VIRsiRNAdb

SpecificityServer - An siRNA design program for determining siRNA specificity
Automatic recommendation
Not OK - siRNA is not specific

15 hits were found for GGACCGACAUUGUGGAGGU (13 guide strand hits and 2 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_014866

KIAA0310

4967

4985

G

G

A

C

C

G

A

C

A

U

U

G

c

G

G

A

G

c

U

86

2

12

false

<90%

9059

NM_001556

IKBKB

1799

1817

a

G

A

C

C

G

A

C

A

U

U

G

U

G

G

A

c

u

U

71

3

15

ac

false

<90%

3916

NM_001017423

ALDH18A1

1255

1273

u

c

A

C

a

G

A

C

A

U

U

G

U

G

G

A

G

G

g

30

4

13

bc

false

<90%

3464

NM_002860

ALDH18A1

1261

1279

u

c

A

C

a

G

A

C

A

U

U

G

U

G

G

A

G

G

g

30

4

13

bc

false

<90%

3470

NM_003866

INPP4B

360

378

G

c

A

C

C

G

A

a

A

U

U

G

U

G

G

A

G

G

g

21

3

10

bc

false

<90%

2937

NM_030819

GFOD2

784

802

G

G

A

C

C

u

A

C

A

U

U

G

U

G

G

A

c

c

U

10

3

10

c

false

<90%

2118

XM_046531

KIAA1614

1920

1938

G

G

A

C

C

G

A

C

A

g

U

G

a

G

G

A

G

G

c

1

3

9

false

<90%

6999

XM_942569

KIAA1614

1920

1938

G

G

A

C

C

G

A

C

A

g

U

G

a

G

G

A

G

G

c

1

3

9

false

<90%

7000

XM_378080

LOC402377

560

578

G

G

A

C

u

G

A

C

u

U

U

G

U

G

G

A

G

G

a

-16

3

9

bc

false

<90%

1275

XM_936890

LOC402377

560

578

G

G

A

C

u

G

A

C

u

U

U

G

U

G

G

A

G

G

a

-16

3

9

bc

false

<90%

1275

NM_002332

LRP1

4404

4422

G

G

A

C

C

G

A

C

g

U

g

G

U

G

G

A

G

G

a

-26

3

8

c

false

<90%

14905

NM_002020

FLT4

1575

1593

G

G

A

C

C

G

A

g

u

U

U

G

U

G

G

A

G

G

g

-27

3

9

bc

false

<90%

4510

NM_182925

FLT4

1575

1593

G

G

A

C

C

G

A

g

u

U

U

G

U

G

G

A

G

G

g

-27

3

9

bc

false

<90%

5833

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_021245

MYOZ1

357

375

A

C

C

U

C

C

A

C

A

A

U

G

c

C

G

c

U

C

u

58

3

12

false

<90%

1661

NM_003236

TGFA

1787

1805

A

C

C

U

C

C

A

C

u

A

U

G

U

g

G

G

U

C

u

15

3

8

c

false

<90%

4119

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 318
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_020133	AGPAT4	3
NM_033129	SCRT2	2
NM_173065	IL28RA	2
NM_198715	PTGER3	2
NM_013313	YPEL1	2
XM_945193	LOC645967	2
XM_933310	LOC645967	2
NM_147161	ACOT11	1
NM_004778	GPR44	1
NM_001627	ALCAM	1
NM_006569	CGREF1	1
NM_201629	TJP2	1
NM_004817	TJP2	1
NM_004805	POLR2D	1
NM_021945	C6orf85	1
NM_001109903		1
NM_018054	ARHGAP17	1
NM_001006634	ARHGAP17	1
NM_022468	MMP25	1
NM_017765	PQLC2	1
NM_001040126	PQLC2	1
NM_001040125	PQLC2	1
NM_032020	FUCA2	1
XM_942502	LOC642757	1
XM_926793	LOC642757	1
NM_052907	TMEM132B	1
NM_015149	RGL1	1
NM_004051	BDH1	1
NM_203315	BDH1	1
NM_203314	BDH1	1
XM_930959	LOC400831	1
XM_943808	LOC400831	1
NM_032367	ZBED3	1
NM_017521	FEV	1
NM_182830	MDGA2	1
XM_001131439	FLJ34048	1
XM_001130034	FLJ34048	1
XM_001131637	FLJ34048	1
NM_001040665	STEAP2	1
NM_152999	STEAP2	1
NM_005224	ARID3A	1
NM_001013661	VSIG8	1
NM_000115	EDNRB	1
NM_001794	CDH4	1
NM_001110781		1
NM_016091	EIF3S6IP	1
NM_173064	IL28RA	1
NM_170743	IL28RA	1
NM_020778	ALPK3	1
NM_145695	DGKB	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
NM_017491	WDR1	1
NM_005112	WDR1	1
NM_001042669	ARHGAP24	1
NM_001025616	ARHGAP24	1
NM_031305	ARHGAP24	1
NM_002092	GRSF1	1
NM_001098477		1
NM_012323	MAFF	1
NM_152878	MAFF	1
NM_007175	ERLIN2	1
NM_032221	CHD6	1
NM_018663	PXMP2	1
XM_001126107	PXMP2	1
NM_133367	PAQR8	1
NM_000061	BTK	1
NM_024821	CCDC134	1
NM_001077199	SFRS12	1
NM_139168	SFRS12	1
NM_024792	FAM57A	1
XM_930505	LOC645676	1
XM_941520	LOC645676	1
NM_006032	CPNE6	1
NM_024933	ANKRD53	1
NM_080871	ASB10	1
XM_941733	LOC647115	1
XM_930136	LOC647115	1
NM_006802	SF3A3	1
NM_014578	RHOD	1
NM_020810	TRMT5	1
XM_926142	LOC642691	1
NM_020705	TBC1D24	1
NM_020131	UBQLN4	1
NM_002651	PIK4CB	1
NM_001002034	FAM109B	1
NM_052909	KIAA1909	1
NM_001111308		1
NM_001111309		1
NM_001111307		1
NM_006202	PDE4A	1
NM_031464	RPS6KL1	1
NM_021135	RPS6KA2	1
NM_001006932	RPS6KA2	1
NM_015330	SPECC1L	1
NM_000278	PAX2	1
NM_003989	PAX2	1
NM_003990	PAX2	1
NM_003987	PAX2	1
NM_003988	PAX2	1
NM_178841	RNF166	1
NM_175898	C15orf37	1
NM_006861	RAB35	1
NM_003668	MAPKAPK5	1
NM_139078	MAPKAPK5	1
NM_006402	HBXIP	1
NM_024665	TBL1XR1	1
NM_003173	SUV39H1	1
NM_019026	TMCO1	1
NM_000875	IGF1R	1
NM_080607	C20orf102	1
NM_153265	EML3	1
NM_001421	ELF4	1
NM_000451	SHOX	1
NM_020530	OSM	1
NM_175922	MGC35308	1
NM_005495	SLC17A4	1
NM_152222	TNFRSF19L	1
NM_032871	TNFRSF19L	1
NM_001406	EFNB3	1
NM_207335	KLHDC6	1
XM_938374	LOC644010	1
NM_001099737		1
NM_032332	MORG1	1
NM_001077196	PDE11A	1
NM_001077197	PDE11A	1
NM_016953	PDE11A	1
NM_012306	FAIM2	1
NM_017849	TMEM127	1
NM_173564	FLJ37538	1
NM_002378	MATK	1
NM_139354	MATK	1
NM_139355	MATK	1
NM_177543	PPAP2C	1
NM_003712	PPAP2C	1
NM_177526	PPAP2C	1
NM_004296	RGS6	1
NM_152233	SNX6	1
NM_021249	SNX6	1
NM_022748	TNS3	1
XM_001132864	HIP1R	1
NM_003959	HIP1R	1
NM_080833	C20orf151	1
NM_001085372		1
NM_014292	CBX6	1
NM_199262	SP6	1
NM_015629	PRPF31	1
NM_198681	PLEKHG5	1
NM_020631	PLEKHG5	1
NM_001042664	PLEKHG5	1
NM_001042663	PLEKHG5	1
NM_001042665	PLEKHG5	1
XM_001131713	LOC730410	1
NM_002634	PHB	1
NM_020839	WDR48	1
NM_175609	ARFGAP1	1
NM_018209	ARFGAP1	1
NM_024551	ADIPOR2	1
NM_001767	CD2	1
NM_005185	CALML3	1
XM_930027	LOC151234	1
XM_938725	LOC151234	1
XM_379029	LOC400879	1
NM_015246	MGRN1	1
NM_177967	UBAC2	1
NM_014858	TMCC2	1
NM_018073	TRIM68	1
NM_020381	PDSS2	1
NM_003459	SLC30A3	1
NM_015094	HIC2	1
NM_030798	WBSCR16	1
NM_182970	RIMS4	1
NM_030651	PRRT1	1
NM_014766	SCRN1	1
NM_031313	ALPPL2	1
NM_024943	TMEM156	1
NM_001035534	FAM129B	1
NM_022833	FAM129B	1
NM_146388	MRPL4	1
NM_001044370	MPPED1	1
XM_001130582	LOC728392	1
XM_001132379	LOC730994	1
NM_145239	PRRT2	1
XM_934805	LOC645227	1
XM_946140	LOC645227	1
NM_032295	SLC37A3	1
NM_207113	SLC37A3	1
NM_014655	SLC25A44	1
NM_001025433	NQO1	1
NM_000903	NQO1	1
NM_001025434	NQO1	1
NM_032980	DTNA	1
NM_001390	DTNA	1
NM_032975	DTNA	1
NM_014405	CACNG4	1
NM_018302	C4orf19	1
NM_001104629		1
NM_004789	LHX2	1
NM_006454	MXD4	1
NM_004886	APBA3	1
NM_001841	CNR2	1
NM_031304	DOHH	1
NM_015393	DKFZP564O0823	1
NM_199138	FAM123A	1
NM_152704	FAM123A	1
NM_013237	PRELID1	1
NM_012405	ICMT	1
NM_004975	KCNB1	1
NM_033512	TSPYL5	1
NM_001042682	RERE	1
NM_012102	RERE	1
NM_001042681	RERE	1
NM_152988	SPPL2B	1
NM_001077238	SPPL2B	1
NM_003897	IER3	1
NM_032552	DAB2IP	1
NM_003311	PHLDA2	1
NM_133457	EMID2	1
NM_023076	C16orf28	1
NM_001009610		1
NM_133369	UNC5A	1
XM_001132928	LOC728969	1
NM_004807	HS6ST1	1
NM_012172	FBXO24	1
NM_015079	TBC1D2B	1
NM_032286	MED10	1
XM_001132790	LOC729117	1
NM_014867	KBTBD11	1
NM_001478	B4GALNT1	1
NM_015297		1
NM_022574	PERQ1	1
XM_930678	LOC642441	1
NM_033100	PCDH21	1
NM_052839	PANX2	1
NM_033315	RASL10B	1
NM_139174	LOC161931	1
NM_015321	CRTC1	1
NM_001098482		1
XM_001127668	LOC728119	1
XM_001131429	LOC731118	1
XM_379543	LOC401442	1
NM_001795	CDH5	1
NM_002566	P2RY11	1
NM_144653	BTBD14A	1
NM_002973	ATXN2	1
NM_177550	SLC13A5	1
NM_001079843	CASZ1	1
NM_017699	SIDT1	1
NM_016135	ETV7	1
NM_015554	GLCE	1
XM_001127284	CXorf31	1
XM_001127244	CXorf31	1
NM_002579	PALM	1
NM_001040134	PALM	1
NM_014901	RNF44	1
NM_000787	DBH	1
NM_024742	ARMC5	1
NM_032102	SFRS2B	1
NM_013373	ZDHHC8	1
NM_138417	KTI12	1
NM_014351	SULT4A1	1
XM_498491	LOC439994	1
XM_930748	LOC642361	1
NM_025251	KIAA1688	1
NM_015025	MYT1L	1
NM_001025266	LOC285382	1
NM_005100	AKAP12	1
NM_144497	AKAP12	1
NM_020473	PIGA	1
NM_002641	PIGA	1
NM_014452	TNFRSF21	1
NM_015064	ERC1	1
NM_178039	ERC1	1
NM_178040	ERC1	1
NM_178038	ERC1	1
NM_178037	ERC1	1
NM_001039350	DPP6	1
NM_001936	DPP6	1
NM_130797	DPP6	1
NM_014286	FREQ	1
NM_199461	NANOS1	1
XM_001132564	LOC728882	1
XM_001133521	MGC51338	1
NM_014548	TMOD2	1
NM_016734	PAX5	1
NM_000500	CYP21A2	1
NM_144681	CCDC42	1
NM_001002860	BTBD7	1
NM_013276	CARKL	1
NM_003040	SLC4A2	1
NM_173598	KSR2	1
NM_178169	RASSF3	1
NM_001001694	FLJ41993	1
NM_033551	LARP1	1
NM_015315	LARP1	1
NM_006245	PPP2R5D	1
NM_180976	PPP2R5D	1
NM_180977	PPP2R5D	1
NM_015379	BRI3	1
NM_004799	ZFYVE9	1
NM_007324	ZFYVE9	1
NM_025106	SPSB1	1
NM_031459	SESN2	1
NM_020993	BCL7A	1
NM_001024808	BCL7A	1
NM_020477	ANK1	1
NM_020475	ANK1	1
NM_000037	ANK1	1
NM_020476	ANK1	1
NM_020478	ANK1	1
NM_020480	ANK1	1
NM_001024941	TRIM17	1
NM_001024940	TRIM17	1
NM_016102	TRIM17	1
NM_144973	MGC24039	1
NM_145061	C13orf3	1
NM_015039	NMNAT2	1
NM_170706	NMNAT2	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