
GCACAGTAAATACCCACTATT
HeLa
View, Order

cdk1 (1)

NM_001786

125-147

aaggggttcctagtactgcaa

Human HeLa

CENP-E (1)

NM_001813

944-966

aaactcttactgctctccagt

Human HeLa
CHO1 (20)
 
138-156
AAGGUCAGUAAUACAACGGUG
CHO
corin, mouse (12)
  
 
AACCACCGCCCUCCGUGCA
HL-5 and 293
   
Cyclin B1 (5)
199-217
CTCGTACAGCCTTGGGAGACA
Xenopus embryo
  
Cyclin B2 (5)
252-270
ATGTTAAGACTAAGCATGTAC
Xenopus embryo
  

cytoplasmic dynein 1 heavy chain (1)

U53530

509-531

aaggccaaggaggcgctggaa

Human HeLa
DIP13-alpha (DCC interacting protein) (25)     AAGUGCAGCAACACACCUGAC
DLD1
View, Order
DIP13-beta (DCC interacting protein) (25)     AAGCAGCACCUCUCCUCCCUU
DLD1
View, Order
Dishevelled (hDv-1 and hDv-3) (16)
 
 
AACAAGATCACCTTCTCCGAG
A293
hDv-2 (16)
 
 
AACTTTGAGAACATGAGCAAC
A293

Eg5 (1)

NM_004523

1547-1569

aactggatcgtaagaaggcag

Human HeLa

emerin (1)

NM_000117

628-650

aaccgtgctcctggggctggg

Human HeLa
eve (11)
 
 
AACUCCUUGAACGGCAGCCGC
Drosophila embryos
hFbw7 (cyclin E ubiquitination) (26)  
713-735
HeLa
   
Fortilin (35)  
121-141
AAGGUAACAUUGAUGACUCGC
U2OS
GalTII (galactosyltransferase II) (27)  
65-87
AAGCACGCGACGCUGGCGCGC
HeLa
View, Order
GalTII (galactosyltransferase II) (27)
461-482
AAGGCGGACGACGACUCCUUC
HeLa
View, Order

GAS41 (1)

NM_006530

327-349

aagacctgtaaccctgtatca

Human HeLa
Hec-1 (36) NM_006101
1517-1539
 
HeLa-S3
   
HPV E6 (38)    
AAGAGGUAUAUGACUUUGCUU
CaSKi, SiHa, NDF, HCT116
HPV E7 (38)    
AAAGGAGGAUGAAAUAGAUGG
CaSKi, SiHa, NDF, HCT116
HtrA2 (28)     AAAACGGCUCAGGAUUCGUGG
U2OS
View, Order
HtrA2 (28)     AAGGGGAGTTTGTTGTTGCCA
U2OS
View, Order
HtrA2 (28)     AAGCTTTCCCGATGTTCAGCA   View, Order

keratin 18 (1)

NM_000224

1154-1176

aagatggcgaggactttaatc

Human HeLa
Kinase interacting stathmin (hKIS) (39)  
160-180
AAGCAGTTCTTGCCGCCAGGA
HEK293
Kinase interacting stathmin (mKIS) (39)  
160-180
AAGCAGTTCCTGCCTCGGGGA
HEK293
lamin A (13)
260-280
GAAGCAGCUUCAGGAUGAGAU
Human HeLa S3
 
 
lamin A (19)
 
 
AAGGACCUGGAGGUCUGCUG
Hep3B
 
 

lamin A/C (1)

NM_005572

608-630

aactggacttccagaagaaca
(90% reduction; 2)

Human HeLa

lamin B1 (1)

NM_005573

672-694

aacgcgcttggtagaggtgga

Human HeLa

lamin B2 (1)

M94362

1457-1479

aagaggaggaggaagccgagt

Human HeLa

LAP2 (1)

NM_003276

37-59

aaagacaagttgaagagtgag

Human HeLa
Mad1 (41)
1843-1865
HeLa-S3
   
Mammalian septin (MSF) (44)
472-492
HeLa
   
Methyl-CpG-binding protein 2 (MeCP2) (19)
 
 
AAGCAUGAGCCCGUGCAGCCA
Hep3B
Methyl-CpG binding domain protein 2 (MBD2) (19)
 
 
AAGAGGAUGGAUUGCCCGGCC
Hep3B
Microtubule-associated protein 2 (MAP2) (42)    
AAUCCUUCGUCUUUCCUCUCG
primary neuronal cells
Myc-induced nuclear antigen 53 (mina53) (40)  
45-63
HeLa, MycB
   
MPS1 kinase (hMps1) (8)
 
133-155
Human HeLa S3
 
 
Myeloid cell leukemia protein 1 (MCL1) (43)  
456-476
AACCCGUCCGUACUGGUGUUA
U2OS
Nicastrin (Nct) (45)    
AAGGGCAAGTTTCCCGTGCAG
HEK293

NuMA (1)

Z11583

3988-4010

aaggcgtggcaggagaagttc

Human HeLa

Nup153 (1)

NM_005124

2593-2615

aaggcagactctaccaaatgt

Human HeLa
Origin recognition complex protein 6 (Orc6) (46)    
AAUGGUAGCCACAUCCGGUGU
HeLa
Origin recognition complex protein 6 (Orc6) (46)    
AAGATTGGACAGCAGGUCGAC
HeLa
P160 ROCK (47)  
566-584; 639-657; 1958-1976; 2780-2798
     
Polo-like Kinase1 (hPlk1) (37) NM_005030
181-203
AAGGGCGGCTTTGCCAAGTGC
HeLa, U2OS
Protein Kinase Receptor (PKR) (9)
 
931-949
AAGATCAAGTTTTGCCAATG
Human HeLa
 
 
hRad9 (29)
232-252
AAGUCUUUCCUGUCUGUCUUU
MCF-7
View, Order
Rad17 (7)
 
 
AACAGACUGGGUUGACCCAUC
Human HeLa
Signalling Adapter/scaffold protein (h/m Shc) (3)
677-697
tcctacttggttcggtacatggg
Human HeLa
  
p66 ShcA (3)
236-256
CGGAATGAGTCTCTGTCATCGTC
Human HeLa
  
Sphingosine kinase 1 (hSK1) (15)
 
70 nt downstream of start codon
AAGAGCUGCAAGGCCUUGCCC
HUVEC
Steroid receptor coactivator (SRC-1) (30)     CCUCAGGGCAGAGAACCAUCUTT
Ishikawa
   
ß-tubulin (6)
3'-UTR
GACAGAGCCAAGUGGACUCAC
Mouse P19
 
 
Tissue Factor (hTF) (18)
 
AAGCGCUUCAGGCACUACAAA
HeLa, 293, Cos-1, HaCaT
Tissue Factor (hTF) (18)
 
AAGAAGCAGACGUACUUGGCA
HeLa, 293, Cos-1, HaCaT
ß-transducin repeat-containing protein (ß-TrCP), human (10)
 
 
GUGGAAUUUGUGGAACAUCTT
293
TSG101 (a ubiquitin enzyme 2 variant protein) (14)
 
413-433
AACCUCCAGUCUUCUCUCGUC
Human HeLa-M & HeLa KK3

VASP (1)

XM_009141

1087-1109

aaagaggaaatcattgaagcc

Human HeLa

vimentin (1)

NM_003380

346-368

aactacatcgacaaggtgcgc
(No silencing observed; 1,2)

Human HeLa

vimentin (1)

NM_003380

1145-1167

aataccaagacctgctcaatg

Human HeLa

vimentin (1)

NM_003380

863-885

aagaatggtacaaatccaagt

Human HeLa

vimentin (1)

NM_003380

1037-1059

aaatggaagagaactttgccg

Human HeLa

vinculin, mouse (1)

L18880

2923-2945

aagcggattagaaccaatctc

Mouse 3T3

zyxin, mouse (1)

X99063

1357-1379

aaagcctaccacccacagtgc

Mouse 3T3
*"View" shows the sense and antisense strands of the siRNA corresponding to the Gene Target. "Order" leads to a custom siRNA order form with the appropriate siRNA sequence pre-filled out. See Ambion's Custom siRNA Oligonucleotide Synthesis Service for details.

**Template sequences for the Silencer™ siRNA Construction Kit.

References

  1. Harborth J, Elbashir SM, Bechert K, Tuschl T, and Weber K. (2001) Identification of essential genes in cultured mammalian cells using small interfering RNAs. J Cell Science 114: 4557-4565.

  2. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, and Tuschl T. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498.

  3. Kisielow M, Kleiner S, Nagasawa M, Faisal A, and Nagamine Y. (2002) Isoform-specific knockdown and expression of adapter protein ShcA using small interfering RNA. Biochem. J. 363:1-5.

  4. Cortez D, Guntuku S, Qin J, and Elledge SJ. (2001) ATR and ATRIP: partners in checkpoint signaling. Science 294:1713-1716.

  5. Zhou Y, Ching Y-P, Kok KH, Kung H-F, Jin D-Y. (2002). Post-transcriptional suppression of gene expression in Xenopus embryos by small interfering RNA. Nucleic Acids Res 30(7):1664-1669.

  6. Yu J-Y, DeRuiter SL, Turner DL. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99(9):6047-6052.

  7. Zou L, Cortez D, and Elledge SJ. (2002). Regulation of ATR substrate selection by Rad17-dependent loading of Rad9 complexes onto chromatin. Genes & Devel. 16:198-208.

  8. Stucke VM, Sillje HHW, Arnaud L, and Nigg EA. (2002). Human Mps1 kinase is required for the spindle assembly checkpoint but not for centrosome duplication. EMBO 21(7):1723-1732.

  9. Donze O, and Picard D. (2002). RNA interference in mammalian cells using siRNAs synthesized with T7 polymerase. Nucl. Acids Res. 30(10): e46.

  10. Fong A, and Sun S-C. (May 6, 2002). Genetic evidence for the essential role of beta-transducin repeat-containing protein in the inducible processing of NF-kB2/p100. J. Biol. Chem. (preprint).

  11. Williams R, and Rubin GM. (2002). ARGONAUTE1 is required for efficient RNA interference in Drosophila embryos. Proc. Natl. Acad. Sci. USA 99(10):6889-6894.

  12. Wu F, Yan W, Pan J, Morser J, and Wu Q. (2002). Processing of pro-atrial natriuretic peptide by corin in cardiac myocytes. J. Biol. Chem. 277(19):16900-16905.

  13. Bai, X, Zhou, D, Brown, JR, Crawford, BE, Hennet, T, and Esko, JD. (2001). Biosynthesis of the linkage region of glycosaminoglycans. J. Biol. Chem. 276(51):48189-48195.

  14. Hewitt EW, Duncan L, Mufti D, Baker J, Stevenson PG, and Lehner PJ. (2002). Ubiquitylation of MHC class I by the K3 viral protein signals internalization and TSG101-dependent degradation. EMBO 21(10): 2418-2429.

  15. Ancellin, N, Colmont, C, Su, J, Li, Q, Mittereder, N, Chae, S-S, Stefansson, S, Liau, G, and Hla, T. (2002). Extracelllular export of sphingosine kinase-1 enzyme. J. Biol. Chem. 277(8):6667-6675.

  16. Li L, Mao J, Sun L, Liu W, and Wu D. (2002). Second cysteine-rich domain of Dickkopf-2 activates canonical Wnt signaling pathway via LRP-6 independently of Dishevelled. J. Biol. Chem. 277(8):5977-5981.

  17. Eide EJ, Bielhaber EL, Hinz W, and Virshup DM. (2002). The circadian regulatory proteins BMAL1 and Cryptochromes are substrates of casein kinase I epsilon. J. Biol. Chem. 277(19):17248-17254.

  18. Holen T, Amarzguioui M, Wiige, MT, Babaie E, and Prydz H. (2002). Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucl. Acids Res. 30(8):1757-1766.

  19. Bakker J, Lin X, and Nelson WG. (2002). Methyl-CpG binding domain protein 2 represses transcription from hypermethylated p-class glutathione-S-transferase gene promoters in hepatocellular carcinoma cells. J. Biol. Chem. (in press).

  20. Matuliene J, and Kuriyama R. (17 April 2002). Kinesin-like protein CHO1 is required for the formation of midbody matrix and the completion of cytokinesis in mammalian cells. Mol. Biol. Cell. (in press).

  21. Yu, J-Y, DeRuiter, SL, Turner, DL. (2002). RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99(9):6047-6052.

  22. Shang Y and Brown M. (2002). Molecular determinants for the tissue specificity of SERMs. Science 295:2465-2468.

  23. Mailand N, Lukas C, Kaiser BK, Jackson PK, Bartek J, and Lukas J. (2002). Deregulated human Cdc14A phosphatase disrupts centrosome separation and chromosome segregation. Nature Cell Biol. 4:317-322.

  24. Chang T-S, Jeong W, Choi SY, Yu S, Kang SW, and Rhee SG. (2002). Regulation of peroxiredoxin I activity by Cdc2-mediated phosphorylation. J. Biol. Chem. 277(28):25370-25376.

  25. Liu J, Yao F, Wu R, Morgan M, Thorburn A, Finely RL, Chen YQ. (2002). Mediation of the DCC apoptotic signal by DIP13 alpha. J. Biol. Chem. 277(29):26281-26285.

  26. Koepp DM, Schaefer LK, Ye X, Keyomarsi K, Chu C, Harper JW, and Elledge SJ. (2001). Phosphorylation-dependent ubiquitination of cyclin E by the SCF-Fbw7 ubiquitin ligase. Science 294(5540):173-177.

  27. Bai, X, Zhou, D, Brown, JR, Crawford, BE, Hennet, T, and Esko, JD. (2001). Biosynthesis of the linkage region of glycosaminoglycans. J. Biol. Chem. 276(51):48189-48195.

  28. Martins et al. (2002). The serine protease Omi/HtrA2 regulates apoptosis by binding XIAP through a reaper like motif. J. Biol. Chem. 277:439-444.

  29. Hirai H and Wang H-G. (2002). A role of the C-terminal region of human Rad9 (hRad9) in nuclear transport of the hRad9 checkpoint complex. J. Biol. Chem. 277(28):25722-25727.

  30. Shang Y and Brown M. (2002). Molecular determinants for the tissue specificity of SERMs. Science 295:2465-2468.

  31. Lassus P, Opitz-Araya X, and Lazebnik Y. (2002). Requirement for caspase-2 in stress-induced apoptosis before mitochondrial permeabilization. Science 297:1352-1354.

  32. Scherr M, Battmer K, Winkler T, Heidenreich O, Ganser A, and Eder M. (2002). Specific inhibition of bcr-abl gene expression by small interfering RNA. Blood (online September 26, 2002 issue)

  33. Heinonen JE, Smith CIE, and Nore BF. (2002). Silencing of Bruton's tyrosine kinase (Btk) using short interfering RNA duplexes (siRNA). FEBS Lett 527:274-278.

  34. Lassus P, Opitz-Araya X, and Lazebnik Y. (2002). Requirement for caspase-2 in stress-induced apoptosis before mitochondrial permeabilization. Science 297:1352-1354.

  35. Zhang D, Li F, Weidner D, Mnjoyan ZH, and Fujise K. (2002). Physical and functional interaction between myeloid cell leukemia 1 protein (MCL1) and fortilin. J. Biol. Chem. 277(40):37430-37438.

  36. Martin-Lluesma S, Stucke VM, and Nigg EA. (2002). Role of Hec1 in spindle checkpoint signaling and kinetochore recruitment of Mad1/Mad2. Science 297:2267-2270.

  37. Liu X and Erikson RL. (2002). Activation of Cdc2/cyclin B and inhibition of centromere amplification in cells depleted of Plk1 by siRNA. Proc. Natl. Acad. Sci. USA 99(13):8672-8676.

  38. Jiang M and Milner J. (2002). Selective silencing of viral gene expression in HPV-positive human cervical carcinoma cells treated with siRNA, a primer of RNA interference. Oncogene 21:6041-6048.

  39. Boehm M, Yoshimoto T, Crook MF, Nallamshetty S, True A, Nabel G, and Nabel EG. (2002). A growth factor-dependent nuclear kinase phosphorylates p27kip1 and regulates cell cycle progression. EMBO J. 21(13):3390-3401.

  40. Tsuneoka M, Koda Y, Soejima M, Teye K, and Kimura H. (2002). A novel Myc target gene, mina53, that is involved in cell proliferation. J. Biol. Chem. 277(38):35450-35459.

  41. Martin-Lluesma S, Stucke VM, and Nigg EA. (2002). Role of Hec1 in spindle checkpoint signaling and kinetochore recruitment of Mad1/Mad2. Science 297:2267-2270.

  42. Krichevsky AM and Kosik KS. (2002). RNAi functions in cultured mammalian neurons. Proc. Natl. Acad. Sci USA 99(18):11926-11929.

  43. Zhang D, Li F, Weidner D, Mnjoyan ZH, and Fujise K. (2002). Physical and functional interaction between myeloid cell leukemia 1 protein (MCL1) and fortilin. J. Biol. Chem. 277(40):37430-37438.

  44. Surka MC, Tsang CW, and Trimble WS. (2002). The mammalian septin MSF localizes with microtubules and is required for completion of cytokinesis. Mol Biol. Cell 13:3532-3545.

  45. Edbauer D, Winkler E, Haass C, and Steiner H. (2002). Presenilin and nicastrin regulate each other and determine amyloid b-peptide production via complex formation. Proc. Natl. Acad. Sci. USA 99(13):8666-8671.

  46. Prasanth SG, Prasanth KV, and Stillman B. (2002). Orc6 involved in DNA replication, chromosome segregation, and cytokinesis. Science 297:1026-1031.

  47. Chevrier V, Piel M, Collomb N, Saoudi Y, Frank R, Paintrand M, Narumiya S, Bornens M, and Job D. (2002). The Rho-associated protein kinase p160ROCK is required for centrosome positioning. J. Cell Biol. 157:807-817.

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