VIRsiRNAdb

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

16 hits were found for GACUUCGGCUUUGGCAUCA (10 guide strand hits and 6 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_012301

MAGI2

3042

3060

G

g

C

U

U

C

G

G

C

U

U

U

G

u

C

A

U

C

A

69

2

11

c

false

<90%

6880

NM_001006932

RPS6KA2

1797

1815

G

A

C

U

U

C

G

G

C

U

U

U

G

c

C

A

a

g

c

49

4

13

c

false

<90%

5735

NM_021135

RPS6KA2

1879

1897

G

A

C

U

U

C

G

G

C

U

U

U

G

c

C

A

a

g

c

49

4

13

c

false

<90%

5817

NM_001748

CAPN2

1424

1442

a

c

C

a

U

C

G

G

C

U

U

U

G

G

C

A

U

C

u

44

4

14

bc

false

<90%

3419

NM_001520

GTF3C1

2729

2747

G

A

C

U

U

C

G

G

C

U

U

U

G

G

C

u

g

g

g

42

4

15

c

false

<90%

7106

NM_005529

HSPG2

1601

1619

u

g

C

U

U

C

u

G

C

U

U

U

G

G

C

A

U

C

A

20

3

12

bc

false

<90%

14294

NM_024654

NOL9

1832

1850

u

g

C

U

U

g

G

G

C

U

U

U

G

G

C

A

U

C

u

18

4

12

bc

false

<90%

2837

NM_001080436

WTIP

661

679

u

A

C

U

U

C

G

G

C

a

U

U

u

G

C

A

U

C

A

4

3

8

false

<90%

2204

XM_939855

WTIP

1591

1609

u

A

C

U

U

C

G

G

C

a

U

U

u

G

C

A

U

C

A

4

3

8

false

<90%

3134

NM_031459

SESN2

1545

1563

c

A

C

U

g

C

G

u

C

U

U

U

G

G

C

A

U

C

A

-15

3

11

bc

false

<90%

3503

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_006328

RBM14

466

484

a

G

A

U

G

C

C

A

A

A

G

C

C

G

c

A

a

U

C

49

3

13

c

false

<90%

2811

NM_001008396

WDHD1

2877

2895

U

G

A

U

u

C

C

A

A

A

G

C

C

G

A

A

G

c

C

45

2

12

c

false

<90%

4641

NM_007086

WDHD1

2970

2988

U

G

A

U

u

C

C

A

A

A

G

C

C

G

A

A

G

c

C

45

2

12

c

false

<90%

4734

XR_016860

LOC441884

828

846

U

G

A

U

G

C

C

A

A

A

u

C

C

G

A

A

G

U

a

33

2

10

c

false

<90%

1429

XR_019308

LOC441884

828

846

U

G

A

U

G

C

C

A

A

A

u

C

C

G

A

A

G

U

a

33

2

10

c

false

<90%

1429

NM_002203

ITGA2

3515

3533

U

G

A

U

G

a

g

A

A

A

G

C

C

G

A

A

G

U

a

-34

3

11

bc

false

<90%

7878

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 372
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_012425	RSU1	2
NM_152724	RSU1	2
NM_022764	MTHFSD	2
NM_032271	TRAF7	2
NM_013238	DNAJC15	1
NM_004172	SLC1A3	1
NM_018303	EXOC2	1
NM_032423	ZNF528	1
XM_945302	LOC652225	1
XM_934407	LOC647131	1
NM_032042	C5orf21	1
NM_013989	DIO2	1
NM_001007023	DIO2	1
NM_000793	DIO2	1
NM_003342	UBE2G1	1
NM_020722		1
NM_031991	PTBP1	1
NM_002819	PTBP1	1
NM_175847	PTBP1	1
NM_031990	PTBP1	1
NM_207406	CCDC4	1
NM_020956	PRX	1
NM_001004298	C10orf90	1
NM_015635	GAPVD1	1
NM_000182	HADHA	1
NM_006822	RAB40B	1
NM_201613	IKIP	1
XM_926521	LOC653137	1
XM_928267	LOC653270	1
NM_012292	HMHA1	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_006516	SLC2A1	1
XM_001133565	LOC731440	1
NM_002507	NGFR	1
XM_001126137	LOC284952	1
XM_001129340	LOC284952	1
NM_004612	TGFBR1	1
NM_032802	SPPL2A	1
NM_004928	C21orf2	1
NM_153265	EML3	1
NM_018370	DRAM	1
NM_004999	MYO6	1
NM_000554	CRX	1
NM_015562		1
NM_078469	BCCIP	1
NM_178864	NPAS4	1
NM_003099	SNX1	1
NM_152826	SNX1	1
NM_148955	SNX1	1
NM_015520	MAGI1	1
NM_001024071	GCH1	1
NM_001024024	GCH1	1
NM_001024070	GCH1	1
NM_000161	GCH1	1
NM_014817	KIAA0644	1
NM_020734	FAM80B	1
NM_022844	MYH11	1
NM_002474	MYH11	1
NM_001040114	MYH11	1
NM_001040113	MYH11	1
NM_152253	CHKB	1
NM_000317	PTS	1
NM_003291	TPP2	1
NM_003107	SOX4	1
NM_005188	CBL	1
NM_152991	EED	1
NM_005054	RGPD5	1
XM_001133591	LOC729540	1
XM_001133590	LOC729540	1
XM_001126221	LOC727851	1
XM_001126260	LOC727851	1
XM_001126233	LOC727851	1
XM_001126248	LOC727851	1
XM_001126272	LOC727851	1
XM_929931	LOC653489	1
NM_001013659	ZNF793	1
NM_005197	CHES1	1
NM_001085471		1
NM_021167	GATAD1	1
NM_032595	PPP1R9B	1
NM_006624	ZMYND11	1
NM_015516	TSKU	1
XM_496960	FAM90A11P	1
NM_001099666		1
NM_006335	TIMM17A	1
NM_004721	MAP3K13	1
NM_006234	POLR2J	1
NM_021260	ZFYVE1	1
NM_178441	ZFYVE1	1
NM_025136	OPA3	1
NM_033131	WNT3A	1
NM_005858	AKAP8	1
NM_005477	HCN4	1
NM_003328	TXK	1
NM_000455	STK11	1
NM_003910	BUD31	1
NM_145175	FAM84A	1
NM_002428	MMP15	1
NM_024820	DENND1A	1
NM_005740	DNAL4	1
NM_153367	C10orf56	1
NM_152475	ZNF417	1
NM_001957	EDNRA	1
NM_001039350	DPP6	1
NM_001936	DPP6	1
NM_130797	DPP6	1
NM_000025	ADRB3	1
NM_130773	CNTNAP5	1
NM_002891	RASGRF1	1
NM_153815	RASGRF1	1
NM_032323	TMEM79	1
NM_030819	GFOD2	1
NM_052847	GNG7	1
NM_183413	FBXO44	1
NM_033182	FBXO44	1
NM_001014765	FBXO44	1
NM_183412	FBXO44	1
NM_031945	TSPAN10	1
NM_001104647		1
NM_018155	SLC25A36	1
NM_005439	MLF2	1
NM_000232	SGCB	1
NM_178120	DLX1	1
NM_001038493	DLX1	1
NM_194457	UBE2J2	1
NM_194315	UBE2J2	1
NM_058167	UBE2J2	1
NM_194458	UBE2J2	1
NM_173695	CXorf59	1
NM_009588	LTB	1
NM_006522	WNT6	1
NM_005503	APBA2	1
NM_006160	NEUROD2	1
XM_933935	LOC646778	1
XM_943239	LOC646778	1
NM_147191	MMP21	1
NM_003507	FZD7	1
NM_016442	ARTS-1	1
NM_005329	HAS3	1
NM_000738	CHRM1	1
NM_015719	COL5A3	1
NM_014911	AAK1	1
NM_001010000	ARHGAP28	1
NM_033631	LUZP1	1
NM_017899	TESC	1
NM_001037172	ACPL2	1
NM_152282	ACPL2	1
NM_022473	ZFP106	1
NM_030760	EDG8	1
NM_170672	RASGRP3	1
NM_207436	FLJ42957	1
NM_178438	LCE5A	1
NM_006361	HOXB13	1
NM_014647	KIAA0430	1
NM_000451	SHOX	1
XM_927706	LOC644591	1
NM_013937	OR11A1	1
NM_020459		1
NM_032214	SLA2	1
NM_175077	SLA2	1
NM_002030	FPRL2	1
NM_130799	MEN1	1
NM_130801	MEN1	1
NM_000244	MEN1	1
NM_130803	MEN1	1
NM_130800	MEN1	1
NM_130804	MEN1	1
NM_130802	MEN1	1
NM_032590	FBXL10	1
NM_001005366	FBXL10	1
NM_020899	ZBTB4	1
NM_007028	TRIM31	1
NM_001098784		1
NM_001098785		1
NM_152832	FAM89B	1
NM_001793	CDH3	1
NM_006852	TLK2	1
NM_001112707		1
NM_024522	FAM77C	1
NM_014226	RAGE	1
NM_003277	CLDN5	1
NM_012458	TIMM13	1
NM_019591	ZNF26	1
XM_934743	FBXO46	1
XM_946240	FBXO46	1
NM_001080469	FBXO46	1
XM_946239	FBXO46	1
NM_052865	C20orf72	1
NM_003681	PDXK	1
NM_001776	ENTPD1	1
NM_001098175		1
NM_002760	PRKY	1
NM_005044	PRKX	1
NM_198859	PRICKLE2	1
NM_017749	FLJ20294	1
NM_001080849	LOC728489	1
NM_020700		1
NM_019845	RPRM	1
NM_014859	KIAA0672	1
NM_003897	IER3	1
NM_033130	SIGLEC10	1
NM_018674	ACCN4	1
NM_182847	ACCN4	1
NM_014675	CROCC	1
NM_001013662		1
NM_170731	BDNF	1
NM_001709	BDNF	1
NM_170732	BDNF	1
NM_170733	BDNF	1
NM_170734	BDNF	1
NM_170735	BDNF	1
NM_030806	C1orf21	1
NM_017952	PTCD3	1
NM_005126	NR1D2	1
XM_001130839	NR1D2	1
NM_145232	ATPBD3	1
NM_020127	TUFT1	1
NM_033274	ADAM19	1
NM_005658	TRAF1	1
NM_138473	SP1	1
NM_001306	CLDN3	1
NM_133374	ZNF618	1
NM_002088	GRIK5	1
NM_004716	PCSK7	1
NM_177401	MIDN	1
NM_012429	SEC14L2	1
NM_153685	C12orf53	1
NM_014924	KIAA0831	1
NM_016219	MAN1B1	1
NM_001017916	CYB561	1
NM_001915	CYB561	1
NM_001017917	CYB561	1
XM_930464	LOC645790	1
XM_941347	LOC645790	1
NM_016474	C3orf19	1
XM_001132353	FLJ44450	1
XM_001133195	FLJ44450	1
NM_053045	MGC14327	1
NM_004975	KCNB1	1
NM_025213	SPTBN4	1
NM_152344	LSM12	1
NM_004348	RUNX2	1
NM_001015051	RUNX2	1
NM_001024630	RUNX2	1
XM_209227	LOC653464	1
NM_001033602	KIAA0774	1
NM_015233	KIAA0774	1
NM_014855	KIAA0415	1
NM_001099439		1
NM_013385	PSCD4	1
NM_001042599	ERBB4	1
NM_005235	ERBB4	1
NM_003713	PPAP2B	1
NM_177414	PPAP2B	1
NM_002725	PRELP	1
NM_201348	PRELP	1
NM_014331	SLC7A11	1
NM_001014380	KATNAL1	1
NM_032116	KATNAL1	1
NM_004852	ONECUT2	1
NM_006920	SCN1A	1
NM_012309	SHANK2	1
NM_001046	SLC12A2	1
NM_001356	DDX3X	1
NM_020890	KIAA1524	1
NM_000927	ABCB1	1
NM_022117	TSPYL2	1
XM_001128695	TSPYL2	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_000679	ADRA1B	1
NM_000991	RPL28	1
NM_003908	EIF2S2	1
NM_001040185	ZNF765	1
NM_007038	ADAMTS5	1
NM_005433	YES1	1
NM_000428	LTBP2	1
NM_002265	KPNB1	1
NM_000750	CHRNB4	1
NM_153051	MTMR3	1
NM_021090	MTMR3	1
NM_153050	MTMR3	1
NM_004588	SCN2B	1
NM_032105	PPP1R12B	1
NM_002481	PPP1R12B	1
NM_013277	RACGAP1	1
NM_019036	HMGCLL1	1
NM_001042406	HMGCLL1	1
NM_001008710	RBPMS	1
NM_001008711	RBPMS	1
NM_006867	RBPMS	1
NM_001004351	MGC57359	1
NM_183238	ZNF605	1
NM_001025205	AP2M1	1
NM_004068	AP2M1	1
NM_001111020		1
NM_003169	SUPT5H	1
NM_198542	ZNF773	1
XM_001132247	C1orf108	1
NM_003082	SNAPC1	1
NM_000821	GGCX	1
NM_001039569	AP1S3	1
NM_019067	GNL3L	1
NM_013252	CLEC5A	1
NM_024595	C1orf108	1
NM_016952	CDON	1
NM_032510	PARD6G	1
NM_015161	ARL6IP1	1
XM_001129292	MBOAT2	1
NM_138799	MBOAT2	1
NM_152458	ZNF785	1
NM_032025	EIF2A	1
NM_001042466	PSAP	1
NM_002778	PSAP	1
NM_001042465	PSAP	1
NM_000437	PAFAH2	1
NM_020702	KIAA1161	1
NM_178865	SERINC2	1
NM_001040274	NO145	1
NM_021649	TICAM2	1
NM_003804	RIPK1	1
NM_025249	KIAA1683	1
NM_003559	PIP5K2B	1
NM_016289	CAB39	1
NM_080605	B3GALT6	1
NM_017892		1
NM_001105669		1
NM_145313	RASGEF1A	1
NM_001040628	NCALD	1
NM_001040626	NCALD	1
NM_001040625	NCALD	1
NM_032041	NCALD	1
NM_001040629	NCALD	1
NM_001040624	NCALD	1
NM_001040627	NCALD	1
NM_001040630	NCALD	1
NM_144675	GSG1L	1
NM_001109763		1
NM_144682	SLFN13	1
NM_024811	FLJ12529	1
NM_032828	ZNF587	1
XM_938665	USP6NL	1
NM_001080491	USP6NL	1
XM_927409	USP6NL	1
XM_943800	USP6NL	1
NM_001649	SHROOM2	1
NM_175609	ARFGAP1	1
NM_018209	ARFGAP1	1
NM_018947	CYCS	1
NM_001031716	OBFC2A	1
NM_138572	TBN	1
NM_022766	CERK	1
NM_012129	CLDN12	1
NM_173495	PTCHD1	1
NM_014732	KIAA0513	1
NM_001380	DOCK1	1
NM_015840	ADAR	1
NM_015841	ADAR	1
NM_001025107	ADAR	1
NM_001111	ADAR	1
NM_006761	YWHAE	1
NM_001097611		1
NM_003593	FOXN1	1
NM_006354	TADA3L	1
NM_001001665	FLJ16008	1
NM_015225	KIAA0367	1
NM_001112	ADARB1	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