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 CGCACCGGGGAUCCUAGGC (2 guide strand hits and 5 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_001877

CR2

136

154

C

G

C

A

C

C

G

G

G

G

g

U

C

C

U

c

G

G

g

7

3

10

c

false

<90%

3982

NM_001006658

CR2

136

154

C

G

C

A

C

C

G

G

G

G

g

U

C

C

U

c

G

G

g

7

3

10

c

false

<90%

4159

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_001077621

VPS37D

870

888

c

g

g

U

A

G

G

A

U

C

C

a

C

G

G

U

G

C

G

33

4

8

false

<90%

1609

XM_943032

LOC647805

685

703

G

C

C

U

A

G

c

A

U

C

C

a

C

G

G

U

G

C

G

0

2

7

false

<90%

1182

NM_021872

CDC25B

896

914

u

C

C

U

g

G

G

g

U

C

C

C

C

G

G

U

G

C

G

-15

3

11

bc

false

<90%

3578

NM_004358

CDC25B

896

914

u

C

C

U

g

G

G

g

U

C

C

C

C

G

G

U

G

C

G

-15

3

11

bc

false

<90%

3659

NM_021873

CDC25B

896

914

u

C

C

U

g

G

G

g

U

C

C

C

C

G

G

U

G

C

G

-15

3

11

bc

false

<90%

3701

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 168
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_014844	KIAA0329	3
NM_001031617	COX19	2
NM_001040661	SLC29A4	2
NM_153247	SLC29A4	2
NM_001560	IL13RA1	1
NM_139159	DPP9	1
NM_001042574	CRTC3	1
NM_022769	CRTC3	1
NM_004114	FGF13	1
NM_033642	FGF13	1
NM_001044370	MPPED1	1
NM_002375	MAP4	1
NM_030884	MAP4	1
XM_495918	FLJ13224	1
XM_938169	FLJ13224	1
XM_931281	LOC643072	1
XM_943769	LOC643072	1
NM_207348	SLC25A34	1
NM_001039577	CCNL2	1
NM_004992	MECP2	1
XM_001130238	LOC728283	1
XM_001132687	LOC731087	1
XM_938028	C19orf16	1
NM_000080	CHRNE	1
XM_001132270	LOC730001	1
XM_001131474	LOC730341	1
XM_001131575	LOC731897	1
NM_178448	C9orf140	1
NM_207396	RNF207	1
NM_176871	PDLIM2	1
NM_001082575	HRNBP3	1
NM_013304	ZDHHC1	1
NM_000278	PAX2	1
NM_003989	PAX2	1
NM_003990	PAX2	1
NM_003987	PAX2	1
NM_003988	PAX2	1
NM_153256	C10orf47	1
NM_002688	SEPT5	1
NM_182551	LYCAT	1
NM_001002257	LYCAT	1
NM_005061	RPL3L	1
NM_152219	GJC1	1
NM_173476	CCDC78	1
XM_001128427	LOC728768	1
XM_940977	LOC651758	1
NM_024919	FRMD1	1
NM_001037	SCN1B	1
NM_001008407	BCAP29	1
NM_000832	GRIN1	1
NM_007327	GRIN1	1
NM_021569	GRIN1	1
NM_005036	PPARA	1
NM_001001928	PPARA	1
NM_206833	CTXN1	1
XM_936809	LOC342918	1
XM_292779	LOC342918	1
NM_001042573	FLJ21865	1
NM_005806	OLIG2	1
NM_024329	EFHD2	1
NM_005170	ASCL2	1
NM_001039966	GPR30	1
NM_001505	GPR30	1
NM_001098201		1
NM_020134	DPYSL5	1
NM_016155	MMP17	1
XM_001133320	MMP17	1
NM_001043318	C14orf43	1
NM_194278	C14orf43	1
NM_001045477	FAM22G	1
NM_001846	COL4A2	1
NM_002105	H2AFX	1
XM_930750	LOC642366	1
XM_943652	LOC642366	1
NM_058192	RPUSD1	1
NM_199461	NANOS1	1
NM_001420	ELAVL3	1
NM_032281	ELAVL3	1
NM_002861	PCYT2	1
NM_005226	EDG3	1
NM_012140	SLC25A10	1
NM_005883	APC2	1
NM_198253	TERT	1
NM_198255	TERT	1
XM_495939	KIAA1545	1
XM_936428	KIAA1545	1
NM_006645	STARD10	1
NM_006224	PITPNA	1
NM_024877	CNTD2	1
NM_198850	PHLDB3	1
XM_928224	LOC653583	1
XM_001131797	LOC732075	1
NM_002342	LTBR	1
NM_020230	PPAN	1
XM_931359	LOC338758	1
XM_944677	LOC338758	1
NM_053045	MGC14327	1
XM_936119	LOC642044	1
XM_936165	LOC642075	1
XM_933843	LOC646720	1
XM_945002	LOC651895	1
NM_005479	FRAT1	1
NM_001085377		1
NM_002387	MCC	1
NM_015461	ZNF521	1
NM_014964	EPN2	1
NM_001102664		1
NM_148921	EPN2	1
NM_032389	ZNF289	1
XM_001134463	BAHCC1	1
NM_001080519	BAHCC1	1
XM_936831	IQSEC3	1
NM_014665	LRRC14	1
NM_006943	SOX12	1
NM_032737	LMNB2	1
NM_001004439	ITGA11	1
XM_932244	LOC653160	1
XM_945233	LOC653160	1
NM_001029885	MGC10334	1
NM_182553	CNIH2	1
XM_001129488	CNIH2	1
NM_207333	ZNF320	1
NM_207419	C1QTNF8	1
NM_020908		1
NM_005078	TLE3	1
NM_001105192		1
NM_000151	G6PC	1
NM_004286	GTPBP1	1
NM_001018070	CORO1B	1
NM_020441	CORO1B	1
NM_000748	CHRNB2	1
XM_933935	LOC646778	1
XM_943239	LOC646778	1
NM_014661	FAM53B	1
NM_031215	CABLES2	1
NM_002911	UPF1	1
NM_000599	IGFBP5	1
NM_013435	RAX	1
NM_018027	FRMD4A	1
NM_019884	GSK3A	1
NM_145685	BRF1	1
NM_001519	BRF1	1
NM_001049	SSTR1	1
NM_178500	PHOSPHO1	1
NM_152494	DCST1	1
NM_021025	TLX3	1
NM_017953	C1orf181	1
NM_178167	ZNF598	1
NM_130459	TOR2A	1
NM_181804	PKIG	1
NM_181805	PKIG	1
NM_007066	PKIG	1
NM_001495	GFRA2	1
NM_032246	RKHD3	1
NM_001024227	ARF1	1
NM_001658	ARF1	1
NM_001024228	ARF1	1
NM_001024226	ARF1	1
NM_020132	AGPAT3	1
NM_001037553	AGPAT3	1
NM_000629	IFNAR1	1
NM_004535	MYT1	1
NM_001042413	GLIS3	1
NM_152629	GLIS3	1
NM_003648	DGKD	1
NM_152879	DGKD	1
NM_001040701	FUT6	1
NM_000150	FUT6	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