VIRsiRNAdb

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

27 hits were found for GCGAGUGCCCCGGGAGGUC (13 guide strand hits and 14 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_080749

NEURL2

631

649

c

C

G

c

G

U

G

C

C

C

C

G

G

G

A

G

G

g

C

58

3

13

c

false

<90%

1276

NM_032425

KIAA1822

2

20

G

C

G

A

G

c

G

C

C

C

C

G

G

G

A

G

G

g

g

29

3

11

c

false

<90%

2253

NM_004685

MTMR6

101

119

c

C

G

A

G

U

c

C

C

C

C

G

G

G

A

G

G

c

C

29

3

10

c

false

<90%

5222

NM_001083600

FLJ14154

1609

1627

a

C

c

A

G

U

G

C

C

C

u

G

G

G

A

G

G

U

C

17

3

8

c

false

<90%

2642

NM_024845

FLJ14154

1631

1649

a

C

c

A

G

U

G

C

C

C

u

G

G

G

A

G

G

U

C

17

3

8

c

false

<90%

2664

NM_001083601

FLJ14154

1659

1677

a

C

c

A

G

U

G

C

C

C

u

G

G

G

A

G

G

U

C

17

3

8

c

false

<90%

2692

NM_133456

SHROOM1

620

638

G

C

G

A

G

U

G

C

u

C

C

G

G

G

A

G

a

c

g

8

4

8

c

false

<90%

3190

NM_014603

CDR2L

838

856

G

C

G

A

G

U

G

C

u

C

C

G

G

G

A

G

a

a

g

8

4

8

c

false

<90%

3540

NM_004187

JARID1C

2864

2882

G

C

G

A

G

U

G

g

C

C

C

u

G

G

A

G

G

U

g

0

3

7

false

<90%

6727

NM_017595

NKIRAS2

116

134

G

C

G

g

G

g

G

C

C

C

C

G

G

G

A

G

G

U

u

-5

3

12

bc

false

<90%

2492

NM_007066

PKIG

46

64

G

C

G

A

G

U

G

C

C

g

C

G

G

G

A

G

u

U

C

-6

2

9

c

false

<90%

1206

NM_181804

PKIG

46

64

G

C

G

A

G

U

G

C

C

g

C

G

G

G

A

G

u

U

C

-6

2

9

c

false

<90%

1353

NM_181805

PKIG

46

64

G

C

G

A

G

U

G

C

C

g

C

G

G

G

A

G

u

U

C

-6

2

9

c

false

<90%

1458

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_021205

RHOU

22

40

a

A

C

C

U

C

C

C

G

G

G

c

C

A

g

U

C

G

C

39

3

10

false

<90%

4369

XM_940053

LOC338667

1757

1775

c

A

C

C

U

g

C

C

G

G

G

G

C

A

C

U

C

a

C

32

3

11

c

false

<90%

2802

XM_294675

LOC338667

1922

1940

c

A

C

C

U

g

C

C

G

G

G

G

C

A

C

U

C

a

C

32

3

11

c

false

<90%

2967

NM_001013693

LDLRAD2

2713

2731

c

c

a

C

U

C

C

u

G

G

G

G

C

A

C

U

C

G

C

4

4

11

bc

false

<90%

4012

NM_021116

ADCY1

1698

1716

c

A

C

C

a

C

C

C

c

G

G

G

C

A

C

U

C

G

C

-13

3

10

bc

false

<90%

12499

NM_138322

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

2302

NM_138325

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

2358

NM_138323

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

3208

NM_138324

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

3254

NM_138321

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

3333

NM_138320

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

3372

NM_138319

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

4520

NM_002570

PCSK6

267

285

c

A

C

C

c

C

C

C

G

G

c

G

C

A

C

U

C

G

C

-14

3

8

c

false

<90%

4559

NM_032814

TMEM118

666

684

G

A

C

C

a

C

C

g

G

G

G

G

C

A

C

U

C

G

g

-18

3

10

bc

false

<90%

1761

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 431
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_007033	RER1	2
NM_005737	ARL4C	2
NM_002268	KPNA4	2
XM_937862	LOC644962	2
NM_015094	HIC2	2
NM_144993		2
NM_019008	SMCR7L	2
NM_002428	MMP15	2
NM_005098	MSC	2
NM_020133	AGPAT4	2
NM_003908	EIF2S2	2
NM_015101	GLT25D2	1
NM_007353	GNA12	1
XM_930750	LOC642366	1
XM_943652	LOC642366	1
NM_014212	HOXC11	1
XM_001129796	LOC645513	1
NM_153188	TNPO1	1
NM_002270	TNPO1	1
NM_001100162		1
NM_001100161		1
NM_015024	XPO7	1
NM_025190	KIAA1641	1
XM_938853	LOC285484	1
XM_376303	LOC285484	1
NM_003286	TOP1	1
NM_198337	INSIG1	1
NM_005542	INSIG1	1
NM_198336	INSIG1	1
NM_003189	TAL1	1
NM_000838	GRM1	1
NM_015285	WDR7	1
NM_052834	WDR7	1
NM_002254	KIF3C	1
NM_003853	IL18RAP	1
NM_014468	VENTX	1
NM_138736	GNAO1	1
NM_001670	ARVCF	1
XM_373690	LOC388282	1
XM_001133719	LOC388282	1
NM_031207	HYI	1
NM_004452	ESRRB	1
NM_024830	AYTL2	1
NM_001005404	YPEL2	1
NM_014744	TBC1D5	1
NM_032450		1
NM_004109	FDX1	1
NM_145166	ZBTB47	1
XM_001128645	LOC728145	1
XM_001133876	LOC731845	1
NM_021973	HAND2	1
NM_001128	AP1G1	1
NM_001030007	AP1G1	1
NM_014734	KIAA0247	1
NM_004712	HGS	1
NM_000332	ATXN1	1
NM_138778	WDR85	1
NM_080594	RNPS1	1
NM_006711	RNPS1	1
NM_033271	BTBD6	1
NM_033550	TP53RK	1
XM_001131621	LOC731091	1
XM_001130681	LOC643446	1
XM_001131599	LOC731091	1
XM_001130661	LOC643446	1
XM_001130637	LOC643446	1
XM_001130669	LOC643446	1
XM_932750	LOC643446	1
XM_001131605	LOC731091	1
XM_001131627	LOC731091	1
XM_001131584	LOC731091	1
XM_001131594	LOC731091	1
XM_001131602	LOC731091	1
XM_001130620	LOC643446	1
XM_001131589	LOC731091	1
XM_001130649	LOC643446	1
NM_172239	REXO1L1	1
NM_133468	BMPER	1
NM_006885	ATBF1	1
XM_001131828	BBS5	1
XM_001131846	BBS5	1
NM_152384	BBS5	1
XM_001132516	LOC729049	1
NM_003088	FSCN1	1
NM_017547	FOXRED1	1
NM_005658	TRAF1	1
NM_153023	SPATA13	1
NM_001189	BAPX1	1
NM_015035	ZHX3	1
XM_001125098	LOC730417	1
NM_000991	RPL28	1
NM_001039762	FLJ45557	1
NM_001100878		1
NM_005327	HADH	1
NM_030621	DICER1	1
NM_177438	DICER1	1
NM_005629	SLC6A8	1
NM_032214	SLA2	1
NM_175077	SLA2	1
XM_001131068	LOC729696	1
XM_001129643	LOC731435	1
XM_001128325	LOC283481	1
XM_001133584	LOC283481	1
XM_498961	LOC441005	1
XM_943522	LOC441005	1
XM_001128998	BRUNOL4	1
NM_020180	BRUNOL4	1
NM_012330	MYST4	1
NM_015008	TMCC1	1
NM_001017395	TMCC1	1
NM_004603	STX1A	1
NM_000702	ATP1A2	1
XM_941733	LOC647115	1
XM_930136	LOC647115	1
NM_173650	DNAJC5G	1
NM_014207	CD5	1
NM_001556	IKBKB	1
XM_001132928	LOC728969	1
NM_003077	SMARCD2	1
NM_001098426		1
NM_018899	PCDHAC2	1
NM_018900	PCDHA1	1
NM_018902	PCDHA11	1
NM_031849	PCDHA6	1
NM_018905	PCDHA2	1
NM_018904	PCDHA13	1
NM_031860	PCDHA10	1
NM_018907	PCDHA4	1
NM_018909	PCDHA6	1
NM_018910	PCDHA7	1
NM_018911	PCDHA8	1
NM_018906	PCDHA3	1
NM_018903	PCDHA12	1
NM_018898	PCDHAC1	1
NM_031857	PCDHA9	1
NM_031411	PCDHA1	1
NM_018908	PCDHA5	1
NM_018901	PCDHA10	1
NM_138385	TMEM129	1
NM_000230	LEP	1
NM_014828	TOX4	1
NM_015323	KIAA0776	1
NM_133373	PLCD3	1
NM_025150	TARS2	1
NM_001085377		1
NM_002387	MCC	1
NM_015470	RAB11FIP5	1
NM_152482	C19orf25	1
NM_177999	ASB6	1
NM_002627	PFKP	1
XM_001134172	LOC730034	1
XM_001133186	LOC731345	1
NM_006231	POLE	1
NM_005736	ACTR1A	1
NM_152265	BTF3L4	1
NM_002390	ADAM11	1
NM_006864	LILRB3	1
NM_001081450	LILRB3	1
NM_177538	CYP20A1	1
NM_174934	SCN4B	1
NM_018427	RRN3	1
NM_001010855	C17orf38	1
NM_012140	SLC25A10	1
NM_152396	METTL6	1
NM_207333	ZNF320	1
NM_013313	YPEL1	1
NM_207325	DPY19L3	1
NM_005498	AP1M2	1
NM_004177	STX3	1
NM_145798	OSBPL7	1
NM_015229	KIAA0664	1
XM_931359	LOC338758	1
XM_944677	LOC338758	1
NM_015446	AHCTF1	1
XM_001126456	AHCTF1	1
NM_006869	CENTA1	1
NM_015266	SLC9A8	1
NM_009588	LTB	1
NM_002341	LTB	1
NM_052839	PANX2	1
NM_005515	HLXB9	1
NM_002959	SORT1	1
NM_020119	ZC3HAV1	1
NM_006695	RPIP8	1
NM_001098624		1
NM_033290	MID1	1
NM_000381	MID1	1
NM_001058	TACR1	1
NM_173089	CAPN3	1
NM_173090	CAPN3	1
NM_173088	CAPN3	1
NM_212465	CAPN3	1
NM_212464	CAPN3	1
NM_000070	CAPN3	1
NM_024344	CAPN3	1
NM_212467	CAPN3	1
NM_173087	CAPN3	1
NM_001098801		1
NM_152352	C18orf19	1
NM_005814	GPA33	1
NM_015033	FNBP1	1
NM_032286	MED10	1
NM_001080480	MBOAT1	1
XM_001131050	MBOAT1	1
XM_001131044	MBOAT1	1
NM_002688	SEPT5	1
NM_015241		1
XM_001128811	LOC731210	1
NM_007103	NDUFV1	1
NM_001099336		1
NM_198521	C12orf42	1
NM_144616	JSRP1	1
XM_001131408	LOC730350	1
XM_001127666	LOC730896	1
NM_080829	C20orf175	1
NM_014402	UQCRQ	1
NM_016376	ANKFY1	1
NM_030915	LBH	1
XM_001132517	LBH	1
XM_001132511	LBH	1
NM_001001894	TTC3	1
NM_003316	TTC3	1
NM_080476	PIGU	1
NM_020200	PRTFDC1	1
NM_005168	RND3	1
XM_926954	LOC642969	1
XM_931734	LOC642969	1
NM_002629	PGAM1	1
XM_930111	LOC644914	1
XM_001128558	LOC730740	1
NM_002107	H3F3A	1
NM_006460	HEXIM1	1
NM_025222	TMEM113	1
NM_014913	ZNF508	1
NM_000926	PGR	1
NM_144675	GSG1L	1
NM_001109763		1
NM_006371	CRTAP	1
NM_020764	CASKIN1	1
XM_001128616	LOC401021	1
NM_001002262	ZFYVE27	1
NM_001002261	ZFYVE27	1
NM_144588	ZFYVE27	1
NM_002309	LIF	1
NM_019063	EML4	1
NM_178507	OAF	1
NM_001100408		1
NM_001033046	C17orf62	1
NM_001100407		1
NM_018054	ARHGAP17	1
NM_001006634	ARHGAP17	1
NM_207006	FAM83A	1
NM_014692		1
NM_152233	SNX6	1
NM_021249	SNX6	1
NM_199287		1
NM_006991	ZNF197	1
XM_379623	FLJ41200	1
XM_943473	FLJ41200	1
NM_030626	LRRC27	1
XM_929378	LOC646450	1
NM_000641	IL11	1
NM_031490	LONP2	1
NM_198562	C3orf62	1
NM_022103	ZNF667	1
NM_058182	C21orf51	1
NM_016169	SUFU	1
NM_002147	HOXB5	1
NM_153619	SEMA6D	1
NM_001111019		1
NM_145117	NAV2	1
NM_182964	NAV2	1
NM_001111018		1
NM_016652	CRNKL1	1
NM_001097620		1
NM_025009	CEP135	1
NM_015306		1
NM_000545	TCF1	1
NM_001014812	FAM96A	1
NM_033058	TRIM55	1
NM_001039550	DNAJB2	1
NM_006736	DNAJB2	1
NM_000709	BCKDHA	1
NM_019885	CYP26B1	1
XM_942692	MGC5139	1
NM_001080533	MGC5139	1
NM_017956	TRMT12	1
NM_024963	FBXL18	1
NM_003507	FZD7	1
NM_014665	LRRC14	1
NM_006315	PCGF3	1
NM_012306	FAIM2	1
NM_001042573	FLJ21865	1
NM_021168	RAB40C	1
NM_133633	SYN3	1
NM_003490	SYN3	1
NM_015044	GGA2	1
NM_152264	SLC39A13	1
NM_018658	KCNJ16	1
NM_170742	KCNJ16	1
NM_170741	KCNJ16	1
NM_002469	MYF6	1
NM_007271	STK38	1
NM_018416	FOXJ2	1
NM_006332	IFI30	1
NM_177550	SLC13A5	1
NM_005683	GPR55	1
NM_052899	GPRIN1	1
NM_032349	NUDT16L1	1
NM_012294	RAPGEF5	1
NM_003924	PHOX2B	1
NM_004973	JARID2	1
NM_014772	KIAA0427	1
NM_004672	MAP3K6	1
NM_001610	ACP2	1
NM_000761	CYP1A2	1
NM_001037165	FOXK1	1
NM_000578	SLC11A1	1
NM_001987	ETV6	1
NM_025106	SPSB1	1
NM_203400	RPRML	1
NM_003775	EDG6	1
NM_052896	CSMD2	1
NM_006225	PLCD1	1
NM_032843	FIBCD1	1
NM_012258	HEY1	1
NM_001040708	HEY1	1
NM_001918	DBT	1
NM_001695	ATP6V1C1	1
NM_152496	MANEAL	1
NM_001031740	MANEAL	1
NM_153451	ORAOV1	1
NM_205843	NFIC	1
NM_005597	NFIC	1
XM_001128037	LOC728654	1
XM_001129553	LOC731413	1
NM_194431	RNASE4	1
NM_002937	RNASE4	1
XM_001132127	LOC731061	1
XM_001130048	LOC728350	1
NM_003107	SOX4	1
NM_001040001	MLLT4	1
NM_003927	MBD2	1
NM_015299	KIAA0323	1
NM_001076680	LOC201229	1
NM_006943	SOX12	1
NM_014351	SULT4A1	1
NM_024492	LPAL2	1
NM_173156	SMG7	1
NM_201569	SMG7	1
NM_201568	SMG7	1
NM_001543	NDST1	1
NM_198253	TERT	1
NM_198255	TERT	1
NM_016057	COPZ1	1
NM_015695	BRPF3	1
NM_022081	HPS4	1
NM_152841	HPS4	1
NM_031892	SH3KBP1	1
NM_001024666	SH3KBP1	1
NM_006035	CDC42BPB	1
NM_003281	TNNI1	1
NM_022356	LEPRE1	1
NM_207405	FLJ46481	1
NM_004869	VPS4B	1
NM_001098798		1
NM_001098797		1
NM_001098796		1
NM_032883	TOX2	1
NM_032809	FAM73B	1
NM_014636	RALGPS1	1
NM_024544	C1orf166	1
NM_001009554	MFAP3L	1
NM_021647	MFAP3L	1
NM_006732	FOSB	1
NM_018702	ADARB2	1
NM_016510	SCLY	1
NM_152219	GJC1	1
NM_153365	TAPT1	1
NM_000296	PKD1	1
NM_001009944	PKD1	1
NM_005202	COL8A2	1
NM_058180	C21orf58	1
NM_001080530	LOC92017	1
XM_001128282	LOC728138	1
NM_014299	BRD4	1
NM_003224	ARFRP1	1
NM_006013	RPL10	1
NM_153812	PHF13	1
NM_033496	HK1	1
NM_000188	HK1	1
NM_033498	HK1	1
NM_033500	HK1	1
NM_033497	HK1	1
XM_039733	KIAA0953	1
XM_940464	KIAA0953	1
NM_002737	PRKCA	1
NM_005920	MEF2D	1
NM_003216	TEF	1
NM_014293	NPTXR	1
NM_198595	AFAP1	1
NM_021638	AFAP1	1
NM_016035	COQ4	1
NM_001024401	SBK1	1
NM_022648	TNS1	1
NM_000632	ITGAM	1
NM_004430	EGR3	1
XM_001130047	EGR3	1
NM_014316	CARHSP1	1
NM_001042476	CARHSP1	1
NM_001011722	ARHGEF10L	1
NM_018125	ARHGEF10L	1
NM_002094	GSPT1	1
XM_001132013	ANKH	1
XM_001127710	LOC728653	1
NM_016298	FBXO40	1
NM_014033	METTL7A	1
NM_001099415		1
NM_003489	NRIP1	1
NM_001336	CTSZ	1
NM_207012	AP3M1	1
NM_012095	AP3M1	1
NM_002897	RBMS1	1
NM_016839	RBMS1	1
NM_016836	RBMS1	1
NM_024554	PGBD5	1
NM_001457	FLNB	1
NM_000498	CYP11B2	1
NM_005479	FRAT1	1
NM_003036	SKI	1
NM_025232	REEP4	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