VIRsiRNAdb

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

12 hits were found for AGGUCCGUGAGCCGCUUGA (1 guide strand hits and 11 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_006062	SMYD5	832	850	A	G	G	a	C	C	G	U	G	A	G	C	a	G	C	U	U	G	A	52	2	8		false		<90%		2561

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_024963

FBXL18

1839

1857

g

C

A

A

G

C

G

G

C

U

g

A

g

G

G

A

C

C

U

26

3

9

false

<90%

2525

NM_004296

RGS6

1594

1612

g

C

A

A

G

C

G

c

C

U

C

A

C

G

G

g

C

C

U

9

3

7

c

false

<90%

3105

NM_153620

HOXA1

606

624

c

C

A

A

G

C

a

G

C

U

C

A

C

G

G

A

a

C

U

8

3

9

c

false

<90%

2358

NM_005522

HOXA1

809

827

c

C

A

A

G

C

a

G

C

U

C

A

C

G

G

A

a

C

U

8

3

9

c

false

<90%

2561

NM_182811

PLCG1

709

727

g

a

g

A

G

C

G

G

C

U

g

A

C

G

G

A

C

C

U

5

4

8

c

false

<90%

5202

NM_002660

PLCG1

709

727

g

a

g

A

G

C

G

G

C

U

g

A

C

G

G

A

C

C

U

5

4

8

c

false

<90%

5205

XM_940199

KIAA1276

3363

3381

U

C

A

A

G

C

a

G

C

U

C

A

C

G

G

A

a

g

a

2

4

9

c

false

<90%

4236

XM_039169

KIAA1276

3363

3381

U

C

A

A

G

C

a

G

C

U

C

A

C

G

G

A

a

g

a

2

4

9

c

false

<90%

4236

XM_940199

KIAA1276

2484

2502

U

C

A

A

G

C

a

G

C

U

C

u

C

G

G

A

C

C

U

0

2

7

false

<90%

4236

XM_039169

KIAA1276

2484

2502

U

C

A

A

G

C

a

G

C

U

C

u

C

G

G

A

C

C

U

0

2

7

false

<90%

4236

NM_020807

ZNF319

1595

1613

U

C

A

A

G

C

G

G

C

c

C

u

C

G

G

A

C

C

U

-16

2

9

false

<90%

4220

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 265
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_004090	DUSP3	2
NM_052847	GNG7	2
NM_001004354	MGC61598	2
NM_015036		1
NM_020384	CLDN2	1
NM_015245	ANKS1A	1
NM_001806	CEBPG	1
NM_032559	KIF2B	1
NM_012393	PFAS	1
NM_001007097	NTRK2	1
NM_001010866	RP13-15M17.2	1
NM_001007139	IGF2	1
NM_000612	IGF2	1
NM_177538	CYP20A1	1
NM_173829	P18SRP	1
NM_018181	ZNF532	1
NM_001080426	DUSP27	1
XM_942428	DUSP27	1
NM_018146	RNMTL1	1
NM_015429	ABI3BP	1
NM_144507	KLK8	1
XM_928029	RNF187	1
XM_001129309	RNF187	1
NM_002537	OAZ2	1
NM_014604	TAX1BP3	1
NM_182760	SUMF1	1
NM_014906	PPM1E	1
NM_144997	FLCN	1
NM_015833	ADARB1	1
NM_015834	ADARB1	1
NM_001112	ADARB1	1
NM_001033049	ADARB1	1
NM_016734	PAX5	1
NM_006306	SMC1A	1
NM_145270	LOC146325	1
NM_207406	CCDC4	1
NM_031945	TSPAN10	1
NM_020733		1
XM_933539	MGC3032	1
XM_944529	MGC3032	1
NM_000657	BCL2	1
NM_033262	SLC8A3	1
NM_183002	SLC8A3	1
NM_058240	SLC8A3	1
NM_182936	SLC8A3	1
NM_182932	SLC8A3	1
NM_000342	SLC4A1	1
NM_015321	CRTC1	1
NM_001098482		1
NM_001029883	FLJ34931	1
NM_015332	NUDCD3	1
NM_018974	UNC93A	1
NM_014762	DHCR24	1
NM_032575	GLIS2	1
NM_033049	MUC13	1
NM_021949	ATP2B3	1
NM_001001344	ATP2B3	1
NM_006612	KIF1C	1
NM_153442	GPR26	1
NM_000914	OPRM1	1
NM_001079846	CREBBP	1
NM_004380	CREBBP	1
NM_000221	KHK	1
NM_006488	KHK	1
NM_032352	BRMS1L	1
NM_015368	PANX1	1
NM_003724	JRK	1
NM_001004316	FLJ16641	1
NM_022834	VWA1	1
NM_199121	VWA1	1
NM_001100423		1
NM_001100422		1
NM_001100424		1
NM_015535	LOC26010	1
NM_001085372		1
NM_207194	ADAM15	1
NM_207196	ADAM15	1
NM_003815	ADAM15	1
NM_207195	ADAM15	1
NM_207191	ADAM15	1
NM_207197	ADAM15	1
NM_001008492	SEPT2	1
NM_006155	SEPT2	1
NM_001008491	SEPT2	1
NM_004404	SEPT2	1
NM_003382	VIPR2	1
NM_033129	SCRT2	1
NM_025248	SNIP	1
NM_004474	FOXD2	1
NM_001031735	C19orf36	1
NM_001039846	C19orf36	1
NM_003086	SNAPC4	1
NM_020872	CNTN3	1
NM_033420	C19orf6	1
NM_080836	STK35	1
NM_020148	SPIRE1	1
NM_020745	AARS2	1
NM_198055	MZF1	1
NM_003422	MZF1	1
NM_001190	BCAT2	1
NM_032266	C2orf16	1
NM_020664	DECR2	1
NM_000603	NOS3	1
NM_002999	SDC4	1
NM_152272	CHMP7	1
NM_014291	GCAT	1
NM_001025073	C3orf17	1
NM_015412	C3orf17	1
NM_001025072	C3orf17	1
NM_017921	NPLOC4	1
NM_052909	KIAA1909	1
NM_004667	HERC2	1
NM_001001557	GDF6	1
XM_001125832	LOC727764	1
XM_940966	LOC647219	1
XM_065166	KIAA1957	1
XM_939576	KIAA1957	1
NM_000303	PMM2	1
NM_006557	DMRT2	1
NM_005511	MLANA	1
NM_024667	VPS37B	1
NM_148169	FBXO17	1
NM_024907	FBXO17	1
NM_147161	ACOT11	1
NM_001040146	CTF8	1
NM_001039690	CTF8	1
NM_001040144	CTF8	1
NM_013252	CLEC5A	1
NM_203304	RKHD1	1
NM_001085363		1
NM_024906	SCD5	1
NM_144949	SOCS5	1
NM_014011	SOCS5	1
NM_031427	DNAL1	1
NM_013231	FLRT2	1
XM_943278	LOC644727	1
XM_932334	LOC644727	1
NM_016526	BET1L	1
NM_032342	C9orf125	1
NM_000578	SLC11A1	1
NM_002942	ROBO2	1
NM_015453	THUMPD3	1
NM_001962	EFNA5	1
NM_020415	RETN	1
NM_207381	TNFAIP8L3	1
NM_019001	XRN1	1
NM_001042604	XRN1	1
NM_000843	GRM6	1
NM_024750	LRRC2	1
NM_024512	LRRC2	1
NM_022081	HPS4	1
NM_152841	HPS4	1
NM_000702	ATP1A2	1
NM_014331	SLC7A11	1
NM_130807	MOBKL2A	1
NM_017451	BAIAP2	1
NM_033387	FAM78A	1
NM_178120	DLX1	1
NM_001038493	DLX1	1
NM_000278	PAX2	1
NM_003989	PAX2	1
NM_003990	PAX2	1
NM_003987	PAX2	1
NM_003988	PAX2	1
NM_005427	TP73	1
NM_014286	FREQ	1
NM_133374	ZNF618	1
NM_021149	COTL1	1
NM_031229	RBCK1	1
NM_006462	RBCK1	1
XM_001130020	KIAA1147	1
XM_001130081	KIAA1147	1
NM_001080392	KIAA1147	1
NM_207387	C17orf76	1
NM_006224	PITPNA	1
NM_001001563	TIMM50	1
NM_194317	LYPD6	1
NM_174911	FAM84B	1
NM_207519	ZAP70	1
NM_001079	ZAP70	1
NM_175898	C15orf37	1
NM_138383	ABBA-1	1
XM_001133209	LOC646513	1
XM_001132717	LOC646513	1
NM_012293	PXDN	1
NM_020170	NCLN	1
NM_001001561	GGA1	1
NM_004959	NR5A1	1
NM_022490	POLR1E	1
NM_003498	SNN	1
XM_001131316	LOC389203	1
XM_371691	LOC389203	1
NM_017758	ALKBH5	1
XM_379029	LOC400879	1
NM_006618	JARID1B	1
NM_018373	SYNJ2BP	1
NM_203422	LOC221091	1
XM_001130636	LOC221091	1
NM_002975	CLEC11A	1
NM_002243	KCNJ15	1
NM_170736	KCNJ15	1
NM_170737	KCNJ15	1
NM_148886	SMCR7	1
NM_139162	SMCR7	1
NM_021913	AXL	1
NM_001699	AXL	1
NM_033130	SIGLEC10	1
NM_000334	SCN4A	1
NM_015490	SEC31B	1
NM_052864	TIFA	1
NM_001457	FLNB	1
NM_012307	EPB41L3	1
NM_000213	ITGB4	1
NM_001005731	ITGB4	1
NM_001005619	ITGB4	1
NM_004335	BST2	1
NM_014850	SRGAP3	1
NM_001033117	SRGAP3	1
NM_021215	C20orf77	1
NM_012164	FBXW2	1
NM_012218	ILF3	1
NM_017806	LIME1	1
NM_015365	AMMECR1	1
NM_001025580	AMMECR1	1
NM_130830	LRRC15	1
NM_004913	C16orf7	1
NM_032451	SPIRE2	1
NM_001004342	TRIM67	1
NM_033348	KCNK7	1
NM_033455	KCNK7	1
NM_005714	KCNK7	1
NM_014635	GCC2	1
NM_181453	GCC2	1
NM_005054	RGPD5	1
XM_001126221	LOC727851	1
XM_001126260	LOC727851	1
XM_001133591	LOC729540	1
XM_001133590	LOC729540	1
XM_001126233	LOC727851	1
XM_001126248	LOC727851	1
XM_001126272	LOC727851	1
XM_929931	LOC653489	1
NM_173644	C20orf197	1
NM_032023	RASSF4	1
NM_004148	NINJ1	1
XM_001128220	PLEKHM1	1
NM_024548	LRRIQ2	1
NM_004157	PRKAR2A	1
NM_001323	CST6	1
XM_001129442	CST6	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
NM_016540	GPR83	1
XM_001131042	LOC731852	1
NM_015266	SLC9A8	1
NM_052876	BTBD14B	1
NM_014616	ATP11B	1
NM_002251	KCNS1	1
NM_014562	OTX1	1
NM_005491	CXorf6	1
NM_014405	CACNG4	1
NM_031243	HNRPA2B1	1
NM_002137	HNRPA2B1	1
NM_001332	CTNND2	1
XM_001134421	C1orf152	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