VIRsiRNAdb

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

4 hits were found for CGUCCGACCUUGAGGCAUA (3 guide strand hits and 1 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

NR_003369

LOC653390

745

763

u

u

U

C

C

a

A

C

C

U

U

G

A

G

G

C

A

U

g

18

4

12

bc

false

<90%

2262

NM_018427

RRN3

774

792

u

u

U

C

C

a

A

C

C

U

U

G

A

G

G

C

A

U

g

18

4

12

bc

false

<90%

3762

NR_003370

LOC730092

14462

14480

u

u

U

C

C

a

A

C

C

U

U

G

A

G

G

C

A

U

g

18

4

12

bc

false

<90%

26557

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_006649

UTP14A

2249

2267

U

c

U

u

C

C

U

C

A

A

G

G

U

C

G

G

A

C

c

46

3

14

bc

false

<90%

2509

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3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 69
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_144669	GLT1D1	1
NM_003660	PPFIA3	1
NM_152470	RNF165	1
NM_203304	RKHD1	1
NM_001085363		1
NM_002183	IL3RA	1
NM_001042682	RERE	1
NM_012102	RERE	1
NM_001042681	RERE	1
NM_198155	C21orf33	1
NM_004649	C21orf33	1
NM_015144	ZCCHC14	1
NM_201263	WARS2	1
NM_002737	PRKCA	1
NM_018440	PAG1	1
NM_001010911	C10orf114	1
NM_000775	CYP2J2	1
XM_001133211	LOC729003	1
NM_001029861	NANOS2	1
NM_015995	KLF13	1
NM_153367	C10orf56	1
NM_002957	RXRA	1
NM_005515	HLXB9	1
NM_001040001	MLLT4	1
NM_024076	KCTD15	1
NM_003221	TFAP2B	1
NM_030761	WNT4	1
NM_001420	ELAVL3	1
NM_032281	ELAVL3	1
NM_001040152	PEG10	1
NM_001099220		1
NM_032298	SYT3	1
NM_001012508	SPRN	1
NM_001077238	SPPL2B	1
NM_001194	HCN2	1
NM_145685	BRF1	1
NM_001519	BRF1	1
NM_032536	NTNG2	1
NM_053004	GNB1L	1
NM_018423	STYK1	1
NM_003012	SFRP1	1
NM_017844	ANKMY1	1
NM_016552	ANKMY1	1
NM_007284	TWF2	1
NM_001030010	ALDH3B1	1
NM_000694	ALDH3B1	1
XM_497110	LOC441495	1
XM_372214	LOC389857	1
XM_938184	LOC389857	1
XM_001130364	LOC728417	1
XM_001130184	LOC730843	1
NM_178326	ATG4B	1
NM_013325	ATG4B	1
XM_001126088	LOC727737	1
XM_001125996	LOC727737	1
XM_001126099	LOC727737	1
XM_001125933	LOC727737	1
XM_001126076	LOC727737	1
XM_001126139	LOC727737	1
NM_014772	KIAA0427	1
NM_016170	TLX2	1
NM_006298	ZNF192	1
NM_024627	C22orf29	1
NM_003764	STX11	1
NM_001077268	ZFYVE19	1
XM_940609	FLJ25076	1
XM_059689	FLJ25076	1
XM_001133151	LOC729199	1
XM_001133879	LOC731918	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