VIRsiRNAdb

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

18 hits were found for ACUCGUGGUGGACUUCUCU (13 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_130807

MOBKL2A

507

525

u

C

a

C

G

U

G

G

U

G

G

A

C

U

U

C

U

u

U

75

3

14

c

false

<90%

3347

NM_145279

MOBKL2C

399

417

g

C

a

C

G

U

G

G

U

G

G

A

C

U

U

C

U

u

c

70

4

14

c

false

<90%

2804

NM_201403

MOBKL2C

417

435

g

C

a

C

G

U

G

G

U

G

G

A

C

U

U

C

U

u

c

70

4

14

c

false

<90%

2822

NM_012464

TLL1

2496

2514

g

C

U

u

G

U

G

G

U

G

G

A

C

U

U

C

U

u

a

53

4

13

c

false

<90%

6654

XM_001126204

LOC730526

68

86

A

C

c

C

G

U

G

G

U

G

G

A

C

U

U

C

a

u

g

49

4

13

c

false

<90%

369

XM_001126062

LOC730276

68

86

A

C

c

C

G

U

G

G

U

G

G

A

C

U

U

C

a

u

g

49

4

13

c

false

<90%

369

XM_001131919

LOC729969

68

86

A

C

c

C

G

U

G

G

U

G

G

A

C

U

U

C

a

u

g

49

4

13

c

false

<90%

369

NM_032831

TMEM142B

1280

1298

A

C

c

C

G

U

G

G

U

G

G

A

C

U

U

C

a

u

g

49

4

13

c

false

<90%

2527

NM_018167

BTBD7

1328

1346

c

g

a

C

G

U

G

G

U

G

G

A

C

c

U

C

U

C

U

47

4

10

c

false

<90%

2568

NM_001002860

BTBD7

1328

1346

c

g

a

C

G

U

G

G

U

G

G

A

C

c

U

C

U

C

U

47

4

10

c

false

<90%

8448

NM_020726

NLN

1529

1547

c

C

U

C

G

U

G

G

U

G

a

A

C

U

U

C

U

C

a

31

3

9

c

false

<90%

2881

NM_000833

GRIN2A

1867

1885

u

g

a

a

G

U

G

G

U

G

G

A

C

U

U

C

U

C

U

30

4

15

bc

false

<90%

6293

NM_001040709

SYPL2

684

702

c

C

U

C

a

U

G

G

g

G

G

A

C

U

U

C

U

C

U

-13

3

10

bc

false

<90%

3779

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_014909

VASH1

3538

3556

g

G

A

G

A

A

G

U

C

C

A

C

C

A

a

G

A

u

g

65

4

13

c

false

<90%

5746

NM_001051

SSTR3

1746

1764

g

G

A

G

A

A

G

U

C

C

A

g

C

A

C

G

A

u

g

56

4

10

false

<90%

2123

NM_020820

PREX1

955

973

c

a

A

G

A

A

G

U

C

C

A

C

C

A

a

G

A

G

g

56

4

12

c

false

<90%

6633

NM_014771

RNF40

200

218

g

G

A

G

A

A

G

a

C

C

A

C

C

A

C

G

A

c

U

33

3

9

c

false

<90%

4256

NM_030767

AKNA

4041

4059

A

G

A

G

A

A

G

g

C

C

A

C

C

A

C

G

A

G

g

32

2

10

bc

false

<90%

5385

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 448
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_014867	KBTBD11	2
NM_014912	CPEB3	2
NM_171998	RAB39B	2
NM_002417	MKI67	2
NM_021629	GNB4	2
NM_198461	LONRF2	2
NM_001007527	LMBRD2	2
NM_153261	TMEM188	1
NM_020918	GPAM	1
NM_173214	NFAT5	1
NM_006599	NFAT5	1
NM_138714	NFAT5	1
NM_001113178		1
NM_138713	NFAT5	1
NM_015094	HIC2	1
NM_032256	TMEM117	1
NM_018941	CLN8	1
NM_032457	PCDH7	1
NM_001649	SHROOM2	1
XM_938519	DKFZP434I0714	1
XM_929673	DKFZP434I0714	1
NM_003846	PEX11B	1
NM_020827		1
NM_033296	MRFAP1	1
NM_024625	ZC3HAV1	1
NM_019083	CCDC76	1
NM_032111	MRPL14	1
NM_001003407	ABLIM1	1
NM_001003408	ABLIM1	1
NM_002313	ABLIM1	1
NM_006720	ABLIM1	1
XM_001130189	LOC731598	1
XM_001129850	LOC729291	1
NM_005840	SPRY3	1
NM_016079	VPS24	1
NM_001005753	VPS24	1
NM_018959	DAZAP1	1
NM_170711	DAZAP1	1
NM_152390	TMEM178	1
NM_004382	CRHR1	1
NM_014636	RALGPS1	1
NM_012293	PXDN	1
NM_012476	VAX2	1
NM_001006623	WDR33	1
NM_175575	WFIKKN2	1
NM_020822	KCNT1	1
NM_000791	DHFR	1
NM_002349	LY75	1
NM_175839	SMOX	1
NM_175840	SMOX	1
NM_175841	SMOX	1
NM_175842	SMOX	1
NM_001109754		1
NM_002837	PTPRB	1
NM_178565	RSPO2	1
NM_001004346	MTHFD2L	1
NM_014758	SNX19	1
NM_052926	PNMA5	1
NM_001103151		1
NM_001103150		1
NM_207401	FLJ45717	1
NM_012309	SHANK2	1
NM_138499	PWWP2	1
NM_001098637		1
NM_005971	FXYD3	1
NM_021910	FXYD3	1
NM_001081686	G6PC2	1
NM_020722		1
NM_020447	C15orf17	1
NM_014235	UBL4A	1
NM_001003698	RREB1	1
NM_001003699	RREB1	1
NM_002955	RREB1	1
NM_004992	MECP2	1
NM_001040157	KIAA1712	1
NM_015471	NSL1	1
NM_001042549	NSL1	1
NM_080605	B3GALT6	1
NM_006355	TRIM38	1
NM_058187	C21orf63	1
NM_003216	TEF	1
NM_000320	QDPR	1
NM_006614	CHL1	1
NM_005504	BCAT1	1
NM_017643	MBTD1	1
XM_929883	LOC339742	1
XM_944606	LOC646482	1
XM_933644	LOC646482	1
NM_014864	FAM20B	1
XM_001132083	LOC732175	1
XM_001131915	LOC729967	1
NM_001718	BMP6	1
NM_004796	NRXN3	1
NM_001105250		1
NM_138970	NRXN3	1
NM_005650	TCF20	1
NM_181492	TCF20	1
NM_002079	GOT1	1
NM_006575	MAP4K5	1
NM_198794	MAP4K5	1
NM_001098620		1
NM_031989	PCBP2	1
NM_005016	PCBP2	1
NM_013263	BRD7	1
NM_014243	ADAMTS3	1
NM_024408	NOTCH2	1
XM_001133349	NOTCH2	1
NM_015257	KIAA0286	1
NM_198468	C6orf167	1
NM_001009554	MFAP3L	1
NM_021647	MFAP3L	1
NM_019595	ITSN2	1
NM_006277	ITSN2	1
XM_936640	LOC647589	1
NM_032508	TMEM185A	1
NM_052876	BTBD14B	1
NM_017780	CHD7	1
NM_015071	ARHGAP26	1
NM_031448	C19orf12	1
NM_001031726	C19orf12	1
NM_005376	MYCL1	1
NM_033244	PML	1
NM_001085460		1
NM_001085469		1
NM_001085465		1
NM_001085466		1
NM_001085462		1
NM_001085461		1
NM_001085458		1
NM_001085468		1
NM_001085463		1
NM_001085467		1
NM_001331	CTNND1	1
NM_001085459		1
NM_001085464		1
NM_152864	C20orf58	1
NM_031300	MXD3	1
NM_031413		1
NM_022719	DGCR14	1
NM_001008537	KIAA2022	1
NM_012129	CLDN12	1
NM_016424	CROP	1
NM_207405	FLJ46481	1
NM_022753	S100PBP	1
NM_014678	SAPS2	1
XM_001129019	SAPS2	1
NM_002342	LTBR	1
NM_001042506	LOC645974	1
XM_001130463	LOC645974	1
XM_001126207	LOC645974	1
NM_001012977	LOC340529	1
NM_182701	GPX6	1
NM_001042574	CRTC3	1
NM_022769	CRTC3	1
NM_001004106	GRK6	1
NM_002082	GRK6	1
NM_001081461	JMJD6	1
NM_015493	ANKRD25	1
NM_003498	SNN	1
XM_001129399	LOC642346	1
XM_928707	LOC642346	1
XM_925879	LOC642346	1
XM_925864	LOC642325	1
XM_001130526	LOC728636	1
XM_001130555	LOC728636	1
XM_001130543	LOC728636	1
XM_001130536	LOC728636	1
NM_172388	NFATC1	1
NM_006162	NFATC1	1
NM_172389	NFATC1	1
NM_172387	NFATC1	1
NM_000192	TBX5	1
NM_080717	TBX5	1
NM_181486	TBX5	1
NM_152914	MGC33894	1
NM_015853	LOC51035	1
NM_006062	SMYD5	1
NM_021931	DHX35	1
NM_001112	ADARB1	1
NM_012234	RYBP	1
NM_004090	DUSP3	1
NM_032554	GPR81	1
NM_000175	GPI	1
NM_015472	WWTR1	1
NM_001012427	FOXP4	1
NM_138457	FOXP4	1
NM_001012426	FOXP4	1
NM_001040146	CTF8	1
NM_001039690	CTF8	1
NM_001040144	CTF8	1
NM_001024227	ARF1	1
NM_001658	ARF1	1
NM_001024228	ARF1	1
NM_001024226	ARF1	1
NM_000302	PLOD1	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_032193	RNASEH2C	1
NM_021030	ZNF14	1
NM_000439	PCSK1	1
NM_003034	ST8SIA1	1
NM_001008493	ENAH	1
NM_018212	ENAH	1
NM_014396	VPS41	1
NM_080631	VPS41	1
NM_181807	DCDC1	1
NM_001005210	LRRC55	1
NM_020823		1
NM_023011	UPF3A	1
NM_080687	UPF3A	1
NM_001003828	PARVB	1
NM_013327	PARVB	1
NM_012308	FBXL11	1
NM_024741	ZNF408	1
NM_014873	LPGAT1	1
NM_021807	EXOC4	1
NM_001099220		1
XM_929902	LOC646938	1
XM_937239	LOC648189	1
NM_007150		1
NM_024531	GPR172A	1
NM_003918	GYG2	1
NM_001079855	GYG2	1
NM_022895	C12orf43	1
NM_152942	TNFRSF8	1
NM_001243	TNFRSF8	1
NM_004782	SNAP29	1
NM_144682	SLFN13	1
NM_020659	TTYH1	1
NM_001005367	TTYH1	1
NM_001040457	RHBDD2	1
NM_001040456	RHBDD2	1
NM_014861	ATP2C2	1
NM_001005408	KIAA1787	1
NM_032442	KIAA1787	1
NM_016433	GLTP	1
NM_018008	FEZF2	1
NM_016037	UTP11L	1
NM_207514	FLJ20186	1
NM_004421	DVL1	1
NM_182779	DVL1	1
NM_182744	NBL1	1
NM_005380	NBL1	1
NM_000901	NR3C2	1
NM_005990	STK10	1
NM_052960	RBP7	1
NM_001098813		1
NM_015146		1
NM_001098812		1
NM_145159	JAG2	1
NM_002226	JAG2	1
NM_003576	STK24	1
NM_001032296	STK24	1
NM_153020	RBM24	1
NM_138790	PLD4	1
NM_020120	UGCGL1	1
NM_001025777	UGCGL1	1
NM_001014831	PAK4	1
NM_001014835	PAK4	1
NM_001014834	PAK4	1
NM_005884	PAK4	1
NM_001014832	PAK4	1
NM_006734	HIVEP2	1
NM_001018003	SORBS3	1
NM_005775	SORBS3	1
NM_005721	ACTR3	1
NM_001010911	C10orf114	1
NM_006337	MCRS1	1
NM_001012300	MCRS1	1
NM_020676	ABHD6	1
NM_014661	FAM53B	1
NM_080819	GPR78	1
XM_001134313	LOC732291	1
XM_938203	C1orf167	1
XM_209234	C1orf167	1
NM_002957	RXRA	1
NM_002657	PLAGL2	1
NM_004710	SYNGR2	1
XM_937698	LOC648629	1
NM_053005	HCCA2	1
NM_175724	IL5RA	1
NM_175727	IL5RA	1
NM_021813	BACH2	1
NM_001030288	SPN	1
NM_003123	SPN	1
NM_001001669	FLJ41603	1
NM_003458	BSN	1
NM_001007248	ZNF599	1
NM_007264	ADMR	1
NM_006950	SYN1	1
NM_133499	SYN1	1
NM_014223	NFYC	1
XM_001134308	LOC732275	1
NM_152422	PTPDC1	1
NM_177995	PTPDC1	1
NM_172239	REXO1L1	1
NM_005561	LAMP1	1
NM_001031694	SCMH1	1
NM_012236	SCMH1	1
NM_003269	NR2E1	1
NM_024989	PGAP1	1
NM_020908		1
NM_005078	TLE3	1
NM_001105192		1
NM_001033113	ENTPD8	1
NM_198585	ENTPD8	1
NM_153487	MDGA1	1
NM_153347	TMEM86A	1
NM_015197	PACS2	1
NM_001100913		1
NM_016095	GINS2	1
NM_024887	DHDDS	1
NM_205861	DHDDS	1
NM_147187	TNFRSF10B	1
NM_003842	TNFRSF10B	1
NM_001004351	MGC57359	1
NM_014517	UBP1	1
NM_001040285	PAPD5	1
NM_001040284	PAPD5	1
NM_001013620	ALG10B	1
NM_018402	IL26	1
NM_001103147		1
NM_001103148		1
NM_001103146		1
NM_015575	TNRC15	1
NM_145687	MAP4K4	1
NM_145686	MAP4K4	1
NM_004834	MAP4K4	1
NM_199131	VAX1	1
NM_144607	CYB5D1	1
NM_007146	VEZF1	1
NM_015458	MTMR9	1
NM_001082480	ZNF623	1
NM_014789	ZNF623	1
NM_023039	ANKRA2	1
NM_138292	ATM	1
NM_000051	ATM	1
NM_000200	HTN3	1
NM_032801	JAM3	1
NM_033020	TRIM33	1
NM_015906	TRIM33	1
NM_015193	ARC	1
NM_001043318	C14orf43	1
NM_194278	C14orf43	1
NM_015892	GALNAC4S-6ST	1
NM_198576	AGRN	1
XM_001126326	AGRIN	1
NM_004091	E2F2	1
NM_032333	C10orf58	1
NM_138727	ST7L	1
NM_138728	ST7L	1
NM_017744	ST7L	1
NM_001010888	ZC3H12B	1
NM_032302	C7orf48	1
NM_005702	ERAL1	1
NM_006557	DMRT2	1
XM_373030	LOC285556	1
XM_939505	LOC285556	1
NM_031845	MAP2	1
NM_031847	MAP2	1
NM_001039538	MAP2	1
NM_002374	MAP2	1
NM_005257	GATA6	1
NM_000934	SERPINF2	1
NM_000216	KAL1	1
NM_003036	SKI	1
XM_001131914	LOC729966	1
XM_001128021	LOC730997	1
NM_145173	DIRAS1	1
NM_022436	ABCG5	1
NM_152667	NANP	1
NM_001039802	CDC42	1
NM_001791	CDC42	1
NM_001089595		1
XM_001126970	LOC728245	1
XM_001130724	LOC731771	1
NM_014964	EPN2	1
NM_001102664		1
NM_148921	EPN2	1
NM_002422	MMP3	1
XM_943661	LRRC38	1
XM_059074	LRRC38	1
NM_020974	SCUBE2	1
NM_005955	MTF1	1
NM_003385	VSNL1	1
NM_000742	CHRNA2	1
NM_018299	UBE2W	1
NM_001001481	UBE2W	1
NM_020431	TMEM63C	1
NM_004590	CCL16	1
NM_014190	ADD1	1
NM_001119	ADD1	1
NM_014189	ADD1	1
NM_176801	ADD1	1
NM_001045477	FAM22G	1
NM_024688	C10orf68	1
NM_001395	DUSP9	1
NM_032932	RAB11FIP4	1
NM_005910	MAPT	1
NM_016841	MAPT	1
NM_016834	MAPT	1
NM_016835	MAPT	1
NM_001099272		1
NM_152733	BTBD9	1
NM_052893		1
NM_001535	PRMT2	1
NM_206962	PRMT2	1
NM_152512	ENTHD1	1
NM_032228	MLSTD2	1
NM_020698	TMCC3	1
NM_005895	GOLGA3	1
NM_001949	E2F3	1
NM_018027	FRMD4A	1
NM_005239	ETS2	1
NM_013231	FLRT2	1
NM_005347	HSPA5	1
NM_152721	DOK6	1
NM_003740	KCNK5	1
NM_015840	ADAR	1
NM_015841	ADAR	1
NM_001025107	ADAR	1
NM_001111	ADAR	1
NM_181353	ID1	1
NM_002165	ID1	1
NM_020870	SH3RF1	1
NM_138341	TMEM116	1
NM_006690	MMP24	1
NM_001040445	ASB1	1
NM_015326	SRGAP2	1
NM_001081	CUBN	1
NM_003310	TSSC1	1
NM_006073	TRDN	1
NM_139075	TPCN2	1
NM_020448	NPAL3	1
NM_022159		1
NM_006203	PDE4D	1
NM_001104631		1
NM_004200	SYT7	1
XM_943686	SYT7	1
NM_025268	TMEM121	1
NM_014510		1
NM_020718	USP31	1
NM_052962	IL22RA2	1
NM_181309	IL22RA2	1
NM_181310	IL22RA2	1
NM_002745	MAPK1	1
NM_006581	FUT9	1
NM_145166	ZBTB47	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