VIRsiRNAdb

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

7 hits were found for UACCGCAGAGUCUAGACUC (0 guide strand hits and 7 sense strand hits.)

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_001005209

MGC99813

1490

1508

c

u

G

U

C

U

A

G

A

C

U

C

U

G

C

a

G

U

c

55

4

13

c

false

<90%

2239

NM_172110

EYA2

1912

1930

G

A

G

U

C

U

A

G

A

C

U

C

U

u

C

u

G

U

A

54

2

13

c

false

<90%

2406

NM_172112

EYA2

1964

1982

G

A

G

U

C

U

A

G

A

C

U

C

U

u

C

u

G

U

A

54

2

13

c

false

<90%

2458

NM_005244

EYA2

1984

2002

G

A

G

U

C

U

A

G

A

C

U

C

U

u

C

u

G

U

A

54

2

13

c

false

<90%

2478

NM_172111

EYA2

2014

2032

G

A

G

U

C

U

A

G

A

C

U

C

U

u

C

u

G

U

A

54

2

13

c

false

<90%

2508

NM_172113

EYA2

2268

2286

G

A

G

U

C

U

A

G

A

C

U

C

U

u

C

u

G

U

A

54

2

13

c

false

<90%

2762

NM_001510

GRID2

2048

2066

a

g

u

c

C

U

A

G

A

C

U

C

U

G

C

G

G

U

A

30

4

15

bc

false

<90%

3024

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3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 185
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_006464	TGOLN2	2
NM_003539	HIST1H4D	1
NM_145025	C6orf199	1
NM_012309	SHANK2	1
NM_001018000	KIAA1026	1
NM_001017999	KIAA1026	1
NM_001018001	KIAA1026	1
NM_015209	KIAA1026	1
XM_001126700	LOC728147	1
XM_001126645	LOC730638	1
NM_032226	ZCCHC7	1
NM_005160	ADRBK2	1
NM_004420	DUSP8	1
NM_198389	PDPN	1
NM_006474	PDPN	1
NM_001006624	PDPN	1
NM_001006625	PDPN	1
NM_024613	PLEKHF2	1
NM_015221	DNMBP	1
NM_020822	KCNT1	1
NM_032239	LARP2	1
NM_052867	NALCN	1
NM_015666	GTPBP5	1
NM_144713	FAM82A	1
NM_020778	ALPK3	1
NM_007087	CALB2	1
NM_007088	CALB2	1
NM_007219	RNF24	1
NM_001037535	SCML1	1
NM_001037540	SCML1	1
NM_006746	SCML1	1
NM_001037536	SCML1	1
NM_007123	USH2A	1
NM_030643	APOL4	1
NM_145660	APOL4	1
NM_001080417	ZNF629	1
XM_938127	ZNF629	1
NM_001557	IL8RB	1
NM_018650	MARK1	1
NM_203305	FAM102A	1
NM_001035254	FAM102A	1
NM_013397	C6orf49	1
NM_002404	MFAP4	1
NM_198525	KIF7	1
NM_015207		1
NM_015554	GLCE	1
NM_003387	WIPF1	1
NM_001077269	WIPF1	1
NM_030613	ZFP2	1
NM_138297	MUC4	1
NM_004532	MUC4	1
NM_018406	MUC4	1
NM_152782	SUNC1	1
NM_001030019	SUNC1	1
NM_015033	FNBP1	1
NM_012334	MYO10	1
NM_182515	ZNF714	1
NM_001007188	DEPDC5	1
NM_001040661	SLC29A4	1
NM_153247	SLC29A4	1
NM_006654	FRS2	1
NM_001042555	FRS2	1
NM_001098819		1
NM_001098818		1
NM_000923	PDE4C	1
NM_020804	PACSIN1	1
NM_015094	HIC2	1
NM_020947	KIAA1609	1
NM_003592	CUL1	1
NM_017929	PEX26	1
NM_001100829		1
NM_153367	C10orf56	1
NM_020722		1
NM_030758	OSBP2	1
NM_002655	PLAG1	1
NM_152996	ST6GALNAC3	1
NM_014413	EIF2AK1	1
NM_012081	ELL2	1
NM_001103147		1
NM_001103148		1
NM_001103146		1
NM_015575	TNRC15	1
NM_182574	FLJ36070	1
NM_017656	ZNF562	1
NM_152470	RNF165	1
NM_001001414	LOC342897	1
NM_024721	ZFHX4	1
NM_001106	ACVR2B	1
NM_002234	KCNA5	1
NM_001009569	MLLT10	1
NM_004641	MLLT10	1
NM_003274	TMEM1	1
NM_001083591	CUGBP2	1
NM_001025077	CUGBP2	1
NM_006561	CUGBP2	1
NM_001025076	CUGBP2	1
NM_032977	CASP10	1
NM_001230	CASP10	1
NM_145912	NFAM1	1
NM_032797	AIFM2	1
NM_138400	NOM1	1
XM_940362	LOC645984	1
XM_928946	LOC645984	1
NM_001003698	RREB1	1
NM_001003699	RREB1	1
NM_002955	RREB1	1
NM_001005476	PKP4	1
NM_003628	PKP4	1
NM_001039842	LOC339229	1
NM_144599	NIPA1	1
NM_001009993	LOC130074	1
NM_174968	ST3GAL3	1
NM_174971	ST3GAL3	1
NM_174964	ST3GAL3	1
NM_174963	ST3GAL3	1
NM_174969	ST3GAL3	1
NM_174965	ST3GAL3	1
NM_174966	ST3GAL3	1
NM_174970	ST3GAL3	1
NM_006279	ST3GAL3	1
NM_174967	ST3GAL3	1
NM_002478	MYOD1	1
NM_014755	SERTAD2	1
NM_033127	LZTR2	1
NM_018269	ADI1	1
NM_001099220		1
NM_015286	DMN	1
NM_145728	DMN	1
NM_004296	RGS6	1
NM_194457	UBE2J2	1
NM_194315	UBE2J2	1
NM_058167	UBE2J2	1
NM_194458	UBE2J2	1
NM_004028	AQP4	1
NM_001650	AQP4	1
NM_020717	SHROOM4	1
XM_926071	LOC642592	1
NM_001099692		1
NM_001040061		1
NM_001013693	LDLRAD2	1
NM_004795	KL	1
NM_080282	ABCA10	1
NM_001039772	LOC643923	1
NM_000950	PRRG1	1
NM_001042599	ERBB4	1
NM_005235	ERBB4	1
NM_000332	ATXN1	1
NM_007345	ZNF236	1
NM_000200	HTN3	1
NM_002159	HTN1	1
NM_018265	C1orf106	1
NM_004100	EYA4	1
NM_172105	EYA4	1
NM_172103	EYA4	1
NM_001025073	C3orf17	1
NM_015412	C3orf17	1
NM_001025072	C3orf17	1
NM_014282	HABP4	1
NM_001099455		1
NM_018340	FLJ11151	1
NM_138328	RHBDL3	1
NM_006544	EXOC5	1
XM_944097	LOC389641	1
NM_001033580	MYOHD1	1
NM_024893	C20orf39	1
NM_001098833		1
NM_020218		1
NM_001018053	PFKFB2	1
NM_152253	CHKB	1
NM_003047	SLC9A1	1
NM_001364	DLG2	1
NM_021238	FAM60A	1
NM_006380	APPBP2	1
NM_024313	NOL12	1
NM_014622	LOH11CR2A	1
XM_001131779	LOC730919	1
NM_014554	SENP1	1
NM_003979	GPRC5A	1
NM_001098525		1
NM_018204	CKAP2	1
NM_172239	REXO1L1	1
NM_003644	GAS7	1
NM_201432	GAS7	1
NM_201433	GAS7	1
NM_001004349	FLJ45422	1

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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