VIRsiRNAdb

SpecificityServer - An siRNA design program for determining siRNA specificity
Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands

20 hits were found for GCGUGAUCAUCCAGGUCAA (10 guide strand hits and 10 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_002545

OPCML

310

328

G

u

G

U

G

A

U

C

A

U

C

C

u

G

G

U

C

A

A

78

2

10

false

<90%

6300

NM_001012393

OPCML

423

441

G

u

G

U

G

A

U

C

A

U

C

C

u

G

G

U

C

A

A

78

2

10

false

<90%

6413

NM_170724

PKHD1

7175

7193

a

C

G

U

G

A

U

C

A

U

C

C

A

G

G

U

u

u

c

66

4

15

ac

false

<90%

11604

NM_138694

PKHD1

7175

7193

a

C

G

U

G

A

U

C

A

U

C

C

A

G

G

U

u

u

c

66

4

15

ac

false

<90%

16235

NM_020214

PARP6

170

188

c

u

G

U

G

A

U

C

A

U

C

C

A

G

a

U

C

A

g

56

4

12

c

false

<90%

2631

NM_000212

ITGB3

1369

1387

G

C

c

U

G

A

U

C

g

U

C

C

A

G

G

U

C

A

c

15

3

9

bc

false

<90%

4894

NM_001001344

ATP2B3

812

830

G

C

G

U

G

c

U

C

A

U

C

C

A

G

G

c

C

A

A

10

2

9

c

false

<90%

6438

NM_021949

ATP2B3

812

830

G

C

G

U

G

c

U

C

A

U

C

C

A

G

G

c

C

A

A

10

2

9

c

false

<90%

6592

NM_003105

SORL1

1951

1969

G

g

c

U

G

A

U

C

c

U

C

C

A

G

G

U

C

A

A

8

3

10

bc

false

<90%

6906

NM_152467

KLHL10

223

241

a

C

G

U

G

g

U

C

A

U

C

a

A

G

G

U

C

A

A

0

3

7

false

<90%

1969

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_000439

PCSK1

3975

3993

c

U

c

A

C

C

U

G

G

A

U

G

A

U

C

A

C

u

a

70

4

14

c

false

<90%

5054

NM_015359

SLC39A14

1153

1171

c

U

G

g

C

C

U

G

G

A

U

G

A

U

C

A

C

u

C

58

3

13

c

false

<90%

4626

NM_004638

BAT2

6275

6293

g

g

G

A

C

C

U

G

G

A

U

c

A

U

C

A

C

G

g

47

4

9

false

<90%

6714

NM_080686

BAT2

6311

6329

g

g

G

A

C

C

U

G

G

A

U

c

A

U

C

A

C

G

g

47

4

9

false

<90%

6750

NM_130843

PTPRN2

4246

4264

U

U

G

A

C

C

a

G

G

A

U

G

A

U

C

A

C

a

u

26

3

10

c

false

<90%

4680

NM_130842

PTPRN2

4282

4300

U

U

G

A

C

C

a

G

G

A

U

G

A

U

C

A

C

a

u

26

3

10

c

false

<90%

4716

NM_002847

PTPRN2

4333

4351

U

U

G

A

C

C

a

G

G

A

U

G

A

U

C

A

C

a

u

26

3

10

c

false

<90%

4767

NM_001636

SLC25A6

728

746

g

U

G

A

g

C

U

G

G

A

U

G

A

U

C

g

C

G

C

20

3

10

c

false

<90%

1455

NM_183243

IMPDH1

398

416

c

U

G

A

C

C

c

G

G

A

a

G

A

U

C

A

C

G

C

-29

3

8

c

false

<90%

2534

NM_000883

IMPDH1

771

789

c

U

G

A

C

C

c

G

G

A

a

G

A

U

C

A

C

G

C

-29

3

8

c

false

<90%

2880

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 438
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_019067	GNL3L	4
NM_030579	CYB5B	2
NM_001037165	FOXK1	2
NM_001102651		2
NM_080927	DCBLD2	2
NM_004230	EDG5	2
NM_177538	CYP20A1	2
XM_929835	LOC284023	2
XM_941810	LOC284023	2
NM_023926	ZSCAN18	2
NM_005994	TBX2	1
NM_001084	PLOD3	1
NM_173344	ST3GAL1	1
NM_003033	ST3GAL1	1
NM_005737	ARL4C	1
NM_001083603	PTCH1	1
NM_001083607	PTCH1	1
NM_001083602	PTCH1	1
NM_001083605	PTCH1	1
NM_001083606	PTCH1	1
NM_001083604	PTCH1	1
NM_000264	PTCH1	1
NM_032300	TCHP	1
NM_012388	PLDN	1
NM_000391	TPP1	1
NM_030621	DICER1	1
NM_177438	DICER1	1
NM_020546	ADCY2	1
NM_001732	BTN1A1	1
NM_020362	C1orf128	1
NM_016331	ZNF639	1
NM_018398	CACNA2D3	1
NM_001012981	ZKSCAN2	1
NM_001012755	MCART6	1
NM_004012	DMD	1
NM_004016	DMD	1
NM_004009	DMD	1
NM_004017	DMD	1
NM_000109	DMD	1
NM_004011	DMD	1
NM_004015	DMD	1
NM_004023	DMD	1
NM_004022	DMD	1
NM_004020	DMD	1
NM_004021	DMD	1
NM_004007	DMD	1
NM_004006	DMD	1
NM_004013	DMD	1
NM_004014	DMD	1
NM_004018	DMD	1
NM_004010	DMD	1
NM_005314	GRPR	1
NM_139048	HLTF	1
NM_003071	HLTF	1
NM_001079669	TMTC4	1
NM_032813	TMTC4	1
NM_183413	FBXO44	1
NM_033182	FBXO44	1
NM_001014765	FBXO44	1
NM_183412	FBXO44	1
XM_042978	FRMPD3	1
XM_937007	FRMPD3	1
NM_153006	NAGS	1
NM_018246	CCDC25	1
NM_001034841	LOC162073	1
NM_152431	PIWIL4	1
NM_001838	CCR7	1
NM_019044	CCDC93	1
NM_020431	TMEM63C	1
NM_016376	ANKFY1	1
NM_002074	GNB1	1
NM_001100162		1
NM_001100161		1
NM_015024	XPO7	1
NM_173598	KSR2	1
NM_003622	PPFIBP1	1
NM_024616	C3orf52	1
NM_014872	ZBTB5	1
NM_001025433	NQO1	1
NM_000903	NQO1	1
NM_001025434	NQO1	1
NM_006251	PRKAA1	1
NM_206907	PRKAA1	1
NM_021155	CD209	1
NM_152411	ZNF786	1
NM_018999	KIAA1128	1
NM_015289	VPS39	1
NM_013411	AK2	1
NM_080764	SUHW2	1
NM_032430	BRSK1	1
NM_001003793	RBMS3	1
NM_001003792	RBMS3	1
NM_018947	CYCS	1
NM_032287	LDOC1L	1
NM_024895	PDZD7	1
NM_000125	ESR1	1
NM_145207	SPATA5	1
NM_006998	SCGN	1
NM_000953	PTGDR	1
NM_021148	ZNF273	1
NM_001001974	PLEKHA1	1
NM_021622	PLEKHA1	1
NM_198476	C19orf54	1
NM_078470	COX15	1
NM_145865	ANKS4B	1
NM_032167	RUNDC2A	1
NM_030780	SLC25A32	1
NM_020161	DKFZp547H025	1
NM_000761	CYP1A2	1
NM_015016		1
XM_938194	LOC127602	1
XM_059166	LOC127602	1
NM_001009899	KIAA2018	1
NM_152673	MUC20	1
NM_001098516		1
NM_001042697	ZSWIM7	1
NM_001042698	ZSWIM7	1
XM_944900	LOC643770	1
XM_931792	LOC643770	1
NM_021130	PPIA	1
NM_024770	METTL8	1
NM_024917	CXorf34	1
NM_022745	ATPAF1	1
NM_001042546	ATPAF1	1
NM_006452	PAICS	1
NM_001079525	PAICS	1
NM_001079524	PAICS	1
XM_001131828	BBS5	1
XM_001131846	BBS5	1
NM_152384	BBS5	1
NM_020710	LRRC47	1
NM_001040441	ZBTB8	1
XM_001124597	LOC730411	1
NM_004727	SLC24A1	1
NM_001201	BMP3	1
NM_012393	PFAS	1
NM_003023	SH3BP2	1
XM_928871	LOC644038	1
XM_926379	LOC440839	1
XM_001128517	LOC728601	1
XM_001125884	LOC727836	1
XM_926363	LOC642313	1
NM_016216	DBR1	1
NM_003034	ST8SIA1	1
NM_000268	NF2	1
NM_016418	NF2	1
NM_181832	NF2	1
NM_181828	NF2	1
NM_181829	NF2	1
NM_181833	NF2	1
NM_181830	NF2	1
NM_017813	IMPAD1	1
NM_001080125	CASP8	1
NM_001080124	CASP8	1
NM_033355	CASP8	1
NM_001228	CASP8	1
NM_033356	CASP8	1
NM_001007024	GOSR1	1
NM_001007025	GOSR1	1
NM_004871	GOSR1	1
NM_002990	CCL22	1
NM_002349	LY75	1
NM_000767	CYP2B6	1
NM_152565	ATP6V0D2	1
NM_032120	DKFZP564O0523	1
NM_138572	TBN	1
NM_017712	PGPEP1	1
NM_000887	ITGAX	1
NM_001077241	SLC25A45	1
NM_182556	SLC25A45	1
NM_005513	GTF2E1	1
NM_198557	RBM43	1
NM_020894	KIAA1530	1
NM_018711	SVOP	1
NM_002076	GNS	1
NM_016052	RRP15	1
NM_017563	IL17RD	1
NM_001080973	IL17RD	1
XM_941026	ING5	1
XM_001126273	LOC727773	1
NM_032329	ING5	1
NM_006085	BPNT1	1
NM_000961	PTGIS	1
NM_182901	C11orf17	1
NM_020642	C11orf17	1
NM_176081	TRDMT1	1
NM_004412	TRDMT1	1
NM_176083	TRDMT1	1
NM_031912	SYT15	1
NM_001040157	KIAA1712	1
NM_024900	PHF17	1
NM_012334	MYO10	1
NM_005652	TERF2	1
NM_153717	EVC	1
NM_173084	TRIM59	1
NM_152458	ZNF785	1
NM_012164	FBXW2	1
NM_015110	SMC5	1
NM_001077196	PDE11A	1
NM_001077197	PDE11A	1
NM_016953	PDE11A	1
NM_001003795	GTF2IRD2B	1
NM_173537	GTF2IRD2	1
NM_024541	C10orf76	1
XM_001128792	LOC728748	1
XM_001130863	LOC728492	1
NM_022978	SERF1B	1
XM_001130858	LOC728492	1
NM_021967	SERF1A	1
NM_005895	GOLGA3	1
NM_031476	CRISPLD2	1
NM_020231	KTELC1	1
NM_152305	KTELC1	1
NM_004705	PRKRIR	1
NM_198859	PRICKLE2	1
NM_001415	EIF2S3	1
NM_015962	FCF1	1
NM_002957	RXRA	1
NM_001001563	TIMM50	1
NM_021828	HPSE2	1
XM_938519	DKFZP434I0714	1
XM_929673	DKFZP434I0714	1
NM_001042	SLC2A4	1
XM_001128311	LOC731449	1
XM_001129750	LOC728999	1
NM_003417	ZNF264	1
NM_001080391	SP100	1
NM_001030288	SPN	1
NM_003123	SPN	1
NM_012409	PRND	1
NM_025243	SLC19A3	1
NM_014897	ZNF652	1
NM_001010982	AFMID	1
NM_001008528	MXRA7	1
NM_020375	C12orf5	1
NM_002033	FUT4	1
NM_017706	WDR55	1
NM_173657	C3orf33	1
NM_001085377		1
NM_002387	MCC	1
NM_007236	CHP	1
NM_145698	ACBD5	1
NM_001042473	ACBD5	1
NM_000148	FUT1	1
NM_021238	FAM60A	1
NM_001037330	TRIM16L	1
NM_006879	MDM2	1
NM_006881	MDM2	1
NM_002392	MDM2	1
NM_006878	MDM2	1
NM_006882	MDM2	1
NM_021067	GINS1	1
NM_018958	C15orf2	1
NM_001690	ATP6V1A	1
NM_022151	MOAP1	1
NM_080876	DUSP19	1
NM_007167	ZMYM6	1
NM_001039697	SNAPC3	1
NM_144578	C14orf32	1
NM_001025266	LOC285382	1
NM_138428	C1orf212	1
NM_021916	ZNF70	1
NM_000546	TP53	1
NM_006918	SC5DL	1
NM_001024956	SC5DL	1
NM_207491	MGC48628	1
NM_001039884	FLJ44894	1
NM_003423	ZNF43	1
NM_005426	TP53BP2	1
NM_001031685	TP53BP2	1
NM_001008539	SLC7A2	1
NM_003046	SLC7A2	1
NM_001079906	ZNF331	1
NM_018555	ZNF331	1
NM_001079907	ZNF331	1
NM_003107	SOX4	1
NM_001663	ARF6	1
NM_001044387	ZNF557	1
NM_024341	ZNF557	1
NM_001044388	ZNF557	1
NM_020341	PAK7	1
NM_177990	PAK7	1
NM_020960	GPR107	1
NM_006464	TGOLN2	1
NM_173632	ZNF776	1
NM_198468	C6orf167	1
NM_015123		1
NM_052864	TIFA	1
NM_001023567	GOLGA8B	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_016436	PHF20	1
NM_001005920	LOC339123	1
NM_020947	KIAA1609	1
NM_004603	STX1A	1
NM_001025092	MBP	1
NM_002385	MBP	1
NM_001025081	MBP	1
NM_001025090	MBP	1
NM_001025101	MBP	1
XM_001128419	MGC16121	1
XM_938958	MGC16121	1
NM_024306	FA2H	1
NM_018281	ECHDC2	1
NM_000834	GRIN2B	1
NM_002855	PVRL1	1
XM_496960	FAM90A11P	1
NM_032854	CORO6	1
NM_019001	XRN1	1
NM_001042604	XRN1	1
NM_014911	AAK1	1
NM_003929	RAB7L1	1
NM_153259	MCOLN2	1
NM_006952	UPK1B	1
NM_207380	FLJ43339	1
NM_207360		1
NM_001037293	PALM2	1
NM_053016	PALM2	1
NM_018409	LRP2BP	1
NM_001099678		1
NM_002213	ITGB5	1
XM_001129224	ITGB5	1
NM_031490	LONP2	1
NM_138400	NOM1	1
XM_001127604	NFATC2IP	1
NM_032815	NFATC2IP	1
NM_207467	FLJ35530	1
NM_018962	DSCR6	1
NM_052909	KIAA1909	1
NM_005840	SPRY3	1
NM_031845	MAP2	1
NM_031847	MAP2	1
NM_001039538	MAP2	1
NM_002374	MAP2	1
NM_014157	CCDC113	1
NM_001017388	TLR10	1
NM_030956	TLR10	1
XM_379029	LOC400879	1
NM_024506	GLB1L	1
NM_004735	LRRFIP1	1
NM_152734	C6orf89	1
NM_007107	SSR3	1
NM_001039140	C20orf27	1
NM_183236	RAB27A	1
NM_004580	RAB27A	1
NM_183234	RAB27A	1
NM_183235	RAB27A	1
NM_020859	SHROOM3	1
NM_003498	SNN	1
NM_003648	DGKD	1
NM_152879	DGKD	1
NM_001567	INPPL1	1
NM_178815	ARL5B	1
NM_017643	MBTD1	1
NM_033326	SOX6	1
NM_017508	SOX6	1
NM_014945	ABLIM3	1
NM_001009554	MFAP3L	1
NM_021647	MFAP3L	1
NM_033027	AXUD1	1
NM_152253	CHKB	1
NM_030648	SETD7	1
NM_012384	GMEB2	1
NM_173551	ANKS6	1
NM_014665	LRRC14	1
NM_012293	PXDN	1
NM_032826	SLC35B4	1
NM_001099272		1
NM_152733	BTBD9	1
NM_052893		1
NM_001011552	SLC9A4	1
NM_052874	STX1B2	1
NM_138959	VANGL1	1
NM_144642	SYNPR	1
NM_032303	HSDL2	1
NM_001038633	RSPO1	1
NM_182644	EPHA3	1
XM_039908	LOC91664	1
NM_005065	SEL1L	1
NM_001079843	CASZ1	1
NM_032208	ANTXR1	1
NM_007184	NISCH	1
NM_020831	MKL1	1
NM_016426	GTSE1	1
NM_015972	POLR1D	1
NM_012218	ILF3	1
NM_173477	USH1G	1
NM_015576	ERC2	1
NM_147189	FAM110B	1
NM_020348	CNNM1	1
NM_001033582	PRKCZ	1
NM_002744	PRKCZ	1
NM_001033581	PRKCZ	1
NM_001024948	FNBP1L	1
NM_017737	FNBP1L	1
NM_001102371		1
NM_024955	FOXRED2	1
NM_032848	C12orf52	1
NM_014844	KIAA0329	1
NM_024701	ASB13	1
NM_017410	HOXC13	1
NM_000071	CBS	1
NM_014862	ARNT2	1
NM_022445	TPK1	1
NM_001042482	TPK1	1
NM_002084	GPX3	1
NM_018105	THAP1	1
NM_199003	THAP1	1
XM_001129929	LOC728339	1
XM_001133196	LOC731507	1
NM_021003	PPM1A	1
NM_177952	PPM1A	1
NM_018424	EPB41L4B	1
NM_001991	EZH1	1
NM_007273	PHB2	1
NM_024918	DSN1	1
NM_015694	ZNF777	1
NM_021938	BRUNOL5	1
NM_006620	HBS1L	1
NM_003392	WNT5A	1
NM_001905	CTPS	1
NM_006593	TBR1	1
NM_006253	PRKAB1	1
NM_012482	ZNF281	1
NM_032268	ZNRF1	1
XM_001133002	LOC728804	1
NM_018437	HEMGN	1
NM_197978	HEMGN	1
NM_002560	P2RX4	1
NM_001033925	TIAL1	1
NM_003252	TIAL1	1
NM_002933	RNASE1	1
NM_198234	RNASE1	1
NM_198235	RNASE1	1
NM_198232	RNASE1	1
NM_152678	FAM116A	1
XM_001132771	FAM116A	1
NM_178126	LOC162427	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).

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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