VIRsiRNAdb

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

17 hits were found for CGCUUCACCUCUGCACGUC (8 guide strand hits and 9 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_017709

FAM46C

4641

4659

a

G

C

U

U

C

A

C

C

U

C

U

G

C

A

C

u

a

a

66

4

15

ac

false

<90%

5720

XR_019630

LOC391718

635

653

C

G

C

U

U

C

A

C

C

U

C

U

G

C

c

C

c

a

a

44

4

14

c

false

<90%

1392

XR_016226

LOC391718

635

653

C

G

C

U

U

C

A

C

C

U

C

U

G

C

c

C

c

c

a

44

4

14

c

false

<90%

1392

XM_001126826

LOC730695

436

454

C

G

C

U

U

C

A

C

C

U

C

U

G

C

c

g

a

c

C

23

4

14

c

false

<90%

507

XR_019511

LOC652817

974

992

C

G

C

U

U

C

c

C

C

U

C

U

G

C

A

C

a

g

u

2

4

9

c

false

<90%

2721

NM_005957

MTHFR

5287

5305

C

G

C

U

U

C

A

C

C

c

C

U

G

C

A

C

u

U

C

-6

2

9

c

false

<90%

7105

NM_003123

SPN

2997

3015

C

G

C

U

U

C

c

C

C

a

C

U

G

C

A

C

G

U

u

-54

3

8

bc

false

<90%

6871

NM_001030288

SPN

3041

3059

C

G

C

U

U

C

c

C

C

a

C

U

G

C

A

C

G

U

u

-54

3

8

bc

false

<90%

6915

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_015657

ABCA12

3104

3122

G

g

u

G

U

G

C

A

G

A

G

G

U

G

A

A

G

C

c

64

3

15

bc

false

<90%

8097

NM_173076

ABCA12

4119

4137

G

g

u

G

U

G

C

A

G

A

G

G

U

G

A

A

G

C

c

64

3

15

bc

false

<90%

9112

NM_001039141

TRIOBP

4045

4063

G

c

C

G

U

G

C

A

G

A

G

G

U

G

g

A

G

C

G

63

2

12

c

false

<90%

10024

NM_004585

RARRES3

232

250

a

c

a

G

U

G

C

A

G

A

G

G

U

G

A

A

a

C

G

43

4

13

c

false

<90%

768

XM_001128928

USP18

278

296

G

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

38

2

7

false

<90%

690

XM_937988

USP41

203

221

G

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

38

2

7

false

<90%

999

XM_036729

USP41

212

230

G

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

38

2

7

false

<90%

1949

NM_017414

USP18

616

634

G

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

38

2

7

false

<90%

2054

NM_014632

MICAL2

3491

3509

G

A

C

G

g

G

C

A

G

A

G

u

U

G

A

A

G

C

a

9

3

6

false

<90%

3934

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 397
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
XM_001128998	BRUNOL4	3
NM_005955	MTF1	2
XM_944835	LOC648691	2
NM_001004432	LINGO4	2
XM_001127950	LOC730566	2
XM_001133333	LOC729172	2
NM_002581	PAPPA	1
NM_006617	NES	1
NM_001102576		1
NM_153478	CSAG1	1
NM_004909	CSAG2	1
NM_001080848	CSAG2	1
NM_152624	DCP2	1
NM_005065	SEL1L	1
NM_018159	NUDT11	1
NM_015241		1
XM_001128811	LOC731210	1
NM_199000	LHFPL3	1
XM_001133975	LOC729918	1
XM_001134047	LOC732127	1
NM_032153	ZIC4	1
NM_000891	KCNJ2	1
NM_000332	ATXN1	1
NM_032940	POLR2C	1
NM_001419	ELAVL1	1
NM_005990	STK10	1
NM_005333	HCCS	1
NM_002651	PIK4CB	1
XM_946032	LOC644852	1
XM_934218	LOC644852	1
NM_003870	IQGAP1	1
NM_001008539	SLC7A2	1
NM_003046	SLC7A2	1
NM_194318	B3GALTL	1
NM_130440	PTPRF	1
NM_002840	PTPRF	1
NM_000735	CGA	1
NM_004854	CHST10	1
NM_152569	C9orf66	1
NM_001104544		1
NM_001104545		1
NM_017938	FAM70A	1
NM_000566	FCGR1A	1
NM_014904	RAB11FIP2	1
NM_001634	AMD1	1
NM_001033059	AMD1	1
NM_198066	GNPNAT1	1
NM_003108	SOX11	1
NM_020180	BRUNOL4	1
NM_138704	NDNL2	1
NM_004958	FRAP1	1
NM_001002860	BTBD7	1
NM_001007257	PRDM2	1
NM_015866	PRDM2	1
NM_178457	C20orf174	1
NM_017694	FLJ20160	1
NM_013435	RAX	1
NM_003284	TNP1	1
NM_015033	FNBP1	1
NM_001076682	NCAM1	1
XM_941646	LOC649371	1
NM_022719	DGCR14	1
NM_020709		1
NM_004992	MECP2	1
NM_002666	PLIN	1
NM_138809	CMBL	1
NM_001034841	LOC162073	1
NM_005188	CBL	1
NM_032727	INA	1
NM_173511	ALS2CR13	1
NM_018019	MED9	1
NM_024596	MCPH1	1
NM_020733		1
NM_012309	SHANK2	1
NM_145798	OSBPL7	1
NM_001099267		1
NM_017728	TMEM104	1
NM_000598	IGFBP3	1
NM_001013398	IGFBP3	1
NM_005957	MTHFR	1
NM_006087	TUBB4	1
NM_005910	MAPT	1
NM_016841	MAPT	1
NM_016834	MAPT	1
NM_016835	MAPT	1
XM_929947	LOC646976	1
XM_939981	LOC646976	1
XM_927936	LOC644841	1
XM_935685	LOC641933	1
XM_938176	LOC644841	1
NM_001040455	SIDT2	1
XM_946142	SHANK3	1
NM_001080420	SHANK3	1
NM_018193	KIAA1794	1
NM_148903	GREB1	1
NM_015553	PIP3-E	1
NM_182548	LHFPL5	1
NM_015372		1
NM_020810	TRMT5	1
NM_032280	ZCCHC9	1
NM_015074	KIF1B	1
NM_000447	PSEN2	1
NM_012486	PSEN2	1
NM_198337	INSIG1	1
NM_005542	INSIG1	1
NM_198336	INSIG1	1
NM_080797	DIDO1	1
XM_001130020	KIAA1147	1
XM_001130081	KIAA1147	1
NM_001002001	GMPR2	1
NM_016576	GMPR2	1
NM_001002000	GMPR2	1
NM_001002002	GMPR2	1
NM_024707	GEMIN7	1
NM_001007270	GEMIN7	1
NM_001007269	GEMIN7	1
NM_024705	DHRS12	1
NM_181644	MFSD4	1
NM_015141	GPD1L	1
NM_001079512	LOC780776	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_020443	NAV1	1
NM_025054	VCPIP1	1
NM_015316	PPP1R13B	1
NM_014659	HISPPD2A	1
NM_001024463	HISPPD2A	1
NM_016224	SNX9	1
NM_021628	ALOXE3	1
NM_001037967	ALAS2	1
NM_001037968	ALAS2	1
NM_001037969	ALAS2	1
NM_000032	ALAS2	1
NM_020748	INTS2	1
XM_929030	LOC161527	1
XM_933066	LOC643696	1
NM_198181	LOC440295	1
XM_001129399	LOC642346	1
XM_928707	LOC642346	1
XM_925879	LOC642346	1
XM_001130526	LOC728636	1
XM_001130555	LOC728636	1
XM_001130543	LOC728636	1
XM_001130536	LOC728636	1
XM_925864	LOC642325	1
NM_080927	DCBLD2	1
NM_000522	HOXA13	1
NM_030787	CFHR5	1
NM_018293	ZNF654	1
XM_001126706	ZNF654	1
NM_178557	NAT8L	1
XM_001130884	LOC729639	1
XM_001130664	LOC731756	1
NM_001009984		1
NM_194291	TMEM65	1
NM_199050	C21orf25	1
NM_015500	C21orf25	1
XM_032945	C21orf25	1
NM_001037	SCN1B	1
NM_002105	H2AFX	1
NM_001099642		1
NM_018348	FLJ11171	1
NM_004680	CDY1	1
NM_001003895	CDY1B	1
NM_024866	ADM2	1
NM_080392	PTP4A2	1
NM_022153	C10orf54	1
NM_001113239		1
NM_022740	HIPK2	1
NM_001079514	UBN1	1
NM_016936	UBN1	1
XM_379029	LOC400879	1
XM_934388	LOC145783	1
NM_182767	SLC6A15	1
NM_004427	PHC2	1
NM_198040	PHC2	1
NM_002582	PARN	1
NM_015306		1
NM_005270	GLI2	1
NM_014286	FREQ	1
NM_017933	PID1	1
NM_001100818		1
NM_002868	RAB5B	1
XM_001126700	LOC728147	1
XM_001126645	LOC730638	1
NM_033259	CAMK2N2	1
NM_014838	ZBED4	1
XM_378661	C17orf51	1
XM_944416	C17orf51	1
NM_002110	HCK	1
NM_001001396	ATP2B4	1
NM_001684	ATP2B4	1
NM_018361	AGPAT5	1
NM_001305	CLDN4	1
NM_017875	SLC25A38	1
NM_020959	TMEM16H	1
NM_014157	CCDC113	1
NM_024311	MFSD11	1
NM_173667	FLJ37543	1
NM_198488	FAM83H	1
NM_001330	CTF1	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
NM_000843	GRM6	1
NM_006413	RPP30	1
NM_001451	FOXF1	1
NM_003929	RAB7L1	1
NM_001246	ENTPD2	1
NM_203468	ENTPD2	1
NM_014293	NPTXR	1
NM_006700	TRAFD1	1
NM_024419	PGS1	1
XM_001131577	FLJ36644	1
XM_001126095	FLJ36644	1
NM_000944	PPP3CA	1
NM_001626	AKT2	1
NM_173570	ZDHHC23	1
NM_001099857		1
NM_003639	IKBKG	1
NM_001099856		1
NM_152543	FLJ25371	1
NM_003192	TBCC	1
NM_001040102	TMEM10	1
NM_033207	TMEM10	1
NM_001040103	TMEM10	1
NM_001080436	WTIP	1
XM_939855	WTIP	1
NM_007033	RER1	1
NM_022912	REEP1	1
NM_002528	NTHL1	1
NM_022344	C17orf75	1
NM_173855	MORN3	1
NM_178275	DKFZp434B1231	1
NM_019044	CCDC93	1
NM_015375	RIPK5	1
NM_199462	RIPK5	1
NM_148920	PIGQ	1
NM_004204	PIGQ	1
NM_173680	ZNF775	1
NM_004873	BAG5	1
NM_001015049	BAG5	1
NM_001015048	BAG5	1
NM_001037165	FOXK1	1
NM_014240	LIMD1	1
NM_178126	LOC162427	1
NM_001012509	SLC45A2	1
NM_078476	BTN2A1	1
NM_006645	STARD10	1
NM_001010911	C10orf114	1
NM_003893	LDB1	1
NM_194272	RBPMS2	1
NM_182970	RIMS4	1
NM_030636	KIAA1706	1
NM_016545	IER5	1
NM_001004302	ZNF783	1
NM_001991	EZH1	1
NM_017758	ALKBH5	1
NM_032173		1
NM_001100621		1
NM_017941	C17orf80	1
NM_006698	BLCAP	1
NM_015559	SETBP1	1
NM_175876	EXOC8	1
NM_013423	ARHGAP6	1
NM_001174	ARHGAP6	1
NM_013427	ARHGAP6	1
NM_030751	ZEB1	1
NM_001040105	MUC17	1
NM_016176	SDF4	1
NM_016547	SDF4	1
NM_198458	ZNF497	1
NM_206866	BACH1	1
NM_001186	BACH1	1
NM_017596	KIF21B	1
NM_020888	KIAA1522	1
NM_017650	PPP1R9A	1
NM_207401	FLJ45717	1
NM_005596	NFIB	1
NM_033405	PRIC285	1
NM_001037335	PRIC285	1
NM_002779	PSD	1
NM_001895	CSNK2A1	1
NM_177560	CSNK2A1	1
NM_177559	CSNK2A1	1
NM_152793	C7orf41	1
NM_005226	EDG3	1
NM_003610	RAE1	1
NM_001015885	RAE1	1
NM_032840	SPRYD3	1
NM_001334	CTSO	1
NM_005561	LAMP1	1
NM_000280	PAX6	1
NM_001604	PAX6	1
NM_017872	THG1L	1
NM_014280	DNAJC8	1
NM_198243	ASB7	1
NM_172060	EYA1	1
NM_000503	EYA1	1
NM_172058	EYA1	1
NM_172059	EYA1	1
NM_004087	DLG1	1
NM_001098424		1
NM_181809	BMP8A	1
NM_001011713	NAT12	1
NM_080796	DIDO1	1
NM_022105	DIDO1	1
NM_001103	ACTN2	1
NM_001083962		1
NM_003199	TCF4	1
NM_016235	GPRC5B	1
NM_000092	COL4A4	1
NM_001025	RPS23	1
NM_000738	CHRM1	1
NM_198841	FAM120AOS	1
NM_198513	PHF20L1	1
NM_016396	CTDSPL2	1
NM_000356	TCOF1	1
NM_001008656	TCOF1	1
NM_001704	BAI3	1
NM_002711	PPP1R3A	1
NM_004852	ONECUT2	1
NM_015005	KIAA0284	1
NM_001112726		1
NM_004778	GPR44	1
NM_005730	CTDSP2	1
NM_004491	GRLF1	1
NM_002760	PRKY	1
NM_005044	PRKX	1
NM_015516	TSKU	1
NM_006732	FOSB	1
XM_001128488	LOC728254	1
XM_001127513	LOC730581	1
NM_018841	GNG12	1
NM_003908	EIF2S2	1
XM_944677	LOC338758	1
XM_931359	LOC338758	1
NM_015566		1
NM_020834	HOMEZ	1
NM_203327	SLC23A2	1
NM_005116	SLC23A2	1
NM_003009	SEPW1	1
NM_003513	HIST1H2AB	1
NM_003731	SSNA1	1
NM_032357	CCDC115	1
NM_172344	KCNG3	1
NM_133329	KCNG3	1
NM_001085429		1
NM_003706	PLA2G4C	1
NM_001032280	TFAP2A	1
NM_003220	TFAP2A	1
NM_001042425	TFAP2A	1
NM_001017523	BTBD11	1
NM_001018072	BTBD11	1
NM_014981		1
XM_937523	KIAA1679	1
NM_001080427	THSD7B	1
NM_006161	NEUROG1	1
NM_001830	CLCN4	1
NM_002834	PTPN11	1
NM_018487	TMEM176A	1
NM_007203	PALM2-AKAP2	1
NM_147150	PALM2-AKAP2	1
NM_001004065	AKAP2	1
NM_000815	GABRD	1
NM_001033930	UBA52	1
NM_003333	UBA52	1
NM_001077511	TCF19	1
NM_007109	TCF19	1
NM_003916	AP1S2	1
NM_020126	SPHK2	1
NM_182487	OLFML2A	1
NM_001100427		1
NM_021159	RAP1GDS1	1
NM_001100428		1
NM_001100429		1
NM_001100426		1
NM_001100430		1
NM_017902	HIF1AN	1
NM_004220	ZNF213	1
NM_006918	SC5DL	1
NM_001024956	SC5DL	1
NM_000242	MBL2	1
NM_173199	NR4A3	1
XM_001129441	LOC645166	1
XM_946374	LSP1	1
NM_019899	ABCC1	1
NM_019862	ABCC1	1
NM_019898	ABCC1	1
NM_004996	ABCC1	1
NM_019900	ABCC1	1
NM_016399	TRIAP1	1
NM_001715	BLK	1
NM_005725	TSPAN2	1
NM_016076	C1orf121	1
NM_004393	DAG1	1
NM_006079	CITED2	1
NM_001424	EMP2	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