VIRsiRNAdb

SpecificityServer - An siRNA design program for determining siRNA specificity
Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand

22 hits were found for GACCGUGCACCAUGAGCAC (3 guide strand hits and 19 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_001037165

FOXK1

8382

8400

u

g

C

C

a

U

G

C

A

C

C

A

U

G

A

G

C

A

g

30

4

13

bc

false

<90%

11191

NM_001454

FOXJ1

1644

1662

G

A

C

C

c

U

G

C

A

C

C

A

U

G

A

G

a

g

C

22

3

11

c

false

<90%

2401

NM_014429

MORC1

1660

1678

c

A

C

u

G

g

G

C

A

C

C

A

U

G

A

G

C

A

C

-2

3

13

bc

false

<90%

3765

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_198531

ATP9B

2762

2780

c

U

G

C

U

C

A

U

G

G

U

G

C

A

C

G

G

g

C

95

2

16

ac

false

<90%

4378

NM_001025243

IRAK1

2036

2054

G

U

u

C

U

C

A

U

G

G

U

G

C

A

C

G

a

g

u

49

4

13

c

false

<90%

3352

NM_001025242

IRAK1

2183

2201

G

U

u

C

U

C

A

U

G

G

U

G

C

A

C

G

a

g

u

49

4

13

c

false

<90%

3499

NM_001569

IRAK1

2273

2291

G

U

u

C

U

C

A

U

G

G

U

G

C

A

C

G

a

g

u

49

4

13

c

false

<90%

3589

NM_022465

IKZF4

1103

1121

G

U

G

C

U

C

A

U

G

G

U

G

C

A

C

a

a

g

C

47

3

15

c

false

<90%

5506

NM_015466

PTPN23

4023

4041

c

a

G

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

30

4

13

bc

false

<90%

5283

XM_926025

LOC642536

39

57

G

a

G

C

U

C

A

U

a

G

U

G

C

A

C

G

G

U

C

28

2

10

bc

false

<90%

336

XM_937965

LOC648887

39

57

G

a

G

C

U

C

A

U

a

G

U

G

C

A

C

G

G

U

C

28

2

10

bc

false

<90%

336

NM_000120

EPHX1

705

723

u

U

G

C

U

g

A

U

G

G

U

G

C

A

C

G

G

c

u

27

4

11

c

false

<90%

1856

NM_207294

MBNL1

1546

1564

G

U

u

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

23

3

13

bc

false

<90%

5132

NM_207295

MBNL1

1582

1600

G

U

u

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

23

3

13

bc

false

<90%

5168

NM_207296

MBNL1

1596

1614

G

U

u

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

23

3

13

bc

false

<90%

5246

NM_207293

MBNL1

1804

1822

G

U

u

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

23

3

13

bc

false

<90%

5390

NM_207292

MBNL1

2803

2821

G

U

u

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

23

3

13

bc

false

<90%

6368

NM_021038

MBNL1

2839

2857

G

U

u

C

c

C

A

U

G

G

U

G

C

A

C

G

G

U

g

23

3

13

bc

false

<90%

6404

NM_014508

APOBEC3C

719

737

c

U

G

C

U

C

A

U

G

c

U

G

C

A

C

G

G

g

C

12

3

8

c

false

<90%

1127

NM_005049

PWP2

2568

2586

c

U

G

C

U

C

A

U

G

u

U

G

C

A

C

G

G

a

C

12

3

8

c

false

<90%

3277

NM_133486

MBNL3

932

950

G

U

G

C

c

C

A

U

G

a

U

G

C

A

C

G

G

U

g

-39

3

8

bc

false

<90%

1575

NM_018388

MBNL3

1037

1055

G

U

G

C

c

C

A

U

G

a

U

G

C

A

C

G

G

U

g

-39

3

8

bc

false

<90%

2701

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 505
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_199175	C21orf123	2
NM_139179	DAGLB	2
NM_001040101	D4S234E	2
NM_014392	D4S234E	2
NM_014770	CENTG1	2
XM_928464	LOC146517	2
NM_001040431	CCDC56	2
NM_017757	ZNF407	2
NM_032421	CLIP2	2
NM_003388	CLIP2	2
NM_000875	IGF1R	2
XM_370711	LOC650794	2
XM_939879	LOC650794	2
NM_016621	PHF21A	2
NM_001101802		2
NM_024086	METT10D	2
NM_032843	FIBCD1	2
NM_015381	FAM19A5	2
NM_001082967	FAM19A5	2
NM_006795	EHD1	2
NM_173833	SCARA5	2
NM_173565	LOC222967	1
NM_020840		1
NM_031481	SLC25A18	1
NM_001014372	SYT14L	1
NM_000164	GIPR	1
NM_018463	ITFG2	1
NM_018090	NECAP2	1
NM_018690	APOB48R	1
NM_153262	SYT14	1
NM_133259	LRPPRC	1
NM_152253	CHKB	1
NM_015226	KIAA0350	1
NM_000214	JAG1	1
NM_172247	CSF2RA	1
NM_172249	CSF2RA	1
NM_001146	ANGPT1	1
NM_032298	SYT3	1
NM_004277	SLC25A27	1
XM_930678	LOC642441	1
XM_001134399	LOC730257	1
XM_001134398	LOC730256	1
NM_005110	GFPT2	1
NM_001080415	SR140	1
XM_940802	SR140	1
NM_004588	SCN2B	1
NM_203412	UBL4B	1
NM_032656	DHX37	1
NM_021641	ADAM12	1
NM_138764	BAX	1
NM_014732	KIAA0513	1
NM_032207	C19orf44	1
NM_005953	MT2A	1
NM_002371	MAL	1
NM_199287		1
XM_001125719	LOC727751	1
XM_001125942	LOC727849	1
XM_925864	LOC642325	1
XM_001130526	LOC728636	1
XM_001130555	LOC728636	1
XM_001130543	LOC728636	1
XM_001130536	LOC728636	1
XM_001129399	LOC642346	1
XM_928707	LOC642346	1
XM_925879	LOC642346	1
NM_001083909	GPR123	1
NM_024701	ASB13	1
NM_014586	HUNK	1
NM_013364	PNMA3	1
NM_001040445	ASB1	1
XM_001127482	LOC728445	1
XM_001132925	DUSP22	1
NM_144975	SLFN5	1
NM_000693	ALDH1A3	1
NM_153051	MTMR3	1
NM_021090	MTMR3	1
NM_153050	MTMR3	1
NM_018385	LSG1	1
NM_015284	KIAA0467	1
NM_007087	CALB2	1
NM_001740	CALB2	1
NM_007088	CALB2	1
NM_021198	CTDSP1	1
NM_002613	PDPK1	1
NM_031268	PDPK1	1
NM_001100390		1
NM_152558	IQCE	1
NM_005161	AGTRL1	1
NM_198545	C1orf187	1
NM_000831	GRIK3	1
NM_001042690	LOC345222	1
NM_017586	C9orf7	1
NM_000951	PRRG2	1
NM_003791	MBTPS1	1
NM_198406	PAQR6	1
NM_007114	TMF1	1
NM_024653	PRKRIP1	1
NM_001101339		1
NM_178526	SLC25A42	1
NM_153321	PMP22	1
NM_000304	PMP22	1
NM_153322	PMP22	1
NM_198128	RNF138	1
NM_016271	RNF138	1
NM_033637	BTRC	1
NM_003939	BTRC	1
NM_001080498	EMR4	1
NM_016507	CRKRS	1
NM_015083		1
NM_015210	KIAA0802	1
NM_007030	TPPP	1
NM_018319	TDP1	1
NM_001008744	TDP1	1
NM_207318	CXorf39	1
NM_002827	PTPN1	1
NM_006410	HTATIP2	1
NM_001098521		1
NM_001098520		1
NM_001098522		1
NM_178858	SFXN2	1
XM_001132645	ODZ3	1
XM_931600	ODZ3	1
NM_001080477	ODZ3	1
XM_940722	ODZ3	1
NM_018640	LMO3	1
NM_001001395	LMO3	1
NM_001033518	WIPI2	1
NM_001033519	WIPI2	1
NM_015610	WIPI2	1
NM_001033520	WIPI2	1
NM_016003	WIPI2	1
NM_006274	CCL19	1
NM_001010866	RP13-15M17.2	1
NM_013260	SAP30BP	1
NM_018270	C20orf20	1
NM_013227	ACAN	1
NM_001135	ACAN	1
NM_001080395	AATK	1
NM_012227	GTPBP6	1
NM_004443	EPHB3	1
NM_173694	ATP11C	1
NM_001010986	ATP11C	1
NM_004274	AKAP6	1
NM_033255	EPSTI1	1
NM_001099857		1
NM_003639	IKBKG	1
NM_001099856		1
NM_020933	ZNF317	1
NM_198993	STAC2	1
NM_000405	GM2A	1
NM_033437	PDE5A	1
NM_001083	PDE5A	1
NM_033430	PDE5A	1
NM_016263	FZR1	1
NM_006500	MCAM	1
NM_001749	CAPNS1	1
NM_001003962	CAPNS1	1
NM_002086	GRB2	1
NM_203506	GRB2	1
NM_005432	XRCC3	1
NM_001100119		1
NM_001100118		1
XM_001130790	KIAA1881	1
NM_001080400	KIAA1881	1
NM_001008493	ENAH	1
NM_018212	ENAH	1
NM_003131	SRF	1
NM_002386	MC1R	1
NM_203305	FAM102A	1
NM_001035254	FAM102A	1
NM_001005339	RGS10	1
NM_002925	RGS10	1
NM_001806	CEBPG	1
NM_016075	VPS36	1
NM_014550	CARD10	1
NM_019892	INPP5E	1
NM_030810	TXNDC5	1
NM_022085	TXNDC5	1
NM_002221	ITPKB	1
NM_178313	SPTBN1	1
NM_014400	LYPD3	1
NM_020431	TMEM63C	1
NM_004822	NTN1	1
NM_001039966	GPR30	1
NM_001505	GPR30	1
NM_001098201		1
NM_012194		1
NM_153611	CYBASC3	1
NM_019601	SUSD2	1
NM_003768	PEA15	1
NM_018238	AGK	1
NM_015325		1
NM_020941		1
NM_015545	PTCD1	1
NM_001033602	KIAA0774	1
NM_015233	KIAA0774	1
NM_003958	RNF8	1
NM_153350	FBXL16	1
NM_001012756	ZNF260	1
NM_002501	NFIX	1
NM_058219	EXOSC6	1
NM_005588	MEP1A	1
NM_031905	ARMC10	1
XM_371655	LOC389137	1
NM_024915	GRHL2	1
NM_133647	SLC12A6	1
NM_001042495	SLC12A6	1
NM_001042494	SLC12A6	1
NM_001042497	SLC12A6	1
NM_005135	SLC12A6	1
NM_001042496	SLC12A6	1
NM_012414	RAB3GAP2	1
NM_015264	C22orf9	1
NM_001009880	C22orf9	1
NM_015172	BAT2D1	1
NM_014630	ZNF592	1
NM_006750	SNTB2	1
NM_024565	CCNJL	1
NM_017905	TMCO3	1
NM_172057	KCNH2	1
NM_000238	KCNH2	1
NM_001098624		1
NM_033290	MID1	1
NM_000381	MID1	1
XM_001127362	KIAA0574	1
NM_001702	BAI1	1
NM_005614	RHEB	1
NM_017761	PNRC2	1
NM_032211	LOXL4	1
NM_000083	CLCN1	1
NM_021137	TNFAIP1	1
NM_005883	APC2	1
NM_021945	C6orf85	1
NM_002375	MAP4	1
NM_030884	MAP4	1
NM_001079843	CASZ1	1
NM_004304	ALK	1
NM_023934	FUNDC2	1
NM_175064	WBSCR19	1
NM_001099435		1
XM_001127525	LOC730307	1
XM_496899	LOC441258	1
XM_929470	LOC643909	1
XM_001127430	LOC730304	1
XM_499348	MGC57359	1
NM_001004351	MGC57359	1
NM_014935	PLEKHA6	1
NM_002278	KRT32	1
NM_174937	TCERG1L	1
NM_138422	LOC113179	1
NM_012316	KPNA6	1
NM_052937	PCMTD1	1
NM_001099439		1
NM_024585	ARMC7	1
NM_007203	PALM2-AKAP2	1
NM_147150	PALM2-AKAP2	1
NM_001004065	AKAP2	1
NM_017621	ALKBH4	1
NM_018487	TMEM176A	1
NM_021927	GUF1	1
NM_001039397	FLJ40244	1
NM_139057	ADAMTS17	1
NM_001629	ALOX5AP	1
NM_012405	ICMT	1
XM_936706	KLHL17	1
NM_198317	KLHL17	1
NM_003559	PIP5K2B	1
NM_176875	CCKBR	1
NM_178835	LOC152485	1
NM_002319	LRCH4	1
NM_006549	CAMKK2	1
NM_153499	CAMKK2	1
NM_153500	CAMKK2	1
NM_172216	CAMKK2	1
NM_172226	CAMKK2	1
NM_207306		1
NM_130459	TOR2A	1
NM_020777	SORCS2	1
NM_002990	CCL22	1
NM_174953	ATP2A3	1
NM_174956	ATP2A3	1
NM_174954	ATP2A3	1
NM_174957	ATP2A3	1
NM_174958	ATP2A3	1
NM_005173	ATP2A3	1
NM_174955	ATP2A3	1
NM_173595		1
NM_003683	RRP1	1
NM_001077418	FLJ22167	1
NM_001077416	FLJ22167	1
NM_001077419	FLJ22167	1
NM_003036	SKI	1
NM_001103161		1
NM_001103160		1
NM_023076	C16orf28	1
NM_001110514		1
NM_001040000	MLLT4	1
NM_001029864	KIAA1755	1
NM_000843	GRM6	1
NM_014722		1
NM_139284	LGI4	1
NM_013261	PPARGC1A	1
NM_145913	SLC5A8	1
NM_170607	MLX	1
NM_198204	MLX	1
NM_198205	MLX	1
NM_005343	HRAS	1
NM_176795	HRAS	1
NM_003857	GALR2	1
NM_001113239		1
NM_022740	HIPK2	1
NM_000445	PLEC1	1
NM_201379	PLEC1	1
NM_201382	PLEC1	1
NM_201383	PLEC1	1
NM_201380	PLEC1	1
NM_201381	PLEC1	1
NM_201384	PLEC1	1
NM_201378	PLEC1	1
XM_379194	LOC401068	1
NM_153812	PHF13	1
NM_015831	ACHE	1
NM_003644	GAS7	1
NM_201432	GAS7	1
NM_201433	GAS7	1
NM_005458	GABBR2	1
NM_004273	CHST3	1
NM_175062	RASGEF1C	1
NM_012325	MAPRE1	1
NM_172229	KREMEN2	1
NM_024507	KREMEN2	1
NM_001039709	CBFA2T2	1
NM_001032999	CBFA2T2	1
NM_005093	CBFA2T2	1
NM_002348	LY9	1
NM_020639	RIPK4	1
NM_007033	RER1	1
NM_005069	SIM2	1
NM_023926	ZSCAN18	1
NM_198563	TMEM110	1
NM_013423	ARHGAP6	1
NM_001174	ARHGAP6	1
NM_013427	ARHGAP6	1
NM_133330	WHSC1	1
NM_001042424	WHSC1	1
NM_133331	WHSC1	1
NM_133335	WHSC1	1
NM_144641	PPM1M	1
NM_014112	TRPS1	1
NM_017822	C12orf41	1
NM_002052	GATA4	1
NM_015894	STMN3	1
NM_006999	POLS	1
XM_945995	LOC339674	1
XM_934917	LOC339674	1
XM_001133211	LOC729003	1
XM_001133556	LOC729135	1
NM_001017995	SH3PXD2B	1
NM_001003665	C1orf95	1
XM_945031	LOC643464	1
XM_931563	LOC643464	1
NM_194356	STX2	1
NM_001980	STX2	1
XM_001133189	INPP5A	1
NM_005539	INPP5A	1
NM_014674	EDEM1	1
NM_020210	SEMA4B	1
NM_198925	SEMA4B	1
NM_015267	CUTL2	1
NM_024979	MCF2L	1
NM_001112732		1
XM_940456	FLJ22184	1
NM_021200	PLEKHB1	1
NM_006651	CPLX1	1
NM_001023587	ABCC5	1
NM_025250	TTYH3	1
NM_138328	RHBDL3	1
NM_201628	FLJ43806	1
NM_177401	MIDN	1
NM_080792	SIRPA	1
NM_001040023	SIRPA	1
NM_001040022	SIRPA	1
NM_012413	QPCT	1
XM_942692	MGC5139	1
NM_001080533	MGC5139	1
NM_013382	POMT2	1
XM_001134463	BAHCC1	1
NM_001080519	BAHCC1	1
NM_002710	PPP1CC	1
NM_024085	ATG9A	1
NM_001077198	ATG9A	1
NM_005187	CBFA2T3	1
NM_175931	CBFA2T3	1
NM_018660	ZNF395	1
NM_001100162		1
NM_001100161		1
NM_015024	XPO7	1
NM_020851	ISLR2	1
NM_001452	FOXF2	1
NM_018150	C1orf164	1
NM_018941	CLN8	1
NM_138369	FAM44B	1
NM_001040446	MTMR12	1
NM_016025	METTL9	1
NM_001077180	METTL9	1
NM_002346	LY6E	1
NM_030761	WNT4	1
NM_138444	KCTD12	1
NM_005957	MTHFR	1
NM_015099	CAMTA2	1
NM_020064	BARHL1	1
NM_017688	BSPRY	1
NM_001043318	C14orf43	1
NM_194278	C14orf43	1
XM_001132002	LOC732148	1
XM_001129370	LOC729122	1
NM_178568	RTN4RL1	1
NM_005764	PDZK1IP1	1
NM_014937	INPP5F	1
NM_152301	MRFAP1L1	1
NM_020993	BCL7A	1
NM_001024808	BCL7A	1
NM_001077492	KLK5	1
NM_001077491	KLK5	1
NM_012427	KLK5	1
NM_015251	ASCIZ	1
NM_015044	GGA2	1
NM_006918	SC5DL	1
NM_001024956	SC5DL	1
NM_004893	H2AFY	1
NM_138610	H2AFY	1
NM_138609	H2AFY	1
NM_001040158	H2AFY	1
NM_018702	ADARB2	1
NM_006695	RPIP8	1
NM_001280	CIRBP	1
NM_004734	DCLK1	1
NM_182705	FAM101B	1
XM_001126665	FAM101B	1
NM_014636	RALGPS1	1
NM_001918	DBT	1
NM_014866	KIAA0310	1
NM_014869	IQSEC1	1
NM_014397	NEK6	1
NM_001100398		1
NM_015085	GARNL4	1
NM_001031717	CRELD1	1
NM_005105	RBM8A	1
NM_153254	TTLL10	1
NM_015197	PACS2	1
NM_001100913		1
NM_199461	NANOS1	1
NM_014850	SRGAP3	1
NM_001033117	SRGAP3	1
NM_006796	AFG3L2	1
NM_000744	CHRNA4	1
NM_005147	DNAJA3	1
NM_004930	CAPZB	1
NM_000153	GALC	1
NM_001733	C1R	1
NM_004928	C21orf2	1
NM_014183	DYNLRB1	1
NM_022080	NAPB	1
XM_001134363	FOXK2	1
XM_001134364	FOXK2	1
NM_004514	FOXK2	1
NM_001008408	RBM33	1
NM_053043	PRR8	1
NM_015002	FBXO21	1
NM_033624	FBXO21	1
NM_015892	GALNAC4S-6ST	1
NM_033403		1
NM_017649	CNNM2	1
NM_199076	CNNM2	1
NM_207309	UAP1L1	1
NM_004577	PSPH	1
NM_006852	TLK2	1
NM_001112707		1
NM_019117	KLHL4	1
NM_134445	CD99L2	1
NM_134446	CD99L2	1
NM_031462	CD99L2	1
NM_012231	PRDM2	1
NM_152305	KTELC1	1
NM_006948	STCH	1
NM_001003800	BICD2	1
NM_052861	MGC21675	1
NM_018488	TBX4	1
NM_021940	SMAP1	1
NM_001044305	SMAP1	1
NM_007353	GNA12	1
NM_005491	CXorf6	1
NM_005270	GLI2	1
NM_198484	ZNF621	1
NM_001098414		1
NM_014616	ATP11B	1
NM_198194	STOM	1
NM_004099	STOM	1
NM_002518	NPAS2	1
NM_012218	ILF3	1
NM_001012755	MCART6	1
NM_007174	CIT	1
XM_943571	LOC646916	1
XM_001127690	LOC730303	1
NM_001099697		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