VIRsiRNAdb

SpecificityServer - An siRNA design program for determining siRNA specificity
Automatic recommendation
Not OK - siRNA is not specific

13 hits were found for CCCGGUUCAUCCUGGACAA (8 guide strand hits and 5 sense strand hits.)

Hits to Guide strand

Accession

Gene

Start

End

Details of mismatches

Spec. Score

Mismatches

Contiguous

Jackson style specificity

Hits similar gene

HSP Score

HSP % Identity

HSP length

Gene Length

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

NM_004829

NCR1

398

416

C

u

C

G

G

U

U

C

A

U

C

C

U

G

G

A

C

c

c

80

3

15

ac

false

<90%

1135

NM_002068

GNA15

1145

1163

a

g

a

G

G

U

U

C

A

U

C

C

U

G

G

A

C

A

u

62

4

15

bc

false

<90%

2060

NM_032853

MUM1

2149

2167

u

C

C

G

G

U

U

C

A

U

u

C

U

G

G

A

C

g

u

29

4

9

c

false

<90%

4179

NM_002275

KRT15

585

603

C

C

C

G

G

g

U

C

A

U

C

C

U

G

G

A

g

A

u

8

3

10

c

false

<90%

1709

NM_032557

USP38

643

661

C

C

C

G

G

c

U

C

A

U

C

C

U

G

G

A

g

g

g

5

4

10

c

false

<90%

4684

NM_004651

USP11

2081

2099

g

C

C

c

G

U

U

C

c

U

C

C

U

G

G

A

C

A

A

1

3

10

bc

false

<90%

3300

NM_013236

ATXN10

1450

1468

u

C

C

c

G

U

U

g

A

U

C

C

U

G

G

A

C

A

A

0

3

11

bc

false

<90%

2963

NM_080474

SERPINB12

899

917

C

C

C

G

G

U

U

C

A

c

C

C

U

G

G

A

a

g

A

-8

3

9

c

false

<90%

1218

Hits to Sense strand

Accession

Gene

Start

End

Details of mismatches

Spec. Score

Mismatches

Contiguous

Jackson style specificity

Hits similar gene

HSP Score

HSP % Identity

HSP length

Gene Length

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

NM_005510

DOM3Z

1356

1374

U

U

G

U

C

C

A

G

G

A

U

G

A

c

C

C

c

a

G

54

3

13

c

false

<90%

1590

XM_373809

LOC388553

1507

1525

U

U

c

U

g

C

A

G

G

A

U

G

A

A

C

C

G

G

a

23

3

13

bc

false

<90%

1776

XM_944980

LOC388553

1507

1525

U

U

c

U

g

C

A

G

G

A

U

G

A

A

C

C

G

G

a

23

3

13

bc

false

<90%

1776

NM_017699

SIDT1

1936

1954

U

U

G

U

C

C

A

G

G

A

a

G

g

A

C

C

G

G

a

23

3

10

false

<90%

5021

NM_020366

RPGRIP1

113

131

U

U

G

a

g

C

A

G

G

A

U

G

A

A

C

C

G

G

G

11

2

14

bc

false

<90%

3950

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 338
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_145727	LPAL2	2
NM_024492	LPAL2	2
NM_153631	HOXA3	2
NM_153632	HOXA3	2
NM_030661	HOXA3	2
NM_012214	MGAT4A	2
NM_001100398		2
NM_015085	GARNL4	2
NM_000748	CHRNB2	1
NM_000719	CACNA1C	1
XM_001131339	LOC731034	1
XM_001127795	LOC728178	1
NM_152494	DCST1	1
NM_001010906		1
NM_014316	CARHSP1	1
NM_001042476	CARHSP1	1
NM_178520	TMEM105	1
NM_182641	BPTF	1
NM_004459	BPTF	1
NM_000527	LDLR	1
NM_018134	IQCC	1
NM_021070	LTBP3	1
NM_000831	GRIK3	1
NM_006454	MXD4	1
NM_033025	SYDE1	1
NM_025155	WDR71	1
NM_178857	RP1L1	1
XM_001128301	LOC728056	1
NM_019613	WDR45L	1
NM_005430	WNT1	1
NM_139323	YWHAB	1
NM_003404	YWHAB	1
NM_032208	ANTXR1	1
NM_138479	C1orf213	1
NM_025188	TRIM45	1
NM_018438	FBXO6	1
NM_176816	CCDC125	1
NM_004727	SLC24A1	1
NM_138278	BNIPL	1
NM_001031727	MGC3207	1
NM_032285	MGC3207	1
NM_052847	GNG7	1
NM_003423	ZNF43	1
NM_207012	AP3M1	1
NM_012095	AP3M1	1
NM_207313	TMEM132E	1
NM_001013635	LOC387856	1
XM_001128921	LOC387856	1
NM_052845	MMAB	1
XM_929433	LOC644006	1
XM_939111	LOC650020	1
NM_002938	RNF4	1
NM_002827	PTPN1	1
NM_000734	CD247	1
NM_198053	CD247	1
NM_024996	GFM1	1
NM_001188	BAK1	1
NM_031459	SESN2	1
NM_002478	MYOD1	1
NM_020133	AGPAT4	1
NM_004992	MECP2	1
NM_207333	ZNF320	1
XM_001134001	LOC440422	1
XM_001133899	LOC729704	1
XM_498661	LOC440422	1
NM_001029861	NANOS2	1
NM_001009909	LUZP2	1
NM_006310	NPEPPS	1
NM_001543	NDST1	1
NM_016049	C14orf122	1
NM_199205	KIAA1967	1
NM_021174	KIAA1967	1
NM_001029884	PLEKHG1	1
NM_001109	ADAM8	1
NM_031918	KLF16	1
NM_004430	EGR3	1
XM_001130047	EGR3	1
NM_004132	HABP2	1
NM_170607	MLX	1
NM_198204	MLX	1
NM_198205	MLX	1
NM_012306	FAIM2	1
NM_177939	PH-4	1
NM_177938	PH-4	1
NM_173475	DCUN1D3	1
NM_001105079		1
NM_130783	TSPAN18	1
NM_001080452	GPR108	1
NM_020171	GPR108	1
NM_033118	MYLK2	1
NM_012301	MAGI2	1
NM_022097	LOC63928	1
XM_941733	LOC647115	1
XM_930136	LOC647115	1
NM_014891	PDAP1	1
NM_005276	GPD1	1
NM_014665	LRRC14	1
NM_175736	FMNL3	1
NM_198900	FMNL3	1
NM_012219	MRAS	1
NM_001085049		1
NM_015063	SLC8A2	1
NM_006822	RAB40B	1
NM_014798	PLEKHM1	1
XM_001128220	PLEKHM1	1
NM_001003692	ZMAT5	1
NM_019103	ZMAT5	1
NM_016606	REEP2	1
NM_006290	TNFAIP3	1
NM_144577	CCDC114	1
NM_004356	CD81	1
NM_014349	APOL3	1
NM_145642	APOL3	1
NM_145640	APOL3	1
NM_145639	APOL3	1
NM_030644	APOL3	1
NM_145641	APOL3	1
NM_199169	TMEPAI	1
NM_199170	TMEPAI	1
NM_199171	TMEPAI	1
NM_020182	TMEPAI	1
NM_025224	ZBTB46	1
NM_005184	CALM3	1
NM_144578	C14orf32	1
NM_004234	ZNF235	1
NM_178136	POLDIP3	1
NM_032311	POLDIP3	1
NM_001098814		1
NM_006950	SYN1	1
NM_133499	SYN1	1
NM_015175		1
NM_138401	FAM125A	1
NM_001387	DPYSL3	1
NM_052943	FAM46B	1
NM_001045478	LOC644997	1
NM_014850	SRGAP3	1
NM_001033117	SRGAP3	1
XM_001130700	LOC729580	1
XM_001126751	LOC730672	1
XM_001132972	LOC729187	1
XM_001132549	LOC731180	1
NM_173804	TMEM86B	1
NM_006493	CLN5	1
XM_001134449	KBTBD9	1
XM_940375	KBTBD9	1
NM_176806	MOCS2	1
NM_004531	MOCS2	1
NM_014520	MYBBP1A	1
NM_017570	OPLAH	1
NM_052909	KIAA1909	1
NM_052995	CLRN1	1
NM_030981	RAB1B	1
NM_001037165	FOXK1	1
NM_002522	NPTX1	1
XM_001132528	NPTX1	1
NM_014000	VCL	1
NM_003373	VCL	1
NM_017450	BAIAP2	1
NM_007368	RASA3	1
NM_152281	SCYL1BP1	1
NM_007170	TESK2	1
NM_001012418	LOC340156	1
NM_017759	FLJ20309	1
NM_015475	FAM98A	1
NM_003804	RIPK1	1
NM_177549	PRNT	1
NM_001004317	LIN28B	1
NM_031412	GABARAPL1	1
NM_020310	MNT	1
NM_030648	SETD7	1
NM_025179	PLXNA2	1
NM_014153	ZC3H7A	1
NM_182744	NBL1	1
NM_005380	NBL1	1
NM_016263	FZR1	1
NM_001079877	RASA4	1
NM_006989	RASA4	1
NM_005160	ADRBK2	1
NM_000346	SOX9	1
NM_182508	C13orf30	1
NM_018390	PLCXD1	1
NM_018242	FLJ10847	1
NM_003979	GPRC5A	1
XM_379029	LOC400879	1
NM_002081	GPC1	1
NM_003983	SLC7A6	1
NM_001076785	SLC7A6	1
XM_498648	LOC440389	1
NM_178172	LOC338328	1
NM_032037	TSSK6	1
NM_004387	NKX2-5	1
NM_002080	GOT2	1
NM_001001894	TTC3	1
NM_003316	TTC3	1
NM_005596	NFIB	1
NM_030643	APOL4	1
NM_145660	APOL4	1
NM_032242	PLXNA1	1
NM_004455	EXTL1	1
NM_003485	GPR68	1
XM_001131186	LOC729746	1
NM_018715	RCC2	1
NM_138368	DKFZp761E198	1
NM_015316	PPP1R13B	1
NM_018031	WDR6	1
NM_023076	C16orf28	1
NM_015321	CRTC1	1
NM_001098482		1
NM_001042535	CENTG3	1
NM_033387	FAM78A	1
NM_000260	MYO7A	1
NM_025232	REEP4	1
NM_018085	IPO9	1
NM_025058	TRIM46	1
NM_175898	C15orf37	1
NM_001012977	LOC340529	1
XM_001126207	LOC645974	1
NM_001042506	LOC645974	1
XM_001130463	LOC645974	1
NM_018669	WDR4	1
NM_001099220		1
NM_025136	OPA3	1
NM_015172	BAT2D1	1
NM_006133	DAGLA	1
NM_014170	GTPBP8	1
NM_138485	GTPBP8	1
NM_015051	TXNDC4	1
NM_025135	FHOD3	1
NM_172037	RDH10	1
NM_001010922	C1orf178	1
XM_001134215	PDPR	1
NM_017990	PDPR	1
NM_001098213		1
NM_001098212		1
NM_000861	HRH1	1
NM_001098211		1
NM_019607	C8orf44	1
NM_022773	TMEM112	1
NM_002033	FUT4	1
NM_001039362	ATP6V1C2	1
NM_144583	ATP6V1C2	1
NM_001079514	UBN1	1
NM_016936	UBN1	1
NM_022842	CDCP1	1
NM_153274	BEST4	1
NM_001277	CHKA	1
NM_212469	CHKA	1
NM_015056	RRP1B	1
NM_178502	DTX3	1
XM_940028	LOC197350	1
XM_113871	LOC197350	1
XM_001129365	LOC731368	1
XM_001128918	LOC728961	1
NM_020820	PREX1	1
NM_001024071	GCH1	1
NM_001024024	GCH1	1
NM_001024070	GCH1	1
NM_000161	GCH1	1
NM_015015	JMJD2B	1
XM_001133221	LOC730241	1
NM_024770	METTL8	1
NM_001842	CNTFR	1
NM_147164	CNTFR	1
NM_016937	POLA1	1
NM_024103	SLC25A23	1
NM_024993	LRRTM4	1
NM_015227	POFUT2	1
NM_024936		1
NM_014815	THRAP4	1
NM_001079518	THRAP4	1
NM_007158	CSDE1	1
NM_001007553	CSDE1	1
NM_007129	ZIC2	1
NM_014238	KSR1	1
NM_004522	KIF5C	1
NM_002547	OPHN1	1
NM_014506	TOR1B	1
NM_002158	FOXN2	1
NM_152600	ZNF579	1
NM_004928	C21orf2	1
NM_018711	SVOP	1
NM_002068	GNA15	1
NM_001419	ELAVL1	1
XM_379694	LOC401577	1
XM_942510	LOC652827	1
XM_928150	LOC401577	1
NM_020956	PRX	1
NM_005875	EIF1B	1
NM_024119	LGP2	1
NM_003353	UCN	1
NM_175569	XG	1
NM_004822	NTN1	1
NM_007084	SOX21	1
NM_001986	ETV4	1
NM_001079675	ETV4	1
XM_001128273	LOC728719	1
XM_001128242	LOC728704	1
NM_175907	ZADH2	1
NM_015101	GLT25D2	1
XM_001130036	LOC730815	1
XM_001132008	LOC728769	1
NM_131916	PPIL3	1
NM_130906	PPIL3	1
NM_032472	PPIL3	1
NM_014667	VGLL4	1
NM_138383	ABBA-1	1
NM_018293	ZNF654	1
XM_001126706	ZNF654	1
NM_172344	KCNG3	1
NM_133329	KCNG3	1
NM_020211	RGMA	1
NM_021971	GMPPB	1
NM_013334	GMPPB	1
NM_014279	OLFM1	1
NM_005895	GOLGA3	1
NM_033305	VPS13A	1
NM_001018037	VPS13A	1
NM_005354	JUND	1
NM_017892		1
NM_004736	XPR1	1
NM_203327	SLC23A2	1
NM_005116	SLC23A2	1
NM_003221	TFAP2B	1
NM_005715	UST	1
NM_002566	P2RY11	1
NM_001080113	PP8961	1
NM_032595	PPP1R9B	1
NM_020383	XPNPEP1	1
NM_003390	WEE1	1
NM_002146	HOXB3	1
NM_198480	ZNF615	1
NM_020375	C12orf5	1
NM_000567	CRP	1
NM_003074	SMARCC1	1
NM_001085400		1
NM_001009812	LBX2	1
NM_153675	FOXA2	1
NM_021784	FOXA2	1

---

Immunostimulatory motif search results

UGUGU - Judge et al. Sequence-dependent stimulation of the mammalian innate immune response by synthetic siRNA. Nat Biotechnol. 2005 Apr;23(4):457-62. (PMID: 15778705)
No Immunostimulatory motif found (UGUGU).

GUCCUUCAA - Hornung et al. Sequence-specific potent induction of IFN-alpha by short interfering RNA in plasmacytoid dendritic cells through TLR7. Nat Med. 2005 Mar;11(3):263-70. Epub 2005 Feb 20. (PMID: 15723075)
No Immunostimulatory motif found (GUCCUUCAA).

---

---

Settings used for search

Scores were calculated using scoring scheme SS1
Using AVG scoring mode.

Hit scores

Parameter	Spec. Score cut-off	Colour	Comment
Hit to same gene		Colour	Hits to the same accession or genes with 100 percent identity (i.e. likely transcript variants). It is advisable to always check the genes hit.
High scoring hit	≥80	Colour	Hits are very likely to cause an off-target effect
Medium scoring hit	<80¸≥40	Colour	Hits with a small chance of causing an off target effect.
Low scoring hit		Colour	Hits very unlikely to cause an off-target effect

The mismatches are colour coded based on the weighting of that position.

Cut-off	Colour
Match	Colour
Wobble base pairs (G-U)	Colour
Critical bases (none)	Colour
0.6 bits	Colour
0.4 bits	Colour
0.2 bits	Colour

About SpecificityServer

SpecificityServer is designed to help you identify potential non-specific matches to your siRNA. It incorporates the latest information about non-specific matches (sequence-specific only).

Designed by: Alistair Chalk, Quan Du, Zicai Liang and Erik L.L. Sonnhammer

For more details about the algorithm "siRNA specificity searching incorporating mismatch tolerance data" Bioinformatics (2008) 24 (10): 1316-1317