VIRsiRNAdb

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

22 hits were found for CGGCAAAGGCUAUGGAACA (18 guide strand hits and 4 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_001013698

LOC440087

1705

1723

C

G

c

C

A

A

A

G

G

C

U

A

U

G

G

A

A

g

c

72

3

14

c

false

<90%

2104

NM_000339

SLC12A3

1491

1509

C

G

G

C

A

A

A

G

G

C

U

A

U

G

G

c

A

a

g

66

3

15

c

false

<90%

3131

NM_130474

MADD

3238

3256

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5640

NM_130472

MADD

3238

3256

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5710

NM_130471

MADD

3298

3316

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5770

NM_130476

MADD

3378

3396

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5850

NM_130473

MADD

3427

3445

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5899

NM_130475

MADD

3438

3456

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5957

NM_130470

MADD

3501

3519

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

5973

NM_003682

MADD

3427

3445

a

c

c

C

A

A

A

G

G

C

U

A

U

G

G

c

A

C

A

40

4

12

c

false

<90%

6016

NM_002373

MAP1A

2861

2879

u

G

G

C

A

A

A

G

u

C

U

A

U

G

G

A

A

C

g

32

3

9

bc

false

<90%

10275

NM_183004

EIF5

573

591

g

G

G

C

A

A

A

G

G

C

a

A

U

G

G

A

A

u

c

29

4

9

c

false

<90%

5782

NM_001969

EIF5

600

618

g

G

G

C

A

A

A

G

G

C

a

A

U

G

G

A

A

u

c

29

4

9

c

false

<90%

5809

XR_018550

LOC391807

737

755

g

G

c

C

A

u

A

G

G

C

U

A

U

G

G

A

A

C

A

15

3

13

bc

false

<90%

810

NM_003884

PCAF

2189

2207

a

G

u

C

A

A

g

G

G

C

U

A

U

G

G

A

A

C

A

12

3

12

bc

false

<90%

4838

NM_173638

NBPF15

128

146

u

G

G

C

A

A

g

G

G

C

U

c

U

G

G

A

A

C

A

-2

3

7

false

<90%

4046

NM_183372

NBPF11

63

81

u

G

G

C

A

A

g

G

G

C

U

c

U

G

G

A

A

C

A

-2

3

7

false

<90%

4902

XR_017591

LOC391707

133

151

C

G

G

C

c

A

A

G

G

C

a

A

U

G

G

A

A

C

u

-17

3

7

c

false

<90%

394

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_001013641

LOC388595

765

783

c

u

g

g

C

C

A

U

A

G

C

C

U

U

U

G

C

C

G

30

4

15

bc

false

<90%

1520

XM_001133510

ZBTB38

1748

1766

U

G

U

U

C

C

A

a

A

G

C

C

U

U

U

G

a

C

a

9

3

8

c

false

<90%

8113

NM_001080412

ZBTB38

1748

1766

U

G

U

U

C

C

A

a

A

G

C

C

U

U

U

G

a

C

a

9

3

8

c

false

<90%

8113

NM_024718

C9orf86

2536

2554

U

G

U

a

C

C

A

U

c

G

C

C

U

U

U

G

C

C

G

3

2

10

bc

false

<90%

3148

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 315
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_001002860	BTBD7	2
NM_203329	CD59	2
NM_203331	CD59	2
NM_203330	CD59	2
NM_000611	CD59	2
NM_003644	GAS7	2
NM_201432	GAS7	2
NM_201433	GAS7	2
NM_014331	SLC7A11	2
NM_032108	SEMA6B	1
NM_144616	JSRP1	1
NM_000479	AMH	1
NM_001033026	C19orf6	1
NM_033420	C19orf6	1
NM_000099	CST3	1
NM_024872	DOK3	1
NM_032430	BRSK1	1
NM_002083	GPX2	1
NM_015229	KIAA0664	1
XM_058967	LOC126037	1
XM_940654	LOC126037	1
NM_004314	ART1	1
NM_001104538		1
NM_002428	MMP15	1
NM_015191	SNF1LK2	1
NM_182519	C20orf186	1
NM_172089	TNFSF12-TNFSF13	1
NM_003327	TNFRSF4	1
NM_015316	PPP1R13B	1
NM_005036	PPARA	1
NM_001001928	PPARA	1
NM_174983	C19orf28	1
NM_206895	UNQ830	1
NM_014694	ADAMTSL2	1
NM_032366	MGC13114	1
NM_001040161	MGC13114	1
NM_199247	CACNB1	1
NM_001040160	MGC13114	1
NM_001040165	MGC13114	1
NM_001040162	MGC13114	1
NM_021905	GABBR1	1
NM_021904	GABBR1	1
NM_007210	GALNT6	1
NM_005665	EVI5	1
NM_021903	GABBR1	1
NM_001960	EEF1D	1
NM_032378	EEF1D	1
NM_001470	GABBR1	1
NM_005786	TSHZ1	1
NM_017805	RASIP1	1
NM_020751	COG6	1
NM_000478	ALPL	1
NM_025045	BAIAP2L2	1
XM_942692	MGC5139	1
NM_001080533	MGC5139	1
NM_014647	KIAA0430	1
NM_001008738	FNIP1	1
NM_133372	FNIP1	1
NM_015922	NSDHL	1
NM_003488	AKAP1	1
XM_001133370	LOC731336	1
XM_001134093	LOC729879	1
NM_022842	CDCP1	1
NM_006581	FUT9	1
NM_032109	OTP	1
NM_178505	TMEM26	1
NM_172364	CACNA2D4	1
NM_001356	DDX3X	1
NM_001376	DYNC1H1	1
NM_022103	ZNF667	1
NM_032199	ARID5B	1
NM_017563	IL17RD	1
NM_001080973	IL17RD	1
NM_015015	JMJD2B	1
NM_017556	FBLIM1	1
NM_001024216	FBLIM1	1
NM_032977	CASP10	1
NM_001230	CASP10	1
NM_004730	ETF1	1
NM_152445	C14orf44	1
NM_153631	HOXA3	1
NM_153632	HOXA3	1
NM_030661	HOXA3	1
NM_005194	CEBPB	1
NM_000104	CYP1B1	1
NM_001508	GPR39	1
NM_004655	AXIN2	1
NM_003186	TAGLN	1
NM_001001522	TAGLN	1
NM_003918	GYG2	1
NM_001079855	GYG2	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_001093	ACACB	1
NM_030651	PRRT1	1
NM_015440	MTHFD1L	1
NM_001098816		1
NM_054026	CNOT7	1
NM_002531	NTSR1	1
NM_030806	C1orf21	1
NM_138736	GNAO1	1
NM_031366	COL4A3	1
NM_000091	COL4A3	1
NM_031365	COL4A3	1
NM_031362	COL4A3	1
NM_175885	MGC33846	1
NM_152547	BTNL9	1
NM_018988	GFOD1	1
XM_001132907	LOC730202	1
XM_001131136	LOC731887	1
NM_022787	NMNAT1	1
NM_001007139	IGF2	1
NM_000612	IGF2	1
NM_001040272	C9orf94	1
NM_199461	NANOS1	1
NM_001101676		1
NM_024561	NARG1L	1
XM_936119	LOC642044	1
XM_936165	LOC642075	1
XM_933843	LOC646720	1
XM_945002	LOC651895	1
NM_005623	CCL8	1
NM_006898	HOXD3	1
NM_005797	EVA1	1
NM_182574	FLJ36070	1
NM_152833		1
NM_001029881	CIB4	1
NM_020719		1
NM_006113	VAV3	1
NM_001079874	VAV3	1
NM_173683	XKR6	1
NM_003627	SLC43A1	1
NM_080760	DACH1	1
NM_080759	DACH1	1
NM_004392	DACH1	1
NM_138420		1
NM_006963	ZNF22	1
NM_005056	JARID1A	1
NM_001042603	JARID1A	1
XM_946032	LOC644852	1
XM_934218	LOC644852	1
NM_006620	HBS1L	1
NM_020390	EIF5A2	1
NM_016588	NRN1	1
XM_939547	ZNF697	1
NM_001080470	ZNF697	1
NM_013987	PARK2	1
NM_004562	PARK2	1
NM_013988	PARK2	1
NM_014600	EHD3	1
NM_021020	LZTS1	1
NM_183373	C6orf145	1
XM_937537	C6orf145	1
NM_001001712	LCN10	1
NM_152744	SDK1	1
NM_003036	SKI	1
NM_001033518	WIPI2	1
NM_001033519	WIPI2	1
NM_015610	WIPI2	1
NM_001033520	WIPI2	1
NM_016003	WIPI2	1
NM_018029	FLJ10213	1
NM_006092	NOD1	1
NM_001030288	SPN	1
NM_003123	SPN	1
NM_173814	PRTG	1
NM_001030060	SAMD5	1
NM_014391	ANKRD1	1
NM_015341	NCAPH	1
NM_198465	NRK	1
NM_052857	CCDC16	1
NM_000068	CACNA1A	1
NM_023035	CACNA1A	1
NM_024577	SH3TC2	1
NM_001197	BIK	1
NM_182832	PLAC4	1
NM_013372	GREM1	1
NM_007353	GNA12	1
NM_152462	AMAC1	1
NM_178500	PHOSPHO1	1
NM_207406	CCDC4	1
NM_024103	SLC25A23	1
NM_012334	MYO10	1
NM_015193	ARC	1
NM_015178	RHOBTB2	1
NM_000787	DBH	1
NM_003657	BCAS1	1
XM_926142	LOC642691	1
NM_005583	LYL1	1
NM_001009959	KIAA1189	1
NM_020711	KIAA1189	1
XM_001128616	LOC401021	1
NM_015393	DKFZP564O0823	1
NM_201998	SF1	1
NM_004630	SF1	1
NM_006482	DYRK2	1
NM_003583	DYRK2	1
XM_001126712	LOC728154	1
XM_001131924	LOC732122	1
NM_032208	ANTXR1	1
NM_145644	MRPL35	1
NM_016622	MRPL35	1
NM_004323	BAG1	1
NM_020853	KIAA1467	1
NM_020804	PACSIN1	1
NM_199175	C21orf123	1
NM_005188	CBL	1
NM_134268	CYGB	1
NM_001080397	SLC45A1	1
XM_937695	SLC45A1	1
NM_021049	MAGEA5	1
NM_000136	FANCC	1
NM_003439	ZKSCAN1	1
NM_001040185	ZNF765	1
NM_018316	KLHL26	1
NM_001103161		1
NM_001103160		1
NM_001031617	COX19	1
NM_007011	ABHD2	1
NM_152924	ABHD2	1
NM_000457	HNF4A	1
NM_178849	HNF4A	1
NM_182663	RASSF5	1
NM_182664	RASSF5	1
NM_182665	RASSF5	1
NM_005318	H1F0	1
NM_015872	ZBTB7B	1
NM_006256	PKN2	1
NM_001098813		1
NM_015146		1
NM_001098812		1
NM_015866	PRDM2	1
NM_001007257	PRDM2	1
NM_024770	METTL8	1
NM_002067	GNA11	1
NM_024322	CENPO	1
NM_024016	HOXB8	1
NM_004883	NRG2	1
NM_013982	NRG2	1
NM_013983	NRG2	1
NM_013981	NRG2	1
NM_144632	TMEM182	1
NM_033141	MAP3K9	1
NM_020773	TBC1D14	1
NM_020954	KIAA1618	1
NM_203434	IER5L	1
XM_001132315	LOC732226	1
NM_153712	TTL	1
NM_001012415	SOHLH1	1
NM_021189	CADM3	1
NM_002383	MAZ	1
NM_001042539	MAZ	1
NM_138731	MIPOL1	1
NM_003897	IER3	1
NM_031426	C9orf58	1
NM_000578	SLC11A1	1
NM_007368	RASA3	1
NM_004831	CRSP7	1
NM_000031	ALAD	1
NM_001003945	ALAD	1
NM_018959	DAZAP1	1
NM_170711	DAZAP1	1
NM_152374	FLJ38984	1
NM_173167	UNC45B	1
NM_001033576	UNC45B	1
NM_199205	KIAA1967	1
NM_021174	KIAA1967	1
NM_001556	IKBKB	1
NM_015079	TBC1D2B	1
NM_001105573		1
NM_004236	COPS2	1
NM_001001931	MTUS1	1
NM_001001924	MTUS1	1
NM_020749	MTUS1	1
NM_001001925	MTUS1	1
NM_024098	CCDC86	1
NM_024915	GRHL2	1
NM_015202	KIAA0556	1
NM_001610	ACP2	1
NM_198517	TBC1D10C	1
NM_173562	KCTD20	1
NM_138415	PHF21B	1
NM_006375	ENOX2	1
NM_182314	ENOX2	1
NM_001001685	FLJ45079	1
NM_015285	WDR7	1
NM_052834	WDR7	1
NM_025010	KLHL18	1
NM_017420	SIX4	1
NM_145753	PHLDB2	1
NM_183237	RNF7	1
NM_000891	KCNJ2	1
NM_004416	DTX1	1
NM_030964	SPRY4	1
NM_005069	SIM2	1
NM_203305	FAM102A	1
NM_001035254	FAM102A	1
NM_145796	POGZ	1
NM_153449	SLC2A14	1
NM_020731	AHRR	1
NM_018403	DCP1A	1
NM_144607	CYB5D1	1
NM_003983	SLC7A6	1
NM_001076785	SLC7A6	1
NM_015308	FNBP4	1
XM_377073	LOC376475	1
NM_001004301	ZNF813	1
NM_014503	UTP20	1
XM_936222	LOC653877	1
NM_000046	ARSB	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