VIRsiRNAdb

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

20 hits were found for AUCGGCCCUGAAGUAUGAG (10 guide strand hits and 10 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_173833

SCARA5

605

623

g

U

C

G

G

C

C

C

U

G

A

A

G

c

A

U

G

c

u

70

4

12

c

false

<90%

3643

NM_002646

PIK3C2B

3248

3266

A

c

a

G

G

C

C

C

U

G

A

A

G

U

A

U

G

A

a

64

3

15

bc

false

<90%

7618

NM_020800

IFT80

3773

3791

A

U

a

G

G

C

C

C

U

G

A

A

G

U

c

U

G

A

a

50

3

11

c

false

<90%

4314

NM_013312

HOOK2

944

962

A

c

a

G

G

C

C

C

U

G

A

A

G

g

A

U

G

A

G

49

3

10

c

false

<90%

2531

NM_003704

C4orf8

1359

1377

c

a

u

G

G

C

C

C

U

G

A

A

G

g

A

U

G

A

G

47

4

10

c

false

<90%

4742

NM_004066

CETN1

784

802

A

a

g

G

G

C

C

C

U

G

A

A

G

U

u

U

G

A

G

44

3

11

c

false

<90%

1161

XR_019146

LOC651439

1232

1250

c

c

a

G

G

C

C

C

a

G

A

A

G

U

A

U

G

A

G

6

4

10

bc

false

<90%

1451

XR_016729

LOC122592

1232

1250

c

c

a

G

G

C

C

C

a

G

A

A

G

U

A

U

G

A

G

6

4

10

bc

false

<90%

1451

XR_018906

LOC399965

1483

1501

c

c

a

G

G

C

C

C

a

G

A

A

G

U

A

U

G

A

G

6

4

10

bc

false

<90%

1705

XR_016979

LOC399965

1483

1501

c

c

a

G

G

C

C

C

a

G

A

A

G

U

A

U

G

A

G

6

4

10

bc

false

<90%

1705

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_152926

CPNE1

1655

1673

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

1954

NM_152925

CPNE1

1697

1715

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

1996

NM_152928

CPNE1

1750

1768

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

2049

NM_152927

CPNE1

1782

1800

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

2081

NM_152929

CPNE1

1798

1816

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

2097

NM_152931

CPNE1

1893

1911

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

2192

NM_003915

CPNE1

1912

1930

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

2211

NM_152930

CPNE1

1925

1943

C

U

C

A

U

A

C

U

U

C

A

G

G

G

C

C

c

A

g

71

2

16

ac

false

<90%

2224

XM_290546

ENDOD1

1268

1286

C

U

C

A

U

A

C

U

U

C

A

u

G

G

C

C

a

u

U

40

3

11

false

<90%

4693

XM_937098

ENDOD1

1268

1286

C

U

C

A

U

A

C

U

U

C

A

u

G

G

C

C

a

u

U

40

3

11

false

<90%

4694

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 260
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_002536	TBC1D25	2
NM_001017392	SFRS14	2
NM_004220	ZNF213	2
NM_020910		2
NM_000990	RPL27A	2
NM_021006	CCL3L1	2
NM_001001437	CCL3L3	2
XM_001133177	LOC728830	2
XM_001123374	LOC730422	2
NM_015393	DKFZP564O0823	1
NM_001030288	SPN	1
NM_003123	SPN	1
XM_937862	LOC644962	1
NM_015044	GGA2	1
NM_001102421		1
NM_001102420		1
NM_006007	ZFAND5	1
NM_001018065	NTRK2	1
NM_001018066	NTRK2	1
NM_001546	ID4	1
NM_004431	EPHA2	1
NM_032019	HDAC10	1
NM_020207	C9orf102	1
NM_006387	CHERP	1
NM_000876	IGF2R	1
NM_024052	C17orf39	1
NM_001707	BCL7B	1
NM_000330	RS1	1
NM_005291	GPR17	1
NM_177401	MIDN	1
NM_015144	ZCCHC14	1
NM_020655	JPH3	1
NM_018899	PCDHAC2	1
NM_018900	PCDHA1	1
NM_018902	PCDHA11	1
NM_031849	PCDHA6	1
NM_018905	PCDHA2	1
NM_018904	PCDHA13	1
NM_031860	PCDHA10	1
NM_018907	PCDHA4	1
NM_018909	PCDHA6	1
NM_018910	PCDHA7	1
NM_018911	PCDHA8	1
NM_018906	PCDHA3	1
NM_018903	PCDHA12	1
NM_018898	PCDHAC1	1
NM_031857	PCDHA9	1
NM_031411	PCDHA1	1
NM_018908	PCDHA5	1
NM_018901	PCDHA10	1
NM_001814	CTSC	1
NM_001039570	KREMEN1	1
NM_001039571	KREMEN1	1
NM_152371	C1orf93	1
NM_194434	VAPA	1
NM_003574	VAPA	1
NM_001271	CHD2	1
NM_017628	KIAA1546	1
NM_032452	JPH4	1
NM_001001549	GRB10	1
NM_001001555	GRB10	1
NM_001001550	GRB10	1
NM_005311	GRB10	1
NM_182919	TICAM1	1
NM_004360	CDH1	1
NM_019072	SGTB	1
NM_181809	BMP8A	1
NM_182557	BCL9L	1
NM_030631	SLC25A21	1
NM_001688	ATP5F1	1
NM_007024	TMEM115	1
NM_212464	CAPN3	1
NM_212467	CAPN3	1
NM_004655	AXIN2	1
NM_020151	STARD7	1
NM_006206	PDGFRA	1
NM_015458	MTMR9	1
NM_002427	MMP13	1
NM_002265	KPNB1	1
NM_006256	PKN2	1
NM_001080395	AATK	1
NM_012419	RGS17	1
NM_001080480	MBOAT1	1
XM_001131050	MBOAT1	1
XM_001131044	MBOAT1	1
NM_003748	ALDH4A1	1
NM_182501	MTERFD2	1
NM_001103147		1
NM_001103148		1
NM_001103146		1
NM_015575	TNRC15	1
NM_174911	FAM84B	1
NM_133264	WIPF2	1
NM_006234	POLR2J	1
NM_032801	JAM3	1
NM_032823	C9orf3	1
NM_000376	VDR	1
NM_001017535	VDR	1
NM_004024	ATF3	1
NM_001040619	ATF3	1
NM_019032	ADAMTSL4	1
NM_004419	DUSP5	1
NM_002337	LRPAP1	1
NM_001042633	SNX21	1
NM_001042632	SNX21	1
NM_022463	NXN	1
NM_005578	LPP	1
XM_001129151	LOC729047	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
XM_001134396	LOC730254	1
NM_004933	CDH15	1
XM_379636	C9orf122	1
XM_940165	C9orf122	1
NM_014975	MAST1	1
NM_181671	PITPNC1	1
XM_496115	LOC440338	1
XM_940659	LOC440338	1
NM_206918	DEGS2	1
NM_144628	TBC1D20	1
NM_003255	TIMP2	1
XM_001132362	TIMP2	1
NM_005934	MLLT1	1
XM_001130242	LOC729433	1
NM_018201	TBC1D13	1
NM_005873	RGS19	1
NM_001039467	RGS19	1
NM_001015	RPS11	1
NM_005883	APC2	1
NM_000875	IGF1R	1
NM_001002295	GATA3	1
NM_002051	GATA3	1
NM_023931	ZNF747	1
NM_018409	LRP2BP	1
NM_012405	ICMT	1
XM_929878	LOC646915	1
NM_002319	LRCH4	1
NM_023072	ZSWIM4	1
NM_001083913	C10orf26	1
NM_017787	C10orf26	1
NM_001080950	MYO1C	1
NM_033375	MYO1C	1
NM_001080779	MYO1C	1
NM_006640	SEPT9	1
NM_206909	PSD3	1
NM_015310	PSD3	1
XM_943502	LOC646576	1
XM_933718	LOC646576	1
NM_014160	MKRN2	1
NM_004928	C21orf2	1
NM_000068	CACNA1A	1
NM_021008	DEAF1	1
XM_001129197	DEAF1	1
NM_001080113	PP8961	1
NM_145003	TSNARE1	1
NM_024297	PHF23	1
NM_205845	AKR1C2	1
NM_001354	AKR1C2	1
NM_006734	HIVEP2	1
NM_152361	EID2B	1
XM_946142	SHANK3	1
NM_001080420	SHANK3	1
NM_003704	C4orf8	1
NM_018367	PHCA	1
NM_018715	RCC2	1
NM_015313	ARHGEF12	1
NM_018953	HOXC5	1
NM_004441	EPHB1	1
XM_001133309	LOC729305	1
XM_001131633	LOC732024	1
NM_145173	DIRAS1	1
NM_001008539	SLC7A2	1
NM_003046	SLC7A2	1
NM_182663	RASSF5	1
NM_182664	RASSF5	1
NM_182665	RASSF5	1
NM_058219	EXOSC6	1
NM_014106	ZNF770	1
NM_080876	DUSP19	1
NM_013304	ZDHHC1	1
NM_000795	DRD2	1
NM_016574	DRD2	1
NM_016498	MTP18	1
NM_181333	PRR5	1
NM_001017530	PRR5	1
NM_015366	PRR5	1
NM_001017528	PRR5	1
NM_001017529	PRR5	1
NM_000525	KCNJ11	1
NM_001040285	PAPD5	1
NM_001040284	PAPD5	1
NM_024652	LRRK1	1
NM_015385	SORBS1	1
NM_001034954	SORBS1	1
NM_001034957	SORBS1	1
NM_001034955	SORBS1	1
NM_001034956	SORBS1	1
NM_006434	SORBS1	1
NM_024991	SORBS1	1
NM_003901	SGPL1	1
NM_001287	CLCN7	1
NM_030630	C17orf28	1
NM_175064	WBSCR19	1
NM_001099435		1
NM_001031618	MGC119295	1
XM_001127525	LOC730307	1
XM_496899	LOC441258	1
XM_929470	LOC643909	1
XM_001127430	LOC730304	1
XM_499348	MGC57359	1
XM_499356	LOC442609	1
XM_935540	LOC442609	1
NM_001004351	MGC57359	1
NM_152504	C20orf196	1
NM_015681	EPPB9	1
NM_033212	CCDC102A	1
NM_012398	PIP5K1C	1
NM_017413	APLN	1
NM_031455	CCDC3	1
NM_002406	MGAT1	1
NM_213649	SFXN4	1
NM_001002836	ZNF787	1
NM_017443	POLE3	1
NM_001010974	BCAS4	1
NM_198799	BCAS4	1
NM_017843	BCAS4	1
NM_005935	AFF1	1
NM_002983	CCL3	1
NM_144775	SMCR8	1
NM_000944	PPP3CA	1
NM_001014450	SPRR2F	1
NM_003288	TPD52L2	1
NM_199359	TPD52L2	1
NM_199362	TPD52L2	1
NM_199360	TPD52L2	1
NM_199363	TPD52L2	1
NM_199361	TPD52L2	1
NM_012392	PEF1	1
NM_018941	CLN8	1
XM_001130495	LOC728429	1
NM_001039615	LOC440053	1
XM_001130086	LOC728957	1
NM_001004328	ZNF705A	1
NM_014333	CADM1	1
NM_001098517		1
NM_032664	FUT10	1
NM_020846		1
NM_000682	ADRA2B	1
NM_014734	KIAA0247	1
NM_181351	NCAM1	1
NM_000615	NCAM1	1
NM_003470	USP7	1
NM_003042	SLC6A1	1
NM_002957	RXRA	1
NM_003688	CASK	1
NM_021943	ZFAND3	1
NM_152233	SNX6	1
NM_021249	SNX6	1
NM_006717	SPIN1	1
NM_002581	PAPPA	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