VIRsiRNAdb

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

10 hits were found for AGUGUCGUGCAGCCUCCAG (2 guide strand hits and 8 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_015508

TIPARP

282

300

u

G

U

G

U

a

G

U

G

C

A

G

C

C

U

C

C

c

u

27

4

11

c

false

<90%

3855

NM_139321

ATRN

5556

5574

u

G

U

G

U

C

c

U

G

C

A

G

C

C

U

C

C

u

c

24

4

10

c

false

<90%

8645

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_017513

LOC644035

1018

1036

a

U

G

G

A

G

G

C

U

G

C

A

C

G

c

C

A

u

a

65

4

13

c

false

<90%

1853

XR_016002

LOC731725

1018

1036

a

U

G

G

A

G

G

C

U

G

C

A

C

G

c

C

A

u

a

65

4

13

c

false

<90%

1858

NM_007202

AKAP10

322

340

C

U

G

G

A

G

G

C

U

G

C

A

g

G

A

C

c

a

a

58

4

12

false

<90%

2929

XR_017764

LOC285550

1621

1639

u

U

G

G

A

a

G

C

U

G

C

A

C

a

A

C

A

C

U

15

3

7

c

false

<90%

4385

XR_017908

LOC285550

1621

1639

u

U

G

G

A

a

G

C

U

G

C

A

C

a

A

C

A

C

U

15

3

7

c

false

<90%

4385

XR_017763

LOC285550

3358

3376

u

U

G

G

A

a

G

C

U

G

C

A

C

a

A

C

A

C

U

15

3

7

c

false

<90%

4626

XR_017909

LOC285550

3358

3376

u

U

G

G

A

a

G

C

U

G

C

A

C

a

A

C

A

C

U

15

3

7

c

false

<90%

4626

NM_001114

ADCY7

767

785

u

g

G

G

A

G

G

C

U

u

C

A

C

G

A

C

A

C

c

-1

4

8

bc

false

<90%

6138

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 311
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_007184	NISCH	2
NM_031912	SYT15	2
NM_030639	BHLHB9	1
NM_181425	FXN	1
NM_000144	FXN	1
NM_014409	TAF5L	1
NM_001481	GAS8	1
NM_000761	CYP1A2	1
NM_001006657	WDR35	1
NM_020779	WDR35	1
NM_000929	PLA2G5	1
XM_929032	LOC646071	1
XM_001125928	LOC283804	1
XM_001126277	LOC648913	1
NM_001013699	LOC440093	1
NM_018210	FLJ10769	1
NM_012434	SLC17A5	1
NM_032268	ZNRF1	1
NM_001110781		1
XM_001126149	LOC727916	1
XM_001126026	LOC730478	1
NM_032325	MGC11102	1
NM_006425	SLU7	1
NM_014064	C9orf32	1
NM_015071	ARHGAP26	1
NM_019000	FLJ20152	1
NM_001034850	FLJ20152	1
NM_001033518	WIPI2	1
NM_001033519	WIPI2	1
NM_015610	WIPI2	1
NM_001033520	WIPI2	1
NM_016003	WIPI2	1
NM_138344	C14orf152	1
NM_016605	FAM53C	1
NM_002340	LSS	1
NM_014910	ZNF507	1
NM_015912	C8ORFK32	1
NM_176081	TRDMT1	1
NM_004412	TRDMT1	1
NM_176083	TRDMT1	1
NM_007018	CEP110	1
NM_018945	PDE7B	1
NM_001043318	C14orf43	1
NM_194278	C14orf43	1
NM_014730	KIAA0152	1
NM_004805	POLR2D	1
NM_153633	HOXC4	1
NM_014620	HOXC4	1
NM_017548	CDV3	1
NM_005238	ETS1	1
NM_020800	IFT80	1
NM_001033925	TIAL1	1
NM_003252	TIAL1	1
NM_004798	KIF3B	1
NM_001099272		1
NM_152733	BTBD9	1
NM_052893		1
NM_005668	ST8SIA4	1
XM_939259	ZNF469	1
XM_001125745	ZNF469	1
NM_001014372	SYT14L	1
NM_153262	SYT14	1
NM_017736	THUMPD1	1
NM_001011713	NAT12	1
NM_006802	SF3A3	1
XM_001128645	LOC728145	1
XM_001133876	LOC731845	1
NM_021260	ZFYVE1	1
NM_178441	ZFYVE1	1
NM_020429	SMURF1	1
NM_181349	SMURF1	1
NM_014733	ZFYVE16	1
NM_001105251		1
NM_004211	SLC6A5	1
NM_001101387		1
NM_014889	PITRM1	1
NM_031438	NUDT12	1
NM_152293		1
NM_004840	ARHGEF6	1
NM_001106	ACVR2B	1
NM_000918	P4HB	1
NM_207313	TMEM132E	1
NM_145185	MAP2K7	1
NM_178586	PPP2R5C	1
NM_002719	PPP2R5C	1
NM_022062	PKNOX2	1
NM_001034914	KCNIP3	1
NM_013434	KCNIP3	1
NM_018992	KCTD5	1
NM_001127	AP1B1	1
NM_145730	AP1B1	1
XM_941162	LOC400950	1
XM_376049	LOC400950	1
NM_001694	ATP6V0C	1
XM_001130742	ATP6V0C	1
NM_001042404	CEP170	1
NM_014812	CEP170	1
NM_001042405	CEP170	1
NM_020733		1
NM_001040653	ZXDC	1
NM_020981	B3GALT1	1
XM_001125791	LOC642788	1
XM_001127886	LOC728100	1
XM_001132421	LOC388312	1
XM_001133085	LOC728790	1
XM_001128749	LOC728054	1
NM_001002857	ANXA2	1
NM_001002858	ANXA2	1
NM_004039	ANXA2	1
NM_004308	ARHGAP1	1
NM_005986	SOX1	1
NM_194320	ZNF169	1
XM_940609	FLJ25076	1
XM_059689	FLJ25076	1
NM_001669	ARSD	1
NM_030911	CDADC1	1
NM_001080435	WHDC1	1
XM_939866	WHDC1	1
NM_030647	JHDM1D	1
NM_002737	PRKCA	1
NM_006775	QKI	1
NM_170665	ATP2A2	1
NM_015138	RTF1	1
NM_022473	ZFP106	1
NM_001002258	ATP5G3	1
NM_001689	ATP5G3	1
NM_001080498	EMR4	1
NM_138467	TYW3	1
NM_001025780	FAM108B1	1
NM_021814	ELOVL5	1
NM_145273	CD300LG	1
NM_001017923	C14orf28	1
NM_183395	NLRP3	1
NM_004895	NLRP3	1
NM_001079821	NLRP3	1
NM_020956	PRX	1
NM_005036	PPARA	1
NM_001001928	PPARA	1
NM_001045477	FAM22G	1
NM_001009610		1
NM_020148	SPIRE1	1
NM_001277	CHKA	1
NM_212469	CHKA	1
NM_144590	ANKRD22	1
XM_928029	RNF187	1
XM_001129309	RNF187	1
NM_032105	PPP1R12B	1
NM_002481	PPP1R12B	1
NM_014614	PSME4	1
NM_006230	POLD2	1
NM_024922	CES3	1
NM_005740	DNAL4	1
NM_021158	TRIB3	1
NM_005494	DNAJB6	1
NM_144719	CCDC13	1
NM_033387	FAM78A	1
NM_018121	C10orf6	1
NM_130459	TOR2A	1
NM_001085347		1
NM_001083603	PTCH1	1
NM_001083607	PTCH1	1
NM_001083602	PTCH1	1
NM_001083605	PTCH1	1
NM_001083606	PTCH1	1
NM_001083604	PTCH1	1
NM_000264	PTCH1	1
NM_212543	B4GALT4	1
NM_003778	B4GALT4	1
NM_002582	PARN	1
NM_001098510		1
NM_145065	PELI3	1
NM_012293	PXDN	1
NM_182488	USP12	1
NM_212471	PRKAR1A	1
NM_212472	PRKAR1A	1
NM_002734	PRKAR1A	1
NM_021619	PRDM12	1
NM_133265	AMOT	1
NM_001100398		1
NM_015085	GARNL4	1
XM_929714	LOC646762	1
XM_938418	LOC646762	1
XM_935722	LOC646762	1
NM_144781	PDCD2	1
NM_017789	SEMA4C	1
NM_014299	BRD4	1
NM_032454	STK19	1
NM_004197	STK19	1
NM_004824	CDYL	1
NM_170751	CDYL	1
NM_170752	CDYL	1
NM_005789	PSME3	1
NM_176863	PSME3	1
NM_018133	MSL2L1	1
NM_203458	NOTCH2NL	1
NM_173465	COL23A1	1
NM_001247	ENTPD6	1
NM_001080421	UNC13A	1
NM_001001664	LOC339745	1
NM_016621	PHF21A	1
NM_001101802		1
NM_144767	AKAP13	1
NM_006738	AKAP13	1
NM_007200	AKAP13	1
NM_014671	UBE3C	1
NM_001012720	RGR	1
NM_002921	RGR	1
NM_001012722	RGR	1
NM_013255	MKLN1	1
NM_014873	LPGAT1	1
NM_001030288	SPN	1
NM_003123	SPN	1
NM_017952	PTCD3	1
NM_000916	OXTR	1
NM_032408	BAZ1B	1
NM_021962	ABR	1
NM_001092	ABR	1
NM_003052	SLC34A1	1
NM_080625	C20orf160	1
NM_003795	SNX3	1
NM_173688	FAM77D	1
NM_182961	SYNE1	1
NM_015293	SYNE1	1
NM_033071	SYNE1	1
NM_133650	SYNE1	1
NM_004056	CA8	1
NM_058169	LOH12CR1	1
NM_020728	FAM62B	1
NM_014423	AFF4	1
NM_005197	CHES1	1
NM_001085471		1
NM_153051	MTMR3	1
NM_021090	MTMR3	1
NM_153050	MTMR3	1
NM_006544	EXOC5	1
NM_178815	ARL5B	1
NM_003118	SPARC	1
NM_000856	GUCY1A3	1
NM_203395	IYD	1
NM_018238	AGK	1
NM_013336	SEC61A1	1
NM_001097620		1
NM_001008539	SLC7A2	1
NM_003046	SLC7A2	1
NM_016532	SKIP	1
NM_130766	SKIP	1
NM_015932	POMP	1
NM_005867	DSCR4	1
NM_017649	CNNM2	1
NM_199076	CNNM2	1
NM_032826	SLC35B4	1
NM_203497	COMMD6	1
NM_203495	COMMD6	1
NM_018150	C1orf164	1
NM_002196	INSM1	1
NM_214462	DACT2	1
NM_018218	USP40	1
NM_004667	HERC2	1
NM_002813	PSMD9	1
NM_174900	ZFP42	1
NM_052875	VPS26B	1
NM_006643	SDCCAG3	1
NM_001039708	SDCCAG3	1
NM_001039707	SDCCAG3	1
XM_926382	LOC642755	1
NM_001111019		1
NM_145117	NAV2	1
NM_182964	NAV2	1
NM_001111018		1
NM_024917	CXorf34	1
NM_001042633	SNX21	1
NM_033421	SNX21	1
NM_001042632	SNX21	1
NM_152897	SNX21	1
NM_003126	SPTA1	1
NM_198182	GRHL1	1
NM_014552	GRHL1	1
NM_001035	RYR2	1
NM_006035	CDC42BPB	1
NM_002171	IFNA10	1
XM_933796	SLC45A4	1
XM_001129527	KLF11	1
NM_003597	KLF11	1
NM_003918	GYG2	1
NM_001079855	GYG2	1
NM_000369	TSHR	1
NM_001616	ACVR2A	1
NM_001042690	LOC345222	1
NM_001009899	KIAA2018	1
NM_006753	SURF6	1
NM_032866	CGNL1	1
NM_006927	ST3GAL2	1
NM_015695	BRPF3	1
XM_001128614	LOC728845	1
NM_015116	LRCH1	1
NM_004747	DLG5	1
NM_002214	ITGB8	1
NM_024936		1
NM_001003796	NHP2L1	1
NM_005008	NHP2L1	1
NM_003633	ENC1	1
NM_024949	WWC2	1
NM_058191	C21orf66	1
NM_024707	GEMIN7	1
NM_001007270	GEMIN7	1
NM_001007269	GEMIN7	1
NM_014522	PCDH11X	1
NM_139012	MAPK14	1
NM_139014	MAPK14	1
NM_001315	MAPK14	1
NM_153034	ZNF488	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