VIRsiRNAdb

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

12 hits were found for CUACCGUGUGUCUUGGCCA (9 guide strand hits and 3 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

XR_017062

LOC441744

289

307

C

g

u

C

C

G

U

G

U

G

U

C

U

U

G

G

C

u

c

61

4

14

c

false

<90%

786

XR_018951

LOC441744

289

307

C

g

u

C

C

G

U

G

U

G

U

C

U

U

G

G

C

u

c

61

4

14

c

false

<90%

786

NM_000841

GRM4

3689

3707

C

U

g

C

C

G

U

G

U

G

U

C

U

U

G

c

C

C

g

49

3

12

c

false

<90%

3884

NM_207380

FLJ43339

747

765

g

a

g

C

C

c

U

G

U

G

U

C

U

U

G

G

C

C

A

3

4

13

bc

false

<90%

4707

NM_214675

CLEC4M

197

215

C

U

A

C

a

G

g

G

U

G

U

C

U

U

G

G

C

C

A

-17

2

12

bc

false

<90%

1600

NM_214676

CLEC4M

197

215

C

U

A

C

a

G

g

G

U

G

U

C

U

U

G

G

C

C

A

-17

2

12

bc

false

<90%

1861

NM_014257

CLEC4M

197

215

C

U

A

C

a

G

g

G

U

G

U

C

U

U

G

G

C

C

A

-17

2

12

bc

false

<90%

1930

NM_214678

CLEC4M

197

215

C

U

A

C

a

G

g

G

U

G

U

C

U

U

G

G

C

C

A

-17

2

12

bc

false

<90%

2265

NM_214677

CLEC4M

197

215

C

U

A

C

a

G

g

G

U

G

U

C

U

U

G

G

C

C

A

-17

2

12

bc

false

<90%

2349

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_005370

RAB8A

1821

1839

U

G

G

C

C

A

A

G

A

C

A

C

A

a

G

G

c

A

u

51

3

13

c

false

<90%

2194

NM_152557

ZNF746

1106

1124

a

G

G

C

C

A

A

G

c

C

A

C

A

C

G

G

U

u

c

30

4

8

c

false

<90%

3706

NM_181336

LEMD2

2080

2098

a

G

G

C

C

c

A

G

A

C

A

C

A

C

G

G

U

c

c

27

4

11

c

false

<90%

2988

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 219
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_023934	FUNDC2	2
NM_033100	PCDH21	2
NM_058197	CDKN2A	1
NM_058195	CDKN2A	1
NM_000077	CDKN2A	1
XM_496115	LOC440338	1
XM_940659	LOC440338	1
NM_020184	CNNM4	1
NM_021631	FKSG2	1
NM_020947	KIAA1609	1
NM_018036	C14orf103	1
NM_020354	ENTPD7	1
NM_006778	TRIM10	1
NM_052828	TRIM10	1
NM_198098	AQP1	1
NM_022062	PKNOX2	1
NM_138468	ICA1L	1
XM_939208	LOC648149	1
XM_001133680	LOC648149	1
NM_003681	PDXK	1
NM_015154	MESDC2	1
NM_000296	PKD1	1
NM_001009944	PKD1	1
NM_013423	ARHGAP6	1
NM_001174	ARHGAP6	1
NM_013427	ARHGAP6	1
NM_052965	C1orf19	1
NM_033417	NY-SAR-48	1
NM_001011699	NY-SAR-48	1
NM_001642	APLP2	1
NM_153366	SVEP1	1
NM_005156	ROD1	1
NM_001001549	GRB10	1
NM_001001555	GRB10	1
NM_001001550	GRB10	1
NM_005311	GRB10	1
NM_006937	SUMO2	1
NM_001005849	SUMO2	1
XM_001127385	LOC730776	1
XM_001128769	LOC728825	1
NM_201544	LGALS8	1
NM_006499	LGALS8	1
NM_201545	LGALS8	1
NM_201543	LGALS8	1
NM_012234	RYBP	1
NM_001029875	RGS7BP	1
NM_013236	ATXN10	1
NM_031476	CRISPLD2	1
NM_001423	EMP1	1
NM_012074	DPF3	1
NM_021648	TSPYL4	1
NM_006763	BTG2	1
NM_080650	ATPBD4	1
NM_173359	EIF4E3	1
NM_182487	OLFML2A	1
NM_032873	STS-1	1
NM_152421	FAM69B	1
XM_001130258	FAM69B	1
NM_005475	SH2B3	1
NM_020066	FMN2	1
NM_198461	LONRF2	1
NM_014880	CD302	1
NM_207368	LOC348262	1
NM_001093767		1
NM_016598	ZDHHC3	1
NM_198849	LOC283514	1
NM_006742	PSKH1	1
NM_016511	CLEC1A	1
NM_001002901	FCRLB	1
NM_032753	RAXL1	1
NM_000878	IL2RB	1
NM_004444	EPHB4	1
NM_001003407	ABLIM1	1
NM_001003408	ABLIM1	1
NM_002313	ABLIM1	1
NM_006720	ABLIM1	1
NM_004926	ZFP36L1	1
NM_006091	CORO2B	1
XM_001131408	LOC730350	1
XM_001127666	LOC730896	1
NM_015332	NUDCD3	1
NM_015056	RRP1B	1
NM_182924	MICALL2	1
NM_000252	MTM1	1
NM_032799	ZDHHC12	1
NM_000210	ITGA6	1
NM_001079818	ITGA6	1
NM_203284	RBPJ	1
NM_203283	RBPJ	1
NM_015874	RBPJ	1
NM_005349	RBPJ	1
NM_016263	FZR1	1
NM_152710	C10orf27	1
NM_016091	EIF3S6IP	1
NM_020122	KCMF1	1
NM_022481	CENTD3	1
NM_003206	TCF21	1
NM_004565	PEX14	1
NM_145007	NLRP11	1
NM_013318		1
NM_014690	FAM131B	1
NM_001031690	FAM131B	1
NM_001001331	ATP2B2	1
NM_001683	ATP2B2	1
NM_004968	ICA1	1
NM_022307	ICA1	1
NM_001340	CYLC2	1
NM_033429	CALML4	1
NM_001031733	CALML4	1
NM_170740	ALDH5A1	1
NM_001080	ALDH5A1	1
XM_001131068	LOC729696	1
XM_001129643	LOC731435	1
NM_005650	TCF20	1
NM_181492	TCF20	1
NM_000033	ABCD1	1
NM_015328	KIAA0828	1
NM_001100595		1
NM_182620	FAM33A	1
NM_152699	SENP5	1
NM_031495	PCDHA2	1
XM_001130238	LOC728283	1
XM_001132687	LOC731087	1
NM_015891	CDC40	1
NM_005036	PPARA	1
NM_001001928	PPARA	1
NM_001007271	DUSP13	1
NM_005347	HSPA5	1
NM_152283		1
NM_032875	FBXL20	1
NM_024016	HOXB8	1
NM_013995	LAMP2	1
NM_001024455	RGAG4	1
NM_000208	INSR	1
NM_001079817	INSR	1
NM_018110	DOK4	1
NM_138820	HIGD2A	1
XM_001133989	LOC729770	1
XM_001132966	LOC731164	1
NM_004588	SCN2B	1
NM_001097611		1
NM_022803	UCP3	1
NM_014655	SLC25A44	1
NM_175767	IL6ST	1
NM_194318	B3GALTL	1
NM_002254	KIF3C	1
NM_000812	GABRB1	1
NM_152470	RNF165	1
NM_014445	SERP1	1
NM_032514	MAP1LC3A	1
NM_181509	MAP1LC3A	1
NM_025090	USP36	1
NM_004535	MYT1	1
NM_001040633	PRKAG2	1
NM_016203	PRKAG2	1
NM_024429	PRKAG2	1
NM_145351	SCARF1	1
NM_145349	SCARF1	1
NM_020343	C20orf74	1
NM_198066	GNPNAT1	1
NM_024791	PDZD3	1
NM_022818	MAP1LC3B	1
NM_001939	DRP2	1
NM_016433	GLTP	1
NM_001098798		1
NM_001098797		1
NM_001098796		1
NM_032883	TOX2	1
NM_004744	LRAT	1
NM_000918	P4HB	1
XM_001128468	NSF	1
NM_006178	NSF	1
NM_021939	FKBP10	1
NM_002520	NPM1	1
NM_199185	NPM1	1
NM_001008390	CGGBP1	1
NM_003663	CGGBP1	1
NM_138736	GNAO1	1
NM_000021	PSEN1	1
NM_019894	TMPRSS4	1
NM_001083947		1
NM_000956	PTGER2	1
NM_152615	PARP15	1
NM_002977	SCN9A	1
NM_138270	ATRX	1
NM_000489	ATRX	1
NM_003099	SNX1	1
NM_152826	SNX1	1
NM_148955	SNX1	1
NM_003966	SEMA5A	1
NM_018381	FLJ11286	1
NM_203446	SYNJ1	1
NM_003895	SYNJ1	1
NM_004571	PKNOX1	1
NM_000818	GAD2	1
NM_001776	ENTPD1	1
NM_001098175		1
NM_020312	COQ9	1
NM_015409	EP400	1
NM_053056	CCND1	1
NM_013252	CLEC5A	1
NM_016094	COMMD2	1
NM_152716	FLJ36874	1
NM_000522	HOXA13	1
NM_001257	CDH13	1
NM_001002860	BTBD7	1
NM_005180	BMI1	1
NM_053053	TADA1L	1
NM_005109	OXSR1	1
NM_018048	FLJ10292	1
NM_004285	H6PD	1
NM_144661	C10orf82	1
NM_000113	TOR1A	1
XM_001132013	ANKH	1
NM_054027	ANKH	1
NM_012287	CENTB2	1
NM_152293		1
NM_032271	TRAF7	1
NM_000229	LCAT	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)
Motif found in guide strand

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