VIRsiRNAdb

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

5 hits were found for GGUUCGGAUGGUUCGGGAA (0 guide strand hits and 5 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_032873

STS-1

272

290

U

U

C

C

C

G

A

A

C

C

A

U

C

C

G

g

c

u

C

47

3

15

c

false

<90%

6882

XR_015426

LOC731268

1100

1118

c

U

C

C

C

G

A

A

C

C

A

c

C

C

G

c

A

C

C

38

3

10

false

<90%

1622

XR_016856

LOC645129

1100

1118

c

U

C

C

C

G

A

A

C

C

A

c

C

C

G

c

A

C

C

38

3

10

false

<90%

1622

XR_015487

LOC729248

1100

1118

c

U

C

C

C

G

A

A

C

C

A

c

C

C

G

c

A

C

C

38

3

10

false

<90%

1622

NM_001410

MEGF8

176

194

c

U

C

C

u

G

g

A

C

C

A

U

C

C

G

A

A

C

C

-19

3

12

bc

false

<90%

10966

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3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 205
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_001049	SSTR1	3
XM_001127950	LOC730566	2
XM_001133333	LOC729172	2
NM_153451	ORAOV1	2
XM_943571	LOC646916	2
NM_001112	ADARB1	2
XM_943323	LOC646719	1
XM_933842	LOC646719	1
NM_021127	PMAIP1	1
NM_001543	NDST1	1
NM_203400	RPRML	1
NM_203453	PPAPDC2	1
XM_001133556	LOC729135	1
NM_005786	TSHZ1	1
NM_207428	C11orf55	1
NM_006628	ARPP-19	1
NM_007030	TPPP	1
NM_004124	GMFB	1
NM_003298	NR2C2	1
NM_004295	TRAF4	1
XM_946191	FBF1	1
NM_001080542	FBF1	1
NM_005065	SEL1L	1
NM_007086	WDHD1	1
NM_001008396	WDHD1	1
NM_001006616	TSPAN17	1
NM_012171	TSPAN17	1
NM_130465	TSPAN17	1
NM_178469	LCN8	1
NM_144976	ZNF564	1
NM_024729	MYH14	1
NM_001077186	MYH14	1
NM_000088	COL1A1	1
XM_934649	C1orf34	1
XM_945958	C1orf34	1
NM_001008408	RBM33	1
NM_053043	PRR8	1
NM_002843	PTPRJ	1
NM_003200	TCF3	1
NM_014647	KIAA0430	1
NM_031445	AMMECR1L	1
NM_178829	C7orf34	1
NM_033141	MAP3K9	1
NM_006651	CPLX1	1
NM_012158	FBXL3	1
NM_012256	ZNF212	1
NM_032932	RAB11FIP4	1
NM_005076	CNTN2	1
NM_005935	AFF1	1
NM_145239	PRRT2	1
NM_004343	CALR	1
NM_201998	SF1	1
NM_004630	SF1	1
NM_002124	HLA-DRB1	1
NM_020443	NAV1	1
NM_015101	GLT25D2	1
NM_001044722	CSNK1G3	1
NM_001031812	CSNK1G3	1
NM_001044723	CSNK1G3	1
NM_004384	CSNK1G3	1
NM_003347	UBE2L3	1
NM_198157	UBE2L3	1
NM_020894	KIAA1530	1
NM_005168	RND3	1
NM_030782	CLPTM1L	1
NM_015156	RCOR1	1
NM_021059	HIST2H3C	1
NM_001005464	HIST2H3A	1
NM_152771	C19orf34	1
NM_013286	RBM15B	1
NM_001014989	LAT	1
NM_001014987	LAT	1
NM_001014988	LAT	1
NM_014387	LAT	1
NM_001039617	ZDHHC19	1
NM_023004	RTN4R	1
NM_014346	TBC1D22A	1
NM_009588	LTB	1
NM_006774	INMT	1
NM_015963	THAP4	1
XM_001128859	LOC728944	1
NM_005631	SMO	1
NM_014604	TAX1BP3	1
NM_032740	SFT2D3	1
NM_013416	NCF4	1
NM_004385	VCAN	1
NM_020839	WDR48	1
NM_004050	BCL2L2	1
XM_001131577	FLJ36644	1
XM_001126095	FLJ36644	1
NM_001040424	PRDM15	1
NM_015995	KLF13	1
NM_015188		1
NM_000744	CHRNA4	1
NM_021250	LILRA5	1
NM_181985	LILRA5	1
NM_007162	TFEB	1
NM_001004342	TRIM67	1
NM_015090	NFASC	1
NM_130770	HTR3C	1
NM_018667	SMPD3	1
NM_207117	C14orf68	1
NM_199245	VAMP1	1
NM_014661	FAM53B	1
NM_025201	PLEKHQ1	1
NM_000441	SLC26A4	1
NM_001007088	ZNF182	1
NM_006962	ZNF182	1
NM_005722	ACTR2	1
NM_001005386	ACTR2	1
NM_004959	NR5A1	1
NM_030665	RAI1	1
NM_031896	CACNG7	1
XM_001133503	LOC645027	1
NM_144991	C21orf29	1
NM_022822	KLC2	1
NM_021134	MRPL23	1
NM_002105	H2AFX	1
NM_152458	ZNF785	1
NM_020993	BCL7A	1
NM_001024808	BCL7A	1
NM_173473	C10orf104	1
NM_015056	RRP1B	1
NM_000135	FANCA	1
NM_001007169	ZNF483	1
NM_020862		1
NM_032294	CAMKK1	1
NM_172206	CAMKK1	1
NM_152345	ANKRD13B	1
NM_004745	DLGAP2	1
NM_004560	ROR2	1
NM_033178	DUX4	1
NM_002319	LRCH4	1
XM_378661	C17orf51	1
XM_944416	C17orf51	1
NM_001114	ADCY7	1
NM_004947	DOCK3	1
NM_003382	VIPR2	1
NM_004170	SLC1A1	1
NM_032682	FOXP1	1
NM_014207	CD5	1
NM_144993		1
NM_005883	APC2	1
NM_004711	SYNGR1	1
XM_001134338	LOC732242	1
NM_003681	PDXK	1
NM_020120	UGCGL1	1
NM_001025777	UGCGL1	1
NM_138383	ABBA-1	1
XM_001125744	LOC92154	1
NM_013336	SEC61A1	1
NM_033161	SURF4	1
NM_014957	DENND3	1
NM_003924	PHOX2B	1
NM_007189	ABCF2	1
NM_005683	GPR55	1
NM_004160	PYY	1
NM_007168	ABCA8	1
NM_001626	AKT2	1
NM_003234	TFRC	1
NM_020228	PRDM10	1
NM_199438	PRDM10	1
NM_199437	PRDM10	1
NM_199439	PRDM10	1
NM_032824	TMEM87B	1
NM_001005407	CACNA1H	1
NM_021098	CACNA1H	1
NM_006815	TMED2	1
NM_024337	IRX1	1
NM_003034	ST8SIA1	1
NM_024627	C22orf29	1
NM_017776	ZNF673	1
NM_153812	PHF13	1
XM_937998	LOC123855	1
XM_063871	LOC123855	1
NM_014667	VGLL4	1
NM_144575	CAPN13	1
NM_012435	SHC2	1
NM_004455	EXTL1	1
NM_003255	TIMP2	1
XM_001132362	TIMP2	1
XM_943592	LOC649130	1
XM_931990	LOC644058	1
NM_001005404	YPEL2	1
XM_498491	LOC439994	1
NM_013435	RAX	1
NM_012121	CDC42EP4	1
XM_930748	LOC642361	1
NM_144578	C14orf32	1
NM_004472	FOXD1	1
NM_030576	LIMD2	1
NM_000719	CACNA1C	1
NM_033093	TRIM5	1
NM_033034	TRIM5	1
NM_199206	TCL1B	1
NM_004918	TCL1B	1
NM_017813	IMPAD1	1
NM_213649	SFXN4	1
NM_001102	ACTN1	1
NM_030759	NRBF2	1
NM_006658	C7orf16	1
NM_024114	TRIM48	1
XM_001125875	LOC727818	1
XM_379228	LOC401093	1
XM_944985	LOC401093	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