VIRsiRNAdb

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

16 hits were found for UCGCUUCACCUCUGCACGU (7 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

4640

4658

c

a

G

C

U

U

C

A

C

C

U

C

U

G

C

A

C

u

a

78

4

15

ac

false

<90%

5720

XR_019630

LOC391718

634

652

a

C

G

C

U

U

C

A

C

C

U

C

U

G

C

c

C

c

a

64

4

14

c

false

<90%

1392

XR_016226

LOC391718

634

652

a

C

G

C

U

U

C

A

C

C

U

C

U

G

C

c

C

c

c

64

4

14

c

false

<90%

1392

NM_005957

MTHFR

5286

5304

c

C

G

C

U

U

C

A

C

C

c

C

U

G

C

A

C

u

U

34

3

9

c

false

<90%

7105

XR_019511

LOC652817

973

991

c

C

G

C

U

U

C

c

C

C

U

C

U

G

C

A

C

a

g

28

4

9

c

false

<90%

2721

NM_003123

SPN

2996

3014

g

C

G

C

U

U

C

c

C

C

a

C

U

G

C

A

C

G

U

-25

3

8

c

false

<90%

6871

NM_001030288

SPN

3040

3058

g

C

G

C

U

U

C

c

C

C

a

C

U

G

C

A

C

G

U

-25

3

8

c

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

3103

3121

g

u

G

U

G

C

A

G

A

G

G

U

G

A

A

G

C

c

u

78

4

15

ac

false

<90%

8097

NM_173076

ABCA12

4118

4136

g

u

G

U

G

C

A

G

A

G

G

U

G

A

A

G

C

c

u

78

4

15

ac

false

<90%

9112

NM_001039141

TRIOBP

4046

4064

c

C

G

U

G

C

A

G

A

G

G

U

G

g

A

G

C

G

c

73

3

12

c

false

<90%

10024

NM_004585

RARRES3

231

249

c

a

G

U

G

C

A

G

A

G

G

U

G

A

A

a

C

G

g

55

4

13

c

false

<90%

768

NM_004335

BST2

403

421

g

u

c

U

G

C

A

G

A

G

G

U

G

g

A

G

C

G

A

47

4

10

c

false

<90%

983

XM_001128928

USP18

278

296

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

u

24

3

7

false

<90%

690

XM_937988

USP41

203

221

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

u

24

3

7

false

<90%

999

XM_036729

USP41

212

230

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

u

24

3

7

false

<90%

1949

NM_017414

USP18

616

634

A

C

G

a

G

C

A

G

A

G

G

a

G

A

A

G

C

G

u

24

3

7

false

<90%

2054

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 350
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_032840	SPRYD3	2
NM_014280	DNAJC8	2
NM_203327	SLC23A2	2
NM_005116	SLC23A2	2
NM_020714	ZNF490	2
NM_018159	NUDT11	1
NM_000332	ATXN1	1
NM_194318	B3GALTL	1
NM_004854	CHST10	1
NM_152569	C9orf66	1
NM_017694	FLJ20160	1
NM_020709		1
NM_001034841	LOC162073	1
NM_024596	MCPH1	1
NM_005910	MAPT	1
NM_016841	MAPT	1
NM_016834	MAPT	1
NM_016835	MAPT	1
NM_001040455	SIDT2	1
NM_015553	PIP3-E	1
NM_182548	LHFPL5	1
NM_000447	PSEN2	1
NM_012486	PSEN2	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_030787	CFHR5	1
NM_001009984		1
NM_022153	C10orf54	1
XM_379029	LOC400879	1
NM_014286	FREQ	1
XM_001126700	LOC728147	1
XM_001126645	LOC730638	1
NM_002110	HCK	1
NM_018361	AGPAT5	1
NM_024311	MFSD11	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
NM_001451	FOXF1	1
XM_001131577	FLJ36644	1
XM_001126095	FLJ36644	1
NM_022912	REEP1	1
NM_178275	DKFZp434B1231	1
NM_014240	LIMD1	1
NM_078476	BTN2A1	1
NM_001991	EZH1	1
NM_016176	SDF4	1
NM_016547	SDF4	1
NM_198458	ZNF497	1
NM_001334	CTSO	1
NM_000738	CHRM1	1
NM_198513	PHF20L1	1
NM_003731	SSNA1	1
NM_001085429		1
NM_001017523	BTBD11	1
NM_001018072	BTBD11	1
NM_001033930	UBA52	1
NM_003333	UBA52	1
NM_020126	SPHK2	1
NM_182487	OLFML2A	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_016399	TRIAP1	1
NM_004393	DAG1	1
NM_006079	CITED2	1
NM_031277	RNF17	1
NM_031476	CRISPLD2	1
NM_005226	EDG3	1
XM_001131308	LOC730961	1
NM_006035	CDC42BPB	1
NM_004758	BZRAP1	1
NM_001009899	KIAA2018	1
NM_017957	EPN3	1
NM_014961	RUFY3	1
NM_006898	HOXD3	1
NM_003060	SLC22A5	1
NM_153818	PEX10	1
NM_002617	PEX10	1
NM_153607	LOC153222	1
XM_001130728	C20orf119	1
XM_001131956	C20orf119	1
NM_001083621	ZBTB40	1
NM_014870	ZBTB40	1
NM_134431	SLCO1A2	1
NM_021094	SLCO1A2	1
NM_003816	ADAM9	1
NM_001005845	ADAM9	1
NM_006087	TUBB4	1
NM_003023	SH3BP2	1
NM_006657	FTCD	1
NM_020918	GPAM	1
NM_001076787	TP53I11	1
NM_006034	TP53I11	1
NM_000843	GRM6	1
NM_198399	ARPP-21	1
NM_001025069	ARPP-21	1
NM_001025068	ARPP-21	1
NM_018440	PAG1	1
NM_198995	C18orf34	1
NM_001105528		1
NM_152914	MGC33894	1
NM_006160	NEUROD2	1
NM_139280	ORMDL3	1
NM_000915	OXT	1
NM_001007156	NTRK3	1
NM_201628	FLJ43806	1
NM_003277	CLDN5	1
NM_175852	TXLNA	1
NM_021575	AP2S1	1
NM_004069	AP2S1	1
NM_152988	SPPL2B	1
NM_001077238	SPPL2B	1
NM_017857	SSH3	1
XM_001128998	BRUNOL4	1
NM_020180	BRUNOL4	1
NM_002639	SERPINB5	1
NM_080550	AP1GBP1	1
NM_007247	AP1GBP1	1
NM_002221	ITPKB	1
XM_376305	DUB3	1
NM_002021	FMO1	1
NM_152374	FLJ38984	1
NM_018400	SCN3B	1
NM_001040151	SCN3B	1
NM_001033518	WIPI2	1
NM_001033519	WIPI2	1
NM_015610	WIPI2	1
NM_001033520	WIPI2	1
NM_016003	WIPI2	1
NM_194071	CREB3L2	1
NM_014303	PES1	1
NM_213645	WARS	1
NM_004184	WARS	1
NM_173701	WARS	1
NM_213646	WARS	1
NM_007078	LDB3	1
NM_001080114	LDB3	1
NM_014754	PTDSS1	1
NM_145867	LTC4S	1
NM_005336	HDLBP	1
NM_203346	HDLBP	1
XM_943034	LOC643085	1
XM_931304	LOC643085	1
NM_004745	DLGAP2	1
XM_001127597	FLJ32810	1
XM_001127587	FLJ32810	1
XM_925815	FLJ32810	1
XM_001127637	FLJ32810	1
XM_001127623	FLJ32810	1
NM_152219	GJC1	1
NM_003528	HIST2H2BE	1
NM_016532	SKIP	1
NM_130766	SKIP	1
NM_014874	MFN2	1
NM_006060	IKZF1	1
NM_000598	IGFBP3	1
NM_001013398	IGFBP3	1
NM_001042633	SNX21	1
NM_033421	SNX21	1
NM_001042632	SNX21	1
NM_152897	SNX21	1
NM_019116	UBFD1	1
NM_001556	IKBKB	1
NM_021978	ST14	1
NM_178858	SFXN2	1
NM_000362	TIMP3	1
NM_012483	GNLY	1
NM_006433	GNLY	1
NM_019089	HES2	1
NM_012321	LSM4	1
NM_003901	SGPL1	1
NM_021943	ZFAND3	1
NM_003889	NR1I2	1
NM_022002	NR1I2	1
NM_033013	NR1I2	1
NM_003617	RGS5	1
NM_018646	TRPV6	1
XM_001126541	TRPV6	1
NM_014571	HEYL	1
NM_138464		1
NM_173587	RCOR2	1
NM_152437	ZNF664	1
NM_016263	FZR1	1
NM_002339	LSP1	1
NM_001013255	LSP1	1
NM_001013253	LSP1	1
NM_001013254	LSP1	1
XM_001133004	LOC728809	1
NM_003255	TIMP2	1
XM_001132362	TIMP2	1
NM_001124	ADM	1
NM_001099278		1
NM_052870	SNAG1	1
NM_020822	KCNT1	1
NM_001113239		1
NM_022740	HIPK2	1
NM_002417	MKI67	1
XM_944097	LOC389641	1
XM_374260	LOC389641	1
NM_152441	FBXL14	1
NM_001031681	CTNS	1
NM_004937	CTNS	1
NM_015219	EXOC7	1
NM_001013839	EXOC7	1
NM_133509	RAD51L1	1
NM_144993		1
NM_001040446	MTMR12	1
NM_001996	FBLN1	1
NM_024301	FKRP	1
NM_001039885	FKRP	1
NM_019067	GNL3L	1
NM_023067	FOXL2	1
NM_004101	F2RL2	1
NM_020405	PLXDC1	1
NM_177550	SLC13A5	1
NM_015046	SETX	1
NM_003099	SNX1	1
NM_152826	SNX1	1
NM_148955	SNX1	1
NM_025179	PLXNA2	1
NM_025072	PTGES2	1
NM_198940	PTGES2	1
NM_198938	PTGES2	1
XM_377073	LOC376475	1
NM_000259	MYO5A	1
NM_001017416	USP1	1
NM_001017415	USP1	1
NM_003368	USP1	1
NM_022893	BCL11A	1
NM_144582	TEX261	1
NM_001009993	LOC130074	1
NM_004781	VAMP3	1
NM_007353	GNA12	1
NM_183065	TMEM107	1
NM_032354	TMEM107	1
NM_001040283	DMRTC2	1
XM_001130790	KIAA1881	1
NM_001080400	KIAA1881	1
NM_001003800	BICD2	1
NM_024784	ZBTB3	1
NM_030961	TRIM56	1
NM_033129	SCRT2	1
NM_001102421		1
NM_001102420		1
NM_006007	ZFAND5	1
NM_003644	GAS7	1
NM_201432	GAS7	1
NM_201433	GAS7	1
NM_002756	MAP2K3	1
NM_145109	MAP2K3	1
XM_939919	LOC650832	1
NM_030665	RAI1	1
NM_014494	TNRC6A	1
NM_144635	FAM131A	1
NM_002062	GLP1R	1
NM_006212	PFKFB2	1
XM_942072	CPN2	1
NM_001080513	CPN2	1
NM_024544	C1orf166	1
NM_001105529		1
NM_006095	ATP8A1	1
NM_004651	USP11	1
XM_496575	FLJ14082	1
XM_936846	FLJ14082	1
NM_001040653	ZXDC	1
NM_024794	ABHD9	1
NM_014622	LOH11CR2A	1
NM_199332	HOMER2	1
NM_004839	HOMER2	1
NM_199331	HOMER2	1
NM_199330	HOMER2	1
NM_015229	KIAA0664	1
NM_033133	CNP	1
NM_018263	ASXL2	1
NM_012448	STAT5B	1
NM_003926	MBD3	1
XM_001133679	LOC729264	1
XM_001133677	LOC729264	1
NM_001099687		1
XM_001133686	LOC729355	1
NM_016212	TP53TG3	1
NM_004772	C5orf13	1
NM_001387	DPYSL3	1
NM_001711	BGN	1
NM_024516	C16orf53	1
NM_207037	TCF12	1
NM_003205	TCF12	1
NM_207040	TCF12	1
NM_207036	TCF12	1
NM_207038	TCF12	1
NM_014216	ITPK1	1
NM_018218	USP40	1
NM_014661	FAM53B	1
NM_017552		1
NM_173804	TMEM86B	1
NM_001029880	SFMBT2	1
NM_001759	CCND2	1
NM_023076	C16orf28	1
NM_003840	TNFRSF10D	1
NM_005932	MIPEP	1
NM_024561	NARG1L	1
NM_024577	SH3TC2	1
NM_001005920	LOC339123	1
NM_024336	IRX3	1
NM_153213	ARHGEF19	1
NM_053056	CCND1	1
NM_022041	GAN	1
NM_001110781		1
XM_933796	SLC45A4	1
NM_001621	AHR	1
NM_182472	EPHA5	1
NM_004439	EPHA5	1
XM_379078	FLJ41481	1
XM_944401	FLJ41481	1
NM_014786	ARHGEF17	1
XM_926382	LOC642755	1
NM_005902	SMAD3	1
NM_001296	CCBP2	1
NM_020335	VANGL2	1
NM_153038	FLJ32447	1
NM_006235	POU2AF1	1
NM_145257	C1orf96	1
NM_002997	SDC1	1
NM_001006946	SDC1	1
NM_001039569	AP1S3	1
NM_033637	BTRC	1
NM_003939	BTRC	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_004992	MECP2	1
NM_015348		1
NM_015646	RAP1B	1
NM_001010942	RAP1B	1
NM_001089704		1
NM_002509	NKX2-2	1
NM_005927	MFAP3	1
NM_006216	SERPINE2	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