VIRsiRNAdb

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

24 hits were found for CGGAGACAUCAGACAACUA (13 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

XM_291020

LOC339809

3236

3254

a

G

G

A

G

A

C

A

U

C

A

G

c

C

A

A

C

a

u

79

4

11

false

<90%

5135

XM_936940

LOC339809

3240

3258

a

G

G

A

G

A

C

A

U

C

A

G

c

C

A

A

C

a

u

79

4

11

false

<90%

5139

NM_002844

PTPRK

2859

2877

u

G

a

A

G

A

C

A

U

C

A

G

A

C

A

g

C

U

A

52

3

12

c

false

<90%

5982

NM_203388

RNH1

809

827

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

1764

NM_203384

RNH1

861

879

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

1816

NM_203389

RNH1

877

895

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

1832

NM_203385

RNH1

929

947

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

1884

NM_203386

RNH1

982

1000

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

1937

NM_203383

RNH1

1034

1052

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

1989

NM_203387

RNH1

1050

1068

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

2005

NM_002939

RNH1

1102

1120

g

u

G

u

G

A

C

A

U

C

A

G

A

C

A

A

C

U

g

44

4

14

bc

false

<90%

2057

NM_001011725

LOC144983

302

320

a

G

G

A

G

A

C

u

U

C

A

G

A

C

A

A

C

c

A

33

3

9

c

false

<90%

2224

NM_001011724

LOC144983

302

320

a

G

G

A

G

A

C

u

U

C

A

G

A

C

A

A

C

c

A

33

3

9

c

false

<90%

2365

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_000204

CFI

715

733

a

A

G

U

U

G

U

C

U

G

A

U

c

U

C

U

C

u

a

79

4

11

false

<90%

2160

NM_015074

KIF1B

4869

4887

a

A

G

U

U

G

U

C

U

G

A

U

a

U

C

U

C

u

c

79

4

11

false

<90%

10551

NM_001001395

LMO3

3192

3210

U

u

G

U

U

G

U

C

U

G

A

U

G

c

C

U

C

C

a

64

3

11

c

false

<90%

3450

NM_018640

LMO3

3469

3487

U

u

G

U

U

G

U

C

U

G

A

U

G

c

C

U

C

C

a

64

3

11

c

false

<90%

3727

NM_194314

ZBTB41

8335

8353

U

g

G

U

U

G

U

C

U

G

A

U

G

U

u

U

C

C

u

58

3

12

c

false

<90%

8474

NM_003899

ARHGEF7

4286

4304

c

u

c

U

U

G

U

C

U

G

A

U

c

U

C

U

C

C

G

56

4

9

false

<90%

5032

NM_004740

TIAF1

996

1014

U

g

G

g

U

G

U

C

U

G

A

U

G

U

C

U

C

C

a

46

3

14

bc

false

<90%

2110

NM_203318

MYO18A

6434

6452

U

g

G

g

U

G

U

C

U

G

A

U

G

U

C

U

C

C

a

46

3

14

bc

false

<90%

7546

NM_078471

MYO18A

6479

6497

U

g

G

g

U

G

U

C

U

G

A

U

G

U

C

U

C

C

a

46

3

14

bc

false

<90%

7591

NM_024293

C2orf17

1117

1135

c

A

G

c

U

G

a

C

U

G

A

U

G

U

C

U

C

C

G

-5

3

12

bc

false

<90%

2614

NM_007348

ATF6

442

460

U

A

G

U

U

c

U

C

a

G

A

U

G

U

C

U

C

C

c

-28

3

9

bc

false

<90%

2488

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 465
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_001097620		2
NM_030576	LIMD2	2
NM_130807	MOBKL2A	2
NM_205843	NFIC	2
NM_005597	NFIC	2
NM_024979	MCF2L	2
NM_001112732		2
NM_000990	RPL27A	2
NM_014772	KIAA0427	2
NM_031444	C22orf13	2
NM_001319	CSNK1G2	1
NM_015711	GLTSCR1	1
NM_004442	EPHB2	1
NM_017449	EPHB2	1
XM_378914	KIAA0492	1
XM_944290	KIAA0492	1
XM_938689	KIAA1671	1
XM_371461	KIAA1671	1
NM_015907	LAP3	1
NM_182574	FLJ36070	1
NM_024607	PPP1R3B	1
NM_001031690	FAM131B	1
NM_014690	FAM131B	1
NM_021809	TGIF2	1
NM_001097611		1
NM_032728	PPAPDC3	1
NM_213604	ADAMTSL5	1
XM_001127146	IL7R	1
NM_139048	HLTF	1
NM_003071	HLTF	1
XM_379454	LOC401284	1
XM_945609	LOC401284	1
NM_080927	DCBLD2	1
NM_182595	DKFZp564N2472	1
NM_001100417		1
NM_175748	C14orf130	1
XM_001131817	LOC732087	1
XM_001133142	LOC731450	1
NM_014643		1
NM_003108	SOX11	1
NM_015226	KIAA0350	1
NM_024329	EFHD2	1
NM_032296	FLYWCH1	1
NM_001007229	SPOP	1
NM_001007230	SPOP	1
NM_001007226	SPOP	1
NM_003563	SPOP	1
NM_001007228	SPOP	1
NM_001007227	SPOP	1
NM_152654	DAND5	1
NM_000554	CRX	1
XM_927936	LOC644841	1
XM_935685	LOC641933	1
XM_938176	LOC644841	1
NM_020766	PCDH19	1
NM_001105243		1
NM_016529	ATP8A2	1
NM_013248	NXT1	1
NM_032801	JAM3	1
NM_080669	SLC46A1	1
NM_002725	PRELP	1
NM_201348	PRELP	1
XM_001132353	FLJ44450	1
XM_001133195	FLJ44450	1
NM_021020	LZTS1	1
NM_006399	BATF	1
NM_004273	CHST3	1
NM_001018000	KIAA1026	1
NM_001017999	KIAA1026	1
NM_001018001	KIAA1026	1
NM_015209	KIAA1026	1
NM_001018111	PODXL	1
NM_005397	PODXL	1
NM_001024372	BAALC	1
NM_024812	BAALC	1
NM_015071	ARHGAP26	1
NM_001031677	RAB24	1
NM_130781	RAB24	1
NM_020911		1
XM_001133080	LOC731356	1
XM_001133093	LOC731356	1
XM_001133076	LOC731356	1
XM_001133109	LOC731356	1
XM_001133116	LOC731356	1
NM_001082488	LOC728635	1
XM_001133105	LOC731356	1
XM_001133065	LOC731356	1
XM_001131304	LOC728635	1
XM_001133102	LOC731356	1
NM_138413	C10orf65	1
NM_030927	TSPAN14	1
NM_174929	ZMIZ2	1
NM_031449	ZMIZ2	1
NM_152571	C9orf163	1
NM_194286	KIAA1853	1
NM_007325	GRIA3	1
NM_000828	GRIA3	1
NM_006645	STARD10	1
NM_001007271	DUSP13	1
NM_001793	CDH3	1
XM_001129399	LOC642346	1
XM_928707	LOC642346	1
XM_925879	LOC642346	1
XM_925864	LOC642325	1
NM_178013	PRIMA1	1
NM_012069	ATP1B4	1
NM_001706	BCL6	1
NM_138931	BCL6	1
NM_022132	MCCC2	1
NM_006321	ARIH2	1
NM_003061	SLIT1	1
NM_025136	OPA3	1
NM_003234	TFRC	1
NM_138348	FAM105B	1
NM_032223		1
NM_152643	KNDC1	1
NM_145013	C11orf45	1
XM_001127419	FLJ30851	1
XM_001130207	FLJ30851	1
NM_001040710	FLJ30851	1
NM_001174	ARHGAP6	1
NM_020150	SAR1A	1
NM_019069	WDR5B	1
NM_138445	GPR146	1
NM_007249	KLF12	1
XM_001134363	FOXK2	1
XM_001134364	FOXK2	1
NM_004514	FOXK2	1
NM_006565	CTCF	1
NM_145253	FAM100A	1
NM_001014842	TM9SF1	1
XM_925788	LOC400723	1
XM_001127682	LOC728534	1
NM_006586	TNRC5	1
NM_174892	CD300LB	1
NM_031445	AMMECR1L	1
NM_014282	HABP4	1
NM_015227	POFUT2	1
NM_133634	POFUT2	1
NM_032214	SLA2	1
NM_175077	SLA2	1
NM_152335	C15orf27	1
NM_018280	C22orf26	1
NM_015720	PODXL2	1
NM_002918	RFX1	1
NM_001001709	FLJ45537	1
NM_022719	DGCR14	1
NM_022081	HPS4	1
NM_152841	HPS4	1
NM_001023587	ABCC5	1
NM_005276	GPD1	1
NM_015453	THUMPD3	1
XM_932309	LOC644694	1
XM_170840	LOC256223	1
XM_001129825	LOC728817	1
XM_001129242	LOC731171	1
NM_016263	FZR1	1
XM_495888	DKFZp434E1119	1
NM_003038	SLC1A4	1
NM_005883	APC2	1
NM_001039762	FLJ45557	1
NM_001018003	SORBS3	1
NM_005775	SORBS3	1
NM_014572	LATS2	1
NM_198086	JUB	1
NM_032876	JUB	1
XM_940362	LOC645984	1
XM_928946	LOC645984	1
NM_004959	NR5A1	1
NM_003751	EIF3S9	1
NM_001037283	EIF3S9	1
NM_177457	LYNX1	1
NM_177477	LYNX1	1
NM_177476	LYNX1	1
NM_006690	MMP24	1
XM_001134215	PDPR	1
NM_017990	PDPR	1
NM_020845	PITPNM2	1
NM_002478	MYOD1	1
NM_017891	C1orf159	1
XM_001128635	LOC731159	1
XM_001131972	LOC729988	1
NM_004455	EXTL1	1
NM_017765	PQLC2	1
NM_001040126	PQLC2	1
NM_001040125	PQLC2	1
NM_001077445	PHF16	1
NM_014735	PHF16	1
NM_024034	GDAP1L1	1
XM_945995	LOC339674	1
XM_934917	LOC339674	1
NM_023072	ZSWIM4	1
NM_001001692	FLJ45139	1
NM_032515	BOK	1
NM_001085363		1
NM_015260	SIN3B	1
NM_138774	C19orf22	1
NM_024100	WDR18	1
NM_177972	TUB	1
NM_003320	TUB	1
NM_001013717	LOC441108	1
NM_003006	SELPLG	1
NM_207514	FLJ20186	1
NM_079837	BANP	1
NM_017869	BANP	1
NM_015210	KIAA0802	1
NM_006237	POU4F1	1
XM_930431	LOC645195	1
XM_942574	LOC645195	1
NM_207349	PRR17	1
NM_033259	CAMK2N2	1
NM_007086	WDHD1	1
NM_001008396	WDHD1	1
NM_000678	ADRA1D	1
NM_203400	RPRML	1
NM_178557	NAT8L	1
NM_021083	XK	1
NM_004045	ATOX1	1
NM_001124	ADM	1
NM_006093	PRG3	1
NM_005986	SOX1	1
NM_020896	OSBPL5	1
NM_145638	OSBPL5	1
NM_001018112	FANCA	1
NM_004976	KCNC1	1
NM_032389	ZNF289	1
NM_001039029	LRTM2	1
NM_015417	C20orf28	1
NM_198836	ACACA	1
NM_198837	ACACA	1
NM_198834	ACACA	1
NM_198838	ACACA	1
NM_198839	ACACA	1
NM_000599	IGFBP5	1
NM_001042690	LOC345222	1
NM_017723	C9orf167	1
NM_032740	SFT2D3	1
NM_144488	RGS3	1
NM_021106	RGS3	1
NM_130795	RGS3	1
NM_144489	RGS3	1
NM_134427	RGS3	1
NM_080625	C20orf160	1
NM_152253	CHKB	1
NM_020639	RIPK4	1
XM_932244	LOC653160	1
XM_945233	LOC653160	1
NM_199054	MKNK2	1
NM_001008404	LOC400258	1
XM_001131466	LOC728516	1
XM_001132985	LOC731177	1
NM_176823	S100A7A	1
NM_000474	TWIST1	1
NM_004387	NKX2-5	1
NM_002508	NID1	1
NM_005170	ASCL2	1
NM_012194		1
NM_147200	TRAF3IP2	1
NM_147686	TRAF3IP2	1
NM_004058	CAPS	1
NM_080590	CAPS	1
NM_004408	DNM1	1
NM_001005336	DNM1	1
NM_014741	KIAA0652	1
NM_203327	SLC23A2	1
NM_005116	SLC23A2	1
NM_005187	CBFA2T3	1
NM_175931	CBFA2T3	1
NM_007014	WWP2	1
NM_199424	WWP2	1
NM_181704	BAGE4	1
NM_182482	BAGE2	1
NM_182484	BAGE5	1
NM_182481	BAGE3	1
NM_001100875		1
NM_152598	RNF190	1
NM_014207	CD5	1
NM_018013	SOBP	1
NM_152914	MGC33894	1
NM_005189	CBX2	1
NM_031218	ZNF93	1
XM_945302	LOC652225	1
XM_934407	LOC647131	1
NM_006675	TSPAN9	1
NM_012315	KLK9	1
NM_015016		1
XM_001132013	ANKH	1
NM_054027	ANKH	1
NM_030962	SBF2	1
NM_004566	PFKFB3	1
NM_001261	CDK9	1
NM_030767	AKNA	1
NM_015995	KLF13	1
NM_004399	DDX11	1
NM_030653	DDX11	1
NM_152438	DDX11	1
NM_005105	RBM8A	1
XM_001131270	LOC730990	1
NM_015063	SLC8A2	1
NM_005036	PPARA	1
NM_001001928	PPARA	1
NM_032446	MEGF10	1
NM_003897	IER3	1
NM_020993	BCL7A	1
NM_001024808	BCL7A	1
NM_015069	ZNF423	1
NM_030636	KIAA1706	1
NM_002688	SEPT5	1
NM_000332	ATXN1	1
NM_015359	SLC39A14	1
NM_014859	KIAA0672	1
NM_206833	CTXN1	1
NM_006555	YKT6	1
NM_014668	GREB1	1
NM_033229	TRIM15	1
NM_005253	FOSL2	1
NM_002751	MAPK11	1
NM_000911	OPRD1	1
NM_004992	MECP2	1
NM_001080950	MYO1C	1
NM_033375	MYO1C	1
NM_001080779	MYO1C	1
NM_198973	MKNK1	1
NM_020941		1
NM_024847	TMC7	1
NM_003811	TNFSF9	1
NM_005873	RGS19	1
NM_001039467	RGS19	1
NM_015520	MAGI1	1
NM_001386	DPYSL2	1
XM_930111	LOC644914	1
XM_001128558	LOC730740	1
NM_002107	H3F3A	1
NM_001003407	ABLIM1	1
NM_001003408	ABLIM1	1
NM_002313	ABLIM1	1
NM_006720	ABLIM1	1
NM_033133	CNP	1
NM_004822	NTN1	1
NM_013336	SEC61A1	1
NM_080552	SLC32A1	1
NM_012398	PIP5K1C	1
NM_172060	EYA1	1
NM_000503	EYA1	1
NM_172058	EYA1	1
NM_172059	EYA1	1
NM_000623	BDKRB2	1
XM_926711	LOC643382	1
XM_939770	LOC650683	1
NM_207393	IGFL3	1
NM_004311	ARL3	1
NM_004741	NOLC1	1
NM_001098500		1
NM_019590	KIAA1217	1
NM_001098501		1
NM_014585	SLC40A1	1
NM_004433	ELF3	1
NM_130391	PTPRD	1
NM_130393	PTPRD	1
NM_130392	PTPRD	1
NM_002839	PTPRD	1
NM_001040712	PTPRD	1
XM_496575	FLJ14082	1
XM_936846	FLJ14082	1
NM_006749	SLC20A2	1
NM_001031735	C19orf36	1
NM_001039846	C19orf36	1
XM_001130955	LOC730347	1
XM_001127355	LOC728377	1
NM_015170	SULF1	1
NM_012455	PSD4	1
NM_024653	PRKRIP1	1
NM_198859	PRICKLE2	1
XM_001133525	LOC731501	1
NM_001025077	CUGBP2	1
XM_001126853	MAML1	1
NM_018648	NOLA3	1
NM_018715	RCC2	1
XM_946142	SHANK3	1
NM_001080420	SHANK3	1
NM_015710	GLTSCR2	1
XM_944097	LOC389641	1
XM_374260	LOC389641	1
NM_015444	TMEM158	1
NM_000953	PTGDR	1
NM_021943	ZFAND3	1
NM_001761	CCNF	1
NM_024513	FYCO1	1
NM_030629	CMIP	1
NM_198390	CMIP	1
NM_023016	ANKRD57	1
XM_938519	DKFZP434I0714	1
XM_929673	DKFZP434I0714	1
NM_001012994		1
NM_022744	C16orf58	1
NM_024780	TMC5	1
NM_001105249		1
NM_001105248		1
NM_182925	FLT4	1
NM_152345	ANKRD13B	1
NM_015299	KIAA0323	1
NM_147162	IL11RA	1
NM_001079846	CREBBP	1
NM_004380	CREBBP	1
NM_148903	GREB1	1
NM_016499	MGC13379	1
NM_021201	MS4A7	1
NM_206938	MS4A7	1
NM_206940	MS4A7	1
NM_206939	MS4A7	1
NM_145166	ZBTB47	1
NM_052847	GNG7	1
NM_152396	METTL6	1
NM_022777	RABL5	1
NM_145239	PRRT2	1
NM_207380	FLJ43339	1
NM_002111	HD	1
NM_175066	DDX51	1
NM_207360		1
XM_001134365	LOC732283	1
NM_014369	PTPN18	1
NM_013382	POMT2	1
NM_001083909	GPR123	1
NM_024032	C17orf53	1
NM_024771	NAT11	1
NM_033446	FAM125B	1
NM_024768	CCDC48	1
NM_181575	AUP1	1
NM_001707	BCL7B	1
NM_194071	CREB3L2	1
NM_133475	ANKRD24	1
NM_005658	TRAF1	1
NM_213566	DFFA	1
NM_004227	PSCD3	1
NM_001003665	C1orf95	1
NM_005250	FOXL1	1
NM_024833	ZNF671	1
NM_021643	TRIB2	1
NM_006557	DMRT2	1
NM_001039199	C20orf121	1
NM_024331	C20orf121	1
NM_003014	SFRP4	1
NM_144675	GSG1L	1
NM_001109763		1
NM_001112800		1
NM_021097	SLC8A1	1
NM_001112801		1
NM_001112802		1
NM_001003676	C11orf49	1
NM_017699	SIDT1	1
NM_025248	SNIP	1
NM_201628	FLJ43806	1
NM_001426	EN1	1
NM_033481	FBXO9	1
NM_033480	FBXO9	1
NM_012347	FBXO9	1
XM_001133677	LOC729264	1
XM_001133686	LOC729355	1
NM_013397	C6orf49	1
NM_001419	ELAVL1	1
NM_006108	SPON1	1
NM_030797	FAM49A	1
NM_014630	ZNF592	1
NM_002599	PDE2A	1
NM_032737	LMNB2	1

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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