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 GGUCCGUGAGCCGCAUGAC (1 guide strand hits and 19 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_145040

PRKCDBP

198

216

G

G

U

C

C

G

U

G

c

G

C

C

G

C

A

U

c

c

a

8

4

8

c

false

<90%

1039

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

XR_017743

LOC389362

397

415

G

U

C

A

U

G

C

G

G

C

U

g

A

C

G

G

A

C

u

61

2

11

false

<90%

1151

XR_017905

LOC389362

397

415

G

U

C

A

U

G

C

G

G

C

U

g

A

C

G

G

A

C

u

61

2

11

false

<90%

1151

NM_198397

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

5243

NM_198376

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7207

NM_198388

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7450

NM_198387

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7471

NM_198382

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7477

NM_198386

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7492

NM_198378

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7513

NM_198384

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7546

NM_198379

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7588

NM_198383

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7612

NM_198380

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7657

NM_198385

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7690

NM_198377

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7756

NM_018896

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7825

NM_198396

CACNA1G

429

447

u

U

C

A

U

G

C

G

G

C

U

C

A

a

c

G

A

C

C

53

3

12

c

false

<90%

7834

NM_005424

TIE1

170

188

a

a

C

c

U

G

C

G

G

C

U

C

A

C

G

G

A

C

C

49

3

15

bc

false

<90%

3960

NM_002661

PLCG2

2039

2057

G

a

g

c

U

G

C

G

G

C

U

C

A

C

G

G

A

C

C

32

3

15

bc

false

<90%

4263

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 264
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_023076	C16orf28	2
NM_022834	VWA1	2
NM_199121	VWA1	2
XM_001130507	LOC731708	1
XM_001127823	LOC728573	1
NM_014286	FREQ	1
NM_001102371		1
NM_024955	FOXRED2	1
NM_175607	CNTN4	1
NM_175612	CNTN4	1
NM_033130	SIGLEC10	1
NM_153636	CPNE7	1
NM_014427	CPNE7	1
NM_013345	GPR132	1
NM_001098415		1
NM_016596	HDAC7A	1
NM_001098416		1
NM_015401	HDAC7A	1
NM_014844	KIAA0329	1
NM_145206	VTI1A	1
NM_001045477	FAM22G	1
NM_005920	MEF2D	1
NM_030810	TXNDC5	1
NM_022085	TXNDC5	1
NM_000334	SCN4A	1
NM_002359	MAFG	1
NM_032711	MAFG	1
NM_001303	COX10	1
NM_005840	SPRY3	1
NM_178836	LOC201164	1
NM_003410	ZFX	1
NM_017454	STAU1	1
NM_004602	STAU1	1
NM_017452	STAU1	1
NM_001037328	STAU1	1
NM_017453	STAU1	1
NM_181706	DPH4	1
NM_000262	NAGA	1
NM_015490	SEC31B	1
XM_378914	KIAA0492	1
XM_944290	KIAA0492	1
NM_006764	IFRD2	1
NM_052864	TIFA	1
NM_001009984		1
NM_201520	SLC25A35	1
NM_001007271	DUSP13	1
NM_005026	PIK3CD	1
NM_005904	SMAD7	1
NM_004204	PIGQ	1
NM_020946	DENND1A	1
NM_015229	KIAA0664	1
NM_001081755	ELN	1
NM_001081754	ELN	1
NM_001081752	ELN	1
NM_000501	ELN	1
NM_001081753	ELN	1
NM_001039796	FLJ35776	1
NM_001457	FLNB	1
NM_001024401	SBK1	1
NM_006291	TNFAIP2	1
NM_033315	RASL10B	1
NM_012307	EPB41L3	1
NM_152988	SPPL2B	1
NM_001077238	SPPL2B	1
NM_000213	ITGB4	1
NM_001005731	ITGB4	1
NM_001005619	ITGB4	1
NM_080388	S100A16	1
NM_004335	BST2	1
NM_203374	ZNF784	1
NM_032933	C18orf45	1
XM_001134324	LOC732287	1
XM_001131719	LOC728585	1
NM_152482	C19orf25	1
NM_001024227	ARF1	1
NM_001658	ARF1	1
NM_001024228	ARF1	1
NM_001024226	ARF1	1
NM_024417	FDXR	1
NM_004110	FDXR	1
NM_014850	SRGAP3	1
NM_001033117	SRGAP3	1
NM_021215	C20orf77	1
NM_198849	LOC283514	1
NM_003486	SLC7A5	1
NM_012164	FBXW2	1
NM_203293	TRIM7	1
NM_203297	TRIM7	1
NM_203294	TRIM7	1
NM_203296	TRIM7	1
NM_203295	TRIM7	1
NM_002023	FMOD	1
NM_015381	FAM19A5	1
NM_001082967	FAM19A5	1
NM_032795	RPUSD4	1
NM_021951	DMRT1	1
XM_927029	PPP1R3E	1
XM_940069	PPP1R3E	1
NM_001497	B4GALT1	1
NM_020731	AHRR	1
NM_012218	ILF3	1
NM_001105579		1
NM_017806	LIME1	1
NM_015365	AMMECR1	1
NM_001025580	AMMECR1	1
NM_001098844		1
NM_020133	AGPAT4	1
NM_001886	CRYBA4	1
NM_145113	MAX	1
NM_133443	GPT2	1
NM_130830	LRRC15	1
NM_004913	C16orf7	1
NM_001034852	SMOC1	1
NM_022137	SMOC1	1
NM_032451	SPIRE2	1
NM_001004342	TRIM67	1
NM_031283	TCF7L1	1
NM_018207	TRIM62	1
NM_033348	KCNK7	1
NM_033455	KCNK7	1
NM_005714	KCNK7	1
NM_002558	P2RX1	1
NM_003881	WISP2	1
NM_001081686	G6PC2	1
NM_001037165	FOXK1	1
NM_138356	SHF	1
NM_001040427	HAGH	1
NM_005326	HAGH	1
NM_005124	NUP153	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_030962	SBF2	1
NM_002248	KCNN1	1
NM_005161	AGTRL1	1
NM_183397	PXMP4	1
NM_007238	PXMP4	1
NM_144599	NIPA1	1
NM_001975	ENO2	1
NM_021240	DMRT3	1
NM_003178	SYN2	1
NM_004822	NTN1	1
NM_003255	TIMP2	1
XM_001132362	TIMP2	1
NM_002836	PTPRA	1
NM_080840	PTPRA	1
NM_080841	PTPRA	1
NM_024086	METT10D	1
XM_495939	KIAA1545	1
XM_936428	KIAA1545	1
NM_032023	RASSF4	1
NM_004148	NINJ1	1
XM_001128220	PLEKHM1	1
NM_021643	TRIB2	1
NM_012204	GTF3C4	1
NM_017712	PGPEP1	1
NM_024548	LRRIQ2	1
NM_014222	NDUFA8	1
XM_936833	LOC644196	1
XM_927389	LOC644196	1
XM_001130325	LOC728469	1
XM_001132990	LOC731448	1
NM_025079	ZC3H12A	1
NM_004745	DLGAP2	1
NM_004157	PRKAR2A	1
NM_001031679	MSRB3	1
NM_198080	MSRB3	1
NM_002997	SDC1	1
NM_001006946	SDC1	1
NM_004914	RAB36	1
XM_001128879	LOC728903	1
NM_001323	CST6	1
XM_001129442	CST6	1
NM_004090	DUSP3	1
NM_012264	C22orf5	1
NM_001532	SLC29A2	1
NM_004186	SEMA3F	1
NM_153812	PHF13	1
NM_032647	CBX2	1
NM_058175	COL6A2	1
NM_005672	PSCA	1
NM_202003	FOXM1	1
NM_202002	FOXM1	1
NM_021953	FOXM1	1
NM_207521	RTN4	1
NM_153828	RTN4	1
NM_020532	RTN4	1
NM_007008	RTN4	1
NM_207520	RTN4	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
NM_152221	CSNK1E	1
NM_001894	CSNK1E	1
NM_001080452	GPR108	1
NM_020171	GPR108	1
NM_001012427	FOXP4	1
NM_138457	FOXP4	1
NM_001012426	FOXP4	1
NM_001024668	LETMD1	1
NM_015416	LETMD1	1
XM_925795	LOC653051	1
NM_005187	CBFA2T3	1
NM_175931	CBFA2T3	1
NM_016540	GPR83	1
NM_015215	CAMTA1	1
XM_001131042	LOC731852	1
NM_024408	NOTCH2	1
XM_001133349	NOTCH2	1
NM_015266	SLC9A8	1
NM_020462	ERGIC1	1
NM_007084	SOX21	1
NM_052876	BTBD14B	1
NM_002923	RGS2	1
NM_000336	SCNN1B	1
NM_182526	C14orf83	1
NM_001261	CDK9	1
NM_015291	DNAJC16	1
NM_014616	ATP11B	1
NM_002251	KCNS1	1
NM_001080485	ZNF275	1
NM_004319	ASTN1	1
NM_014562	OTX1	1
NM_015318	ARHGEF18	1
NM_005491	CXorf6	1
NM_014405	CACNG4	1
NM_207405	FLJ46481	1
NM_003856	IL1RL1	1
NM_023932	EGFL9	1
NM_206539	EGFL9	1
NM_153693	HOXC6	1
NM_004503	HOXC6	1
NM_004074	COX8A	1
NM_001111308		1
NM_001111309		1
NM_001111307		1
NM_006202	PDE4A	1
NM_031243	HNRPA2B1	1
NM_002137	HNRPA2B1	1
NM_023940	RASL11B	1
NM_181701	QSOX2	1
NM_033393	KIAA1727	1
NM_014767	SPOCK2	1
NM_145306	C10orf35	1
NM_206855	QKI	1
NM_007353	GNA12	1
NM_032680	EFCAB4B	1
NM_020531	C20orf3	1
NM_001332	CTNND2	1
XM_001134421	C1orf152	1
NM_018013	SOBP	1
NM_001001132	ITSN1	1
NM_004862	LITAF	1
NM_001100421		1
NM_001100420		1
NM_017447	C21orf91	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