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 GCGUUCCAAUCAACACCAA (13 guide strand hits and 4 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_014479

ADAMDEC1

1132

1150

a

u

G

U

U

C

C

A

u

U

C

A

A

C

A

C

C

A

A

26

3

10

bc

false

<90%

2175

NM_017634

KCTD9

2101

2119

a

a

G

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

g

21

4

9

bc

false

<90%

3353

XM_001127464

ALOX5

1031

1049

c

C

a

U

U

g

C

A

A

U

C

A

A

C

A

C

C

A

A

15

3

13

bc

false

<90%

2278

NM_000698

ALOX5

1310

1328

c

C

a

U

U

g

C

A

A

U

C

A

A

C

A

C

C

A

A

15

3

13

bc

false

<90%

2568

NM_014522

PCDH11X

1963

1981

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

4603

NM_032971

PCDH11Y

1694

1712

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

4710

NM_032967

PCDH11X

1707

1725

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

4723

NM_032972

PCDH11Y

1948

1966

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

4964

XM_001124844

LOC730420

1961

1979

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

4977

NM_032973

PCDH11Y

1948

1966

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

9056

NM_032969

PCDH11X

1963

1981

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

9146

NM_032968

PCDH11X

1963

1981

a

u

a

U

U

C

C

A

c

U

C

A

A

C

A

C

C

A

A

6

4

10

bc

false

<90%

9176

NM_005446

P2RXL1

2304

2322

u

g

G

U

U

C

C

A

A

a

C

A

A

C

A

C

C

A

c

-1

4

8

bc

false

<90%

3554

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_016061

YPEL5

1097

1115

U

U

G

G

U

G

U

U

G

A

U

U

G

G

A

A

a

c

u

68

3

16

ac

false

<90%

2183

NM_173699

MAGEB18

666

684

U

U

G

G

U

G

U

U

G

A

U

U

u

G

A

A

g

G

a

61

3

12

false

<90%

1826

NM_139248

LIPH

419

437

U

U

G

u

U

G

U

U

G

A

U

U

G

G

A

A

u

c

g

32

4

12

c

false

<90%

2478

NM_005197

CHES1

7633

7651

U

U

G

G

U

G

U

U

G

c

U

U

G

G

A

A

g

G

C

-6

2

9

c

false

<90%

7826

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 377
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_052847	GNG7	2
NM_017797	BTBD2	2
NM_024915	GRHL2	2
NM_133460	ZNF418	1
NM_024949	WWC2	1
NM_001042599	ERBB4	1
NM_005235	ERBB4	1
NM_016081	PALLD	1
NM_020796	SEMA6A	1
NM_005503	APBA2	1
NM_004469	FIGF	1
NM_203304	RKHD1	1
NM_001085363		1
NM_030762	BHLHB3	1
NM_181521	CMTM4	1
NM_001042682	RERE	1
NM_012102	RERE	1
NM_001042681	RERE	1
NM_015110	SMC5	1
NM_015090	NFASC	1
NM_181443	BTBD3	1
NM_014962	BTBD3	1
NM_052926	PNMA5	1
NM_001103151		1
NM_001103150		1
NM_032882	PNMA6A	1
NM_003132	SRM	1
NM_005324	H3F3B	1
NM_003045	SLC7A1	1
NM_174916	UBR1	1
NM_005766	FARP1	1
NM_033064	ATCAY	1
NM_144707	PROM2	1
NM_183337	RGS11	1
NM_003834	RGS11	1
NM_016155	MMP17	1
XM_001133320	MMP17	1
NM_024332	BRCC3	1
NM_001018055	BRCC3	1
NM_138479	C1orf213	1
NM_017770	ELOVL2	1
NM_005297	MCHR1	1
NM_001040167	LFNG	1
NM_033051	SLC46A2	1
NM_003255	TIMP2	1
XM_001132362	TIMP2	1
NM_016823	CRK	1
NM_005206	CRK	1
NM_175609	ARFGAP1	1
NM_018209	ARFGAP1	1
NM_019063	EML4	1
NM_024933	ANKRD53	1
NM_005255	GAK	1
NM_014877	HELZ	1
XM_495908	DDX12	1
NM_004399	DDX11	1
NM_030653	DDX11	1
NM_152438	DDX11	1
NM_002148	HOXD10	1
NM_139071	SMARCD1	1
NM_003076	SMARCD1	1
NM_145245	EVI5L	1
NM_005683	GPR55	1
NM_173553	FLJ25801	1
NM_001012991	LOC400506	1
NM_199205	KIAA1967	1
NM_021174	KIAA1967	1
NM_198147	LOC116236	1
NM_020826	SYT13	1
NM_002340	LSS	1
NM_001004342	TRIM67	1
NM_152262	ZNF439	1
NM_019116	UBFD1	1
NM_001001479	SLC35E4	1
NM_001001795	MGC70857	1
NM_012306	FAIM2	1
NM_003037	SLAMF1	1
NM_004513	IL16	1
NM_172217	IL16	1
NM_182509	THSD3	1
NM_001001438	LSS	1
NM_031301	APH1B	1
NM_001695	ATP6V1C1	1
NM_012465	TLL2	1
NM_004339	PTTG1IP	1
NM_006563	KLF1	1
NM_007203	PALM2-AKAP2	1
NM_147150	PALM2-AKAP2	1
NM_001004065	AKAP2	1
NM_002594	PCSK2	1
NM_032409	PINK1	1
NM_003836	DLK1	1
NM_024910	ZNF767	1
NM_173588	IGSF22	1
NM_032109	OTP	1
NM_018171	APPL2	1
NM_198490	RAB43	1
NM_003253	TIAM1	1
NM_001004019	FBLN2	1
NM_001998	FBLN2	1
NM_173854	SLC41A1	1
NM_002235	KCNA6	1
NM_006836	GCN1L1	1
NM_152592	C14orf49	1
NM_000334	SCN4A	1
NM_002220	ITPKA	1
NM_139029	CD151	1
NM_004357	CD151	1
NM_001039490	CD151	1
NM_139030	CD151	1
NM_001040011		1
NM_001101347		1
XM_001128965	LOC728975	1
NM_182616	C15orf38	1
NM_001044370	MPPED1	1
NM_024076	KCTD15	1
NM_014869	IQSEC1	1
NM_000230	LEP	1
NM_012174	FBXW8	1
NM_153348	FBXW8	1
NM_014755	SERTAD2	1
NM_020429	SMURF1	1
NM_181349	SMURF1	1
NM_018718	TSGA14	1
NM_017919	STX17	1
NM_017958	PLEKHB2	1
NM_001100623		1
NM_001452	FOXF2	1
NM_002052	GATA4	1
NM_015276		1
NM_178457	C20orf174	1
NM_014700	RAB11FIP3	1
NM_004147	DRG1	1
NM_032300	TCHP	1
NM_001081461	JMJD6	1
NM_006071	PKDREJ	1
NM_000451	SHOX	1
NM_080666	WDR89	1
NM_001008726	WDR89	1
NM_032854	CORO6	1
NM_153690	FAM43A	1
NM_005018	PDCD1	1
NM_182487	OLFML2A	1
NM_025081	KIAA1305	1
NM_152219	GJC1	1
NM_023067	FOXL2	1
NM_016831	PER3	1
XM_943034	LOC643085	1
XM_931304	LOC643085	1
NM_017766	CASZ1	1
NM_006315	PCGF3	1
NM_004444	EPHB4	1
NM_024701	ASB13	1
NM_001098844		1
NM_017450	BAIAP2	1
NM_014861	ATP2C2	1
NM_005528	DNAJC4	1
NM_207360		1
NM_001031617	COX19	1
NM_001099682		1
NM_024859	MAGIX	1
NM_001099680		1
NM_001099681		1
NM_175902	FLJ22222	1
NM_006943	SOX12	1
NM_145262	GLYCTK	1
NM_006285	TESK1	1
NM_021623		1
NM_032859	ABHD13	1
NM_170776	GPR97	1
NM_003966	SEMA5A	1
NM_144994	ANKRD23	1
NM_015124	DIP	1
NM_004599	SREBF2	1
NM_016224	SNX9	1
NM_014848	SV2B	1
NM_198207	LASS1	1
NM_003200	TCF3	1
NM_001033518	WIPI2	1
NM_001033519	WIPI2	1
NM_015610	WIPI2	1
NM_001033520	WIPI2	1
NM_016003	WIPI2	1
NM_153812	PHF13	1
NM_206920	MAMDC4	1
NM_012301	MAGI2	1
NM_014023	WDR37	1
NM_002609	PDGFRB	1
NM_002359	MAFG	1
NM_032711	MAFG	1
NM_003485	GPR68	1
NM_030576	LIMD2	1
NM_144578	C14orf32	1
NM_000719	CACNA1C	1
NM_017814	TMEM161A	1
NM_032982	CASP2	1
NM_032983	CASP2	1
NM_005082	TRIM25	1
NM_003131	SRF	1
XM_001134277	LOC221362	1
NM_016647	C8orf55	1
NM_214711	LOC401137	1
NM_012138	AATF	1
NM_207428	C11orf55	1
NM_020528	PCBP3	1
NM_015162	ACSBG1	1
NM_001031680	RUNX3	1
NM_004350	RUNX3	1
NM_001080484	KIAA1751	1
XM_936307	KIAA1751	1
XM_928866	LOC645895	1
XM_938922	LOC645895	1
NM_001014839	NCDN	1
NM_014284	NCDN	1
NM_001014841	NCDN	1
NM_018416	FOXJ2	1
NM_005860	FSTL3	1
NM_022479	WBSCR17	1
NM_001040424	PRDM15	1
NM_022115	PRDM15	1
XM_001131399	LOC731962	1
XM_001131436	LOC729822	1
NM_001080457	LRRC4B	1
XM_936789	LRRC4B	1
NM_138442	CCDC124	1
NM_005806	OLIG2	1
NM_001009877	BRD9	1
NM_023924	BRD9	1
NM_001097638		1
NM_000511	FUT2	1
NM_020773	TBC1D14	1
NM_030660	ATXN3	1
NM_004993	ATXN3	1
NM_004052	BNIP3	1
NM_020825	CRAMP1L	1
NM_152419		1
NM_001449	FHL1	1
NM_001196	BID	1
NM_197967	BID	1
NM_197966	BID	1
NM_016242	EMCN	1
NM_198850	PHLDB3	1
XM_928224	LOC653583	1
XM_001131797	LOC732075	1
NM_198318	PRMT1	1
NM_198319	PRMT1	1
NM_001536	PRMT1	1
NM_006184	NUCB1	1
NM_012473	TXN2	1
NM_017949	CUEDC1	1
NM_006393	NEBL	1
NM_024617	ZCCHC6	1
XM_001133142	LOC731450	1
NM_014310	RASD2	1
NM_006272	S100B	1
NM_004571	PKNOX1	1
NM_174937	TCERG1L	1
NM_003575	ZNF282	1
NM_007129	ZIC2	1
XM_945588	FLJ30375	1
XM_498945	FLJ30375	1
NM_001098498		1
NM_001098497		1
NM_001039948	RUTBC2	1
NM_133454	RUTBC2	1
NM_024017	HOXB9	1
NM_032432	ABLIM2	1
NM_001037165	FOXK1	1
NM_017556	FBLIM1	1
NM_001024216	FBLIM1	1
NM_000168	GLI3	1
NM_175055	HIST3H2BB	1
NM_001328	CTBP1	1
NM_001012614	CTBP1	1
NM_005468	NAALADL1	1
NM_021902	FXYD1	1
NM_005031	FXYD1	1
NM_004423	DVL3	1
NM_003508	FZD9	1
NM_003565	ULK1	1
XM_001133335	ULK1	1
NM_017921	NPLOC4	1
NM_004220	ZNF213	1
NM_001040665	STEAP2	1
NM_152999	STEAP2	1
NM_173570	ZDHHC23	1
NM_005184	CALM3	1
NM_170606	MLL3	1
NM_153181	NETO1	1
NM_138966	NETO1	1
NM_021064	HIST1H2AG	1
NM_005990	STK10	1
NM_005334	HCFC1	1
NM_031432	UCK1	1
NM_178314	FLJ39378	1
NM_006444	SMC2	1
NM_001042550	SMC2	1
NM_001042551	SMC2	1
NM_001933	DLST	1
NM_003089	SNRP70	1
NM_183425	RBM38	1
NM_017495	RBM38	1
NM_001012636	IL32	1
NM_004221	IL32	1
NM_001012631	IL32	1
NM_001012718	IL32	1
NM_001012635	IL32	1
NM_001012633	IL32	1
NM_001012632	IL32	1
NM_001012634	IL32	1
XM_943278	LOC644727	1
XM_932334	LOC644727	1
NM_000115	EDNRB	1
NM_181353	ID1	1
NM_019845	RPRM	1
NM_001039803	CCRK	1
NM_178432	CCRK	1
NM_012119	CCRK	1
NM_133330	WHSC1	1
NM_001042424	WHSC1	1
NM_133331	WHSC1	1
NM_133335	WHSC1	1
XM_097977	FAM59B	1
XM_940578	FAM59B	1
XM_928252	LOC645212	1
XM_939117	LOC645212	1
NM_080539	COLQ	1
NM_080538	COLQ	1
NM_080544	COLQ	1
NM_005677	COLQ	1
NM_080541	COLQ	1
XM_001133551	LOC731754	1
XM_001126119	LOC727757	1
NM_020168	PAK6	1
NM_001025591	LOC284402	1
NM_002739	PRKCG	1
NM_014550	CARD10	1
NM_031476	CRISPLD2	1
NM_013279	C11orf9	1
NM_021259	TMEM8	1
NM_020462	ERGIC1	1
NM_024963	FBXL18	1
XM_936831	IQSEC3	1
NM_018373	SYNJ2BP	1
NM_152253	CHKB	1
NM_152247	CPT1B	1
NM_004657	SDPR	1
XM_001125745	ZNF469	1
XM_939259	ZNF469	1
NM_181491	SURF5	1
NM_133640	SURF5	1
NM_006340	BAIAP2	1
NM_002117	HLA-C	1
NM_032145	FBXO30	1
NM_175876	EXOC8	1
NM_014840	NUAK1	1
NM_006675	TSPAN9	1
NM_024776		1
NM_153620	HOXA1	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_018708	FEM1A	1
NM_015299	KIAA0323	1
XM_001132872	LOC728677	1
NM_006148	LASP1	1
NM_058181	C21orf57	1
NM_020910		1
NM_007159	SLMAP	1
NM_181809	BMP8A	1
NM_001001712	LCN10	1
NM_004263	SEMA4F	1
NM_014333	CADM1	1
NM_001098517		1
NM_012477	WBP1	1
NM_025133	FBXO11	1
NM_171825	CAMK2A	1
NM_015981	CAMK2A	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