VIRsiRNAdb

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

9 hits were found for CCGGUUGGUGAGGUUAAUU (1 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_133334

WHSC1

4004

4022

C

C

G

G

U

U

G

u

U

G

A

G

G

U

g

A

A

U

U

13

2

7

c

false

<90%

8390

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_033290

MID1

798

816

g

A

g

U

A

A

C

C

U

C

A

C

C

A

A

C

C

u

u

70

4

14

c

false

<90%

3117

NM_033291

MID1

858

876

g

A

g

U

A

A

C

C

U

C

A

C

C

A

A

C

C

u

u

70

4

14

c

false

<90%

3352

NM_000381

MID1

858

876

g

A

g

U

A

A

C

C

U

C

A

C

C

A

A

C

C

u

u

70

4

14

c

false

<90%

3452

NM_194072

HILS1

212

230

A

g

a

U

A

A

C

C

U

C

A

C

C

A

A

C

C

c

c

61

4

14

c

false

<90%

873

NM_052817

MID2

931

949

g

A

U

g

A

A

C

C

U

C

A

C

C

A

A

C

C

u

G

58

3

13

c

false

<90%

2433

NM_012216

MID2

931

949

g

A

U

g

A

A

C

C

U

C

A

C

C

A

A

C

C

u

G

58

3

13

c

false

<90%

2523

NM_002677

PMP2

2663

2681

A

A

U

U

A

A

C

C

U

C

A

C

C

A

A

u

a

a

a

42

4

15

c

false

<90%

3579

NM_014909

VASH1

1161

1179

A

A

U

U

u

A

C

C

U

C

A

C

C

A

A

C

a

G

c

20

3

11

c

false

<90%

5746

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 234
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_024577	SH3TC2	2
NM_030643	APOL4	2
NM_145660	APOL4	2
NM_015035	ZHX3	2
NM_001012418	LOC340156	1
NM_024817	THSD4	1
XM_001129847	LOC728834	1
XM_001129267	LOC731181	1
NM_017759	FLJ20309	1
NM_024659	GTDC1	1
NM_001006636	GTDC1	1
NM_000367	TPMT	1
NM_018043	TMEM16A	1
NM_001099694		1
NM_001101654		1
NM_014593	CXXC1	1
NM_182752	FAM79A	1
NM_015475	FAM98A	1
NM_003804	RIPK1	1
NM_004090	DUSP3	1
NM_177549	PRNT	1
NM_018509	LRRC59	1
NM_001001685	FLJ45079	1
NM_031844	HNRPU	1
NM_004501	HNRPU	1
NM_203329	CD59	1
NM_203331	CD59	1
NM_203330	CD59	1
NM_000611	CD59	1
NM_001039844	ACBD7	1
NM_017712	PGPEP1	1
NM_181672	OGT	1
NM_181673	OGT	1
NM_024336	IRX3	1
NM_001004317	LIN28B	1
XM_001131014	LOC729683	1
XM_001130799	LOC731783	1
NM_031412	GABARAPL1	1
NM_015253	WSCD1	1
NM_005297	MCHR1	1
NM_004077	CS	1
NM_198324	CS	1
NM_001099272		1
NM_152733	BTBD9	1
NM_052893		1
NM_017544	NKRF	1
NM_005049	PWP2	1
NM_024513	FYCO1	1
XM_938741	LOC116412	1
XM_375665	LOC116412	1
NM_020310	MNT	1
NM_153705	KDELC2	1
NM_000724	CACNB2	1
NM_201596	CACNB2	1
NM_201571	CACNB2	1
NM_201593	CACNB2	1
NM_201590	CACNB2	1
NM_201572	CACNB2	1
NM_201597	CACNB2	1
NM_201570	CACNB2	1
XM_933903	LOC644662	1
XM_944785	LOC644662	1
NM_030648	SETD7	1
NM_003045	SLC7A1	1
NM_014551	NCAPH2	1
NM_025179	PLXNA2	1
NM_006096	NDRG1	1
NM_006033	LIPG	1
NM_014153	ZC3H7A	1
NM_182744	NBL1	1
NM_005380	NBL1	1
NM_025196	GRPEL1	1
NM_002442	MSI1	1
NM_016263	FZR1	1
NM_001079877	RASA4	1
NM_006989	RASA4	1
NM_001042646	TRAK1	1
NM_015053	PPFIA4	1
NM_005160	ADRBK2	1
NM_000346	SOX9	1
NM_031991	PTBP1	1
NM_002819	PTBP1	1
NM_175847	PTBP1	1
NM_031990	PTBP1	1
NM_020823		1
NM_182508	C13orf30	1
NM_019046	ANKRD16	1
NM_013332	HIG2	1
NM_001098786		1
NM_182515	ZNF714	1
NM_001537	HSBP1	1
NM_020122	KCMF1	1
NM_001001665	FLJ16008	1
NM_018390	PLCXD1	1
NM_014665	LRRC14	1
NM_001037293	PALM2	1
NM_053016	PALM2	1
NM_018242	FLJ10847	1
NM_014417	BBC3	1
NM_003979	GPRC5A	1
NM_002518	NPAS2	1
NM_001081686	G6PC2	1
XM_379029	LOC400879	1
XM_928199	LOC400581	1
NM_207309	UAP1L1	1
NM_002081	GPC1	1
NM_003983	SLC7A6	1
NM_001076785	SLC7A6	1
NM_031448	C19orf12	1
NM_001031726	C19orf12	1
XM_498648	LOC440389	1
NM_001008405	BCAP29	1
NM_018844	BCAP29	1
NM_178172	LOC338328	1
NM_033133	CNP	1
NM_032037	TSSK6	1
NM_004387	NKX2-5	1
NM_001447	FAT2	1
NM_014807	TMEM24	1
NM_018566	YOD1	1
NM_002080	GOT2	1
NM_005961		1
NM_207577	MAP6	1
NM_001001894	TTC3	1
NM_003316	TTC3	1
NM_005596	NFIB	1
NM_018964	SLC37A1	1
NM_004943	DMWD	1
NM_004614	TK2	1
NM_004427	PHC2	1
NM_198040	PHC2	1
NM_153347	TMEM86A	1
NM_019044	CCDC93	1
NM_032242	PLXNA1	1
XM_930496	LOC645752	1
NM_004455	EXTL1	1
NM_020947	KIAA1609	1
NM_015533	DAK	1
NM_000512	GALNS	1
NM_003808	TNFSF13	1
NM_172088	TNFSF13	1
NM_172087	TNFSF13	1
NM_172089	TNFSF12-TNFSF13	1
NM_012405	ICMT	1
NM_007327	GRIN1	1
NM_021569	GRIN1	1
NM_003281	TNNI1	1
NM_080836	STK35	1
NM_194286	KIAA1853	1
NM_003485	GPR68	1
NM_001978	EPB49	1
NM_025149	FLJ20920	1
XM_001131186	LOC729746	1
NM_018715	RCC2	1
NM_138368	DKFZp761E198	1
NM_001083909	GPR123	1
NM_015271	TRIM2	1
NM_030645	SH3BP5L	1
NM_001012514	ITM2C	1
NM_030926	ITM2C	1
NM_001012516	ITM2C	1
NM_006478	GAS2L1	1
NM_152237	GAS2L1	1
NM_152236	GAS2L1	1
NM_003575	ZNF282	1
NM_020132	AGPAT3	1
NM_001037553	AGPAT3	1
NM_003214	TEAD3	1
NM_014957	DENND3	1
NM_016257	HPCAL4	1
NM_020733		1
XM_498841	LOC440748	1
NM_001806	CEBPG	1
NM_024574	C4orf31	1
NM_001319	CSNK1G2	1
NM_001127	AP1B1	1
NM_145730	AP1B1	1
NM_015316	PPP1R13B	1
NM_021738	SVIL	1
NM_003174	SVIL	1
NM_032977	CASP10	1
NM_001230	CASP10	1
XM_943571	LOC646916	1
NM_002628	PFN2	1
NM_053024	PFN2	1
NM_014630	ZNF592	1
XM_498907	LOC284998	1
XM_944715	LOC284998	1
NM_018031	WDR6	1
NM_024297	PHF23	1
NM_006609	MAP3K2	1
XM_001128799	MAP3K2	1
NM_023076	C16orf28	1
NM_015321	CRTC1	1
NM_001098482		1
NM_001789	CDC25A	1
NM_201567	CDC25A	1
NM_152588	TMTC2	1
NM_198859	PRICKLE2	1
NM_005885	MARCH6	1
NM_014232	VAMP2	1
NM_001042535	CENTG3	1
NM_018273	TMEM143	1
NM_053064	GNG2	1
NM_198281	GPRIN3	1
NM_007354	C3orf27	1
NM_033387	FAM78A	1
NM_000260	MYO7A	1
NM_134268	CYGB	1
NM_016621	PHF21A	1
NM_001101802		1
NM_025232	REEP4	1
NM_024591	CHMP6	1
XM_001132548	CHMP6	1
NM_014824	FCHSD2	1
NM_144498	OSBPL2	1
NM_014835	OSBPL2	1
NM_018085	IPO9	1
NM_004973	JARID2	1
NM_015656		1
NM_000877	IL1R1	1
NM_025058	TRIM46	1
NM_014432	IL20RA	1
NM_133334	WHSC1	1
NM_033163	FGF8	1
NM_006119	FGF8	1
NM_033165	FGF8	1
NM_033164	FGF8	1
NM_014804	KIAA0753	1
NM_003882	WISP1	1
XM_941466	METRNL	1
XM_927769	LOC653506	1
NM_021216	ZNF71	1
NM_000599	IGFBP5	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).

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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