VIRsiRNAdb

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

28 hits were found for AACGAUGAAAUAGAUGGAG (12 guide strand hits and 16 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

XM_938907

KIAA1240

1854

1872

u

u

u

G

A

U

G

A

A

A

U

A

G

A

U

G

G

A

u

62

4

15

bc

false

<90%

8103

XM_039676

KIAA1240

1854

1872

u

u

u

G

A

U

G

A

A

A

U

A

G

A

U

G

G

A

u

62

4

15

bc

false

<90%

8103

NM_013309

SLC30A4

940

958

A

A

C

u

A

U

G

A

A

A

U

A

a

A

U

G

G

A

G

52

2

8

false

<90%

4290

NM_017780

CHD7

6070

6088

A

A

a

G

A

U

G

A

A

A

U

A

G

A

U

G

a

A

u

51

3

13

c

false

<90%

10469

NM_015888

HOOK1

1163

1181

A

A

a

G

A

U

G

A

A

A

U

A

G

A

U

G

u

u

c

49

4

13

c

false

<90%

5865

NM_006852

TLK2

1032

1050

A

A

C

G

A

U

u

A

A

A

U

A

G

A

U

G

u

g

u

2

4

9

c

false

<90%

3616

XR_017136

LOC646202

1442

1460

A

A

C

G

A

U

u

A

A

A

U

A

G

A

U

G

u

g

u

2

4

9

c

false

<90%

3851

XR_015709

LOC732083

1451

1469

A

A

C

G

A

U

u

A

A

A

U

A

G

A

U

G

u

g

u

2

4

9

c

false

<90%

3856

NM_015040

PIP5K3

5529

5547

c

A

a

G

A

U

G

A

A

g

U

A

G

A

U

G

G

A

G

-4

3

9

bc

false

<90%

9901

NM_181504

PIK3R1

2156

2174

A

A

C

u

A

U

c

A

A

A

U

A

G

A

U

G

G

A

u

-8

3

11

bc

false

<90%

5663

NM_181524

PIK3R1

2316

2334

A

A

C

u

A

U

c

A

A

A

U

A

G

A

U

G

G

A

u

-8

3

11

bc

false

<90%

5823

NM_181523

PIK3R1

2946

2964

A

A

C

u

A

U

c

A

A

A

U

A

G

A

U

G

G

A

u

-8

3

11

bc

false

<90%

6453

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_000068

CACNA1A

2352

2370

C

U

C

C

A

U

C

U

A

U

U

U

C

A

U

u

G

U

a

68

2

15

c

false

<90%

7807

NM_023035

CACNA1A

2352

2370

C

U

C

C

A

U

C

U

A

U

U

U

C

A

U

u

G

U

a

68

2

15

c

false

<90%

7812

NM_005183

CACNA1F

2266

2284

g

U

g

C

A

U

C

U

A

U

U

U

C

A

U

C

a

U

U

54

3

13

c

false

<90%

6080

NM_001005407

CACNA1H

1433

1451

C

U

u

C

A

U

C

U

A

U

U

U

C

A

U

C

c

U

g

51

3

13

c

false

<90%

8079

NM_021098

CACNA1H

1433

1451

C

U

u

C

A

U

C

U

A

U

U

U

C

A

U

C

c

U

g

51

3

13

c

false

<90%

8097

XM_933399

LOC646098

196

214

C

U

C

C

A

U

C

U

A

U

U

U

C

u

U

C

a

a

c

49

4

13

c

false

<90%

315

XM_943021

LOC646098

196

214

C

U

C

C

A

U

C

U

A

U

U

U

C

u

U

C

a

a

c

49

4

13

c

false

<90%

315

NM_005013

NUCB2

1553

1571

C

a

a

C

A

U

C

U

A

U

U

U

C

A

U

C

u

U

U

45

3

13

c

false

<90%

1612

NM_054020

CATSPER2

1170

1188

C

a

g

C

A

U

C

U

A

U

U

U

C

A

U

C

c

U

U

45

3

13

c

false

<90%

1942

NM_172095

CATSPER2

1170

1188

C

a

g

C

A

U

C

U

A

U

U

U

C

A

U

C

c

U

U

45

3

13

c

false

<90%

1948

NM_017901

TPCN1

1879

1897

g

c

C

C

u

U

C

U

A

U

U

U

C

A

U

C

G

U

g

30

4

13

bc

false

<90%

2810

NM_000678

ADRA1D

447

465

C

a

C

C

A

a

C

U

A

U

U

U

C

A

U

C

G

U

g

20

3

12

bc

false

<90%

2130

NM_006717

SPIN1

1033

1051

C

U

C

C

g

U

C

U

A

U

U

U

C

A

U

C

a

a

g

17

4

11

c

false

<90%

4535

NM_017917

PPP2R3C

128

146

u

U

C

C

A

U

C

U

c

U

U

U

C

A

U

a

G

U

U

11

3

7

c

false

<90%

1843

NM_017938

FAM70A

208

226

C

U

C

C

A

U

C

U

A

U

g

U

C

A

c

C

G

U

g

9

3

10

c

false

<90%

3408

NM_181840

KCNK18

1021

1039

C

U

C

C

A

U

u

U

A

U

a

U

C

A

U

C

G

U

U

-27

2

8

c

false

<90%

1155

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 360
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_033064	ATCAY	3
NM_006838	METAP2	2
NM_022754	SFXN1	1
NM_000896	CYP4F3	1
NM_001082	CYP4F2	1
NM_001112736		1
NM_014912	CPEB3	1
NM_015283		1
NM_152734	C6orf89	1
NM_001802	CDR2	1
NM_080591	PTGS1	1
NM_000962	PTGS1	1
XM_001133059	LOC728772	1
XM_001133074	LOC728772	1
XM_001133066	LOC728772	1
NM_017552		1
NM_001200	BMP2	1
NM_145176	SLC2A12	1
NM_016570	ERGIC2	1
NM_015683	ARRDC2	1
NM_001025604	ARRDC2	1
NM_001945	HBEGF	1
NM_015954	DERA	1
NM_001040202	PAQR3	1
NM_181789	GLDN	1
NM_001963	EGF	1
NM_002414	CD99	1
NM_015949	C7orf20	1
NM_000875	IGF1R	1
NM_000332	ATXN1	1
NM_018010	IFT57	1
NM_025132	WDR19	1
NM_022557	GH2	1
XM_932721	LOC653264	1
XM_931343	LOC653135	1
XM_001132109	LOC730020	1
XM_936831	IQSEC3	1
NM_018451	CENPJ	1
NM_198541	IGFL1	1
NM_052869	TTYH2	1
NM_032646	TTYH2	1
NM_001109754		1
NM_002837	PTPRB	1
NM_017644	KLHL24	1
NM_001083112	GPD2	1
NM_000408	GPD2	1
NM_080491	GAB2	1
NM_012296	GAB2	1
NM_007249	KLF12	1
XM_941540	FLJ90086	1
XM_371820	FLJ90086	1
NM_013286	RBM15B	1
NM_001017405	MAEA	1
NM_005882	MAEA	1
NM_014765	TOMM20	1
NM_015909	NAG	1
NM_032569	N-PAC	1
NM_000570	FCGR3B	1
NM_014805	EPM2AIP1	1
NM_016118	NUB1	1
NM_000569	FCGR3A	1
NM_016399	TRIAP1	1
NM_000599	IGFBP5	1
NM_006122	MAN2A2	1
NM_001100390		1
NM_152558	IQCE	1
NM_001012267	CENPP	1
NM_138440	VASN	1
XM_941733	LOC647115	1
XM_930136	LOC647115	1
NM_194247	HNRPA3	1
NM_004137	KCNMB1	1
NM_001017970	TMEM30B	1
NM_005955	MTF1	1
NM_005151	USP14	1
NM_001037334	USP14	1
NM_001083913	C10orf26	1
NM_017787	C10orf26	1
NM_024653	PRKRIP1	1
NM_015295		1
NM_032329	ING5	1
XM_941026	ING5	1
XM_001126273	LOC727773	1
NM_006773	DDX18	1
NM_006323	SEC24B	1
NM_001042734	SEC24B	1
NM_003238	TGFB2	1
NM_002789	PSMA4	1
NM_001102667		1
NM_001102668		1
NM_014344	FJX1	1
NM_022128	RBKS	1
NM_139279	MCFD2	1
NM_052957	ACRC	1
NM_001364	DLG2	1
NM_173642	FAM80A	1
NM_203463	LASS6	1
XM_001129151	LOC729047	1
NM_014643		1
NM_018452	C6orf35	1
NM_000396	CTSK	1
NM_004460	FAP	1
NM_178006	STARD13	1
NM_178007	STARD13	1
NM_052851	STARD13	1
NM_002763	PROX1	1
NM_020925	CACHD1	1
XM_001131007	LOC729678	1
XM_001127177	LOC730780	1
NM_003180	SYT5	1
XM_495908	DDX12	1
NM_024959	SLC24A6	1
NM_001012709	KRTAP5-4	1
NM_177402	SYT2	1
XM_373973	LOC388923	1
XM_943355	LOC388923	1
NM_144984	C10orf72	1
NM_145245	EVI5L	1
NM_017994	C7orf42	1
NM_174936	PCSK9	1
NM_018697	LANCL2	1
NM_001100829		1
NM_183075	CYP2U1	1
NM_032448	FAM120B	1
NM_032737	LMNB2	1
NM_000578	SLC11A1	1
NM_001032392	PLGLB1	1
NM_002665	PLGLB2	1
NM_003913	PRPF4B	1
XM_001134277	LOC221362	1
NM_001001872	C14orf37	1
NM_002666	PLIN	1
NM_033225	CSMD1	1
NM_004869	VPS4B	1
NM_001455	FOXO3A	1
NM_201559	FOXO3A	1
NM_052905	FMNL2	1
NM_017439	LOC54103	1
NM_018847	KLHL9	1
NM_021813	BACH2	1
NM_018053	XKR8	1
NM_007364	TMED3	1
NM_015057	MYCBP2	1
NM_004522	KIF5C	1
NM_018227	UBE1L2	1
NM_182848	CLDN10	1
NM_006984	CLDN10	1
NM_020911		1
NM_015266	SLC9A8	1
NM_033429	CALML4	1
NM_001031733	CALML4	1
NM_212558	LOC401498	1
NM_005266	GJA5	1
NM_181703	GJA5	1
NM_152534	NEK10	1
XM_001133581	LOC729540	1
NM_020815	PCDH10	1
NM_001098213		1
NM_001098212		1
NM_000861	HRH1	1
NM_001098211		1
NM_005146	SART1	1
XM_001126170	LOC730519	1
XM_001132260	LOC730060	1
NM_152624	DCP2	1
NM_032154	PCGF6	1
NM_001011663	PCGF6	1
NM_033394	TANC1	1
XM_378973	LOC284801	1
XM_944897	LOC284801	1
NM_139179	DAGLB	1
NM_018003	UACA	1
NM_001008224	UACA	1
NM_024627	C22orf29	1
NM_003030	SHOX2	1
NM_006884	SHOX2	1
NM_016575	NT5DC3	1
NM_020552	TCL6	1
NM_020553	TCL6	1
NM_003799	RNMT	1
XM_001126406	LOC727922	1
XM_001126391	LOC727922	1
XM_001126417	LOC727922	1
NM_054016	FUSIP1	1
XM_370909	LOC388177	1
XM_938956	LOC388177	1
NM_206925	CA12	1
NM_001218	CA12	1
NM_006141	DYNC1LI2	1
NM_000428	LTBP2	1
NM_014686	KIAA0355	1
NM_004572	PKP2	1
NM_001005242	PKP2	1
XM_001128720	FLJ22763	1
XM_001128163	FLJ22763	1
NM_030650	KIAA1715	1
NM_004650	PNPLA4	1
NM_206909	PSD3	1
NM_015310	PSD3	1
NM_018202	TMEM57	1
NM_017826	SOHLH2	1
NM_000314	PTEN	1
NM_005407	SALL2	1
NM_018639	WSB2	1
NM_175885	MGC33846	1
NM_002522	NPTX1	1
NM_001098638		1
NM_001336	CTSZ	1
NM_207361	FREM2	1
NM_001042383	CEP63	1
NM_001042400	CEP63	1
NM_025180	CEP63	1
NM_005388	PDCL	1
XM_001134172	LOC730034	1
XM_001133186	LOC731345	1
NM_020773	TBC1D14	1
NM_032107	L3MBTL	1
NM_015478	L3MBTL	1
NM_001037954	DIXDC1	1
NM_033425	DIXDC1	1
NM_018121	C10orf6	1
NM_012129	CLDN12	1
XM_001128311	LOC731449	1
XM_001129750	LOC728999	1
NM_080658	ACY3	1
NM_004842	AKAP7	1
NM_138633	AKAP7	1
NM_016377	AKAP7	1
NM_139280	ORMDL3	1
NM_001025202	LOC442582	1
NM_001013739	LOC442578	1
NM_133265	AMOT	1
NM_003747	TNKS	1
NM_001039362	ATP6V1C2	1
NM_144583	ATP6V1C2	1
NM_021954	GJA3	1
XM_001130699	LOC731761	1
XM_001129872	LOC729296	1
NM_025154	UNC84A	1
NM_020651	PELI1	1
NM_001017995	SH3PXD2B	1
NM_017582	UBE2Q1	1
NM_032781	PTPN5	1
NM_001039970	PTPN5	1
NM_006906	PTPN5	1
XM_939547	ZNF697	1
NM_001080470	ZNF697	1
NM_000369	TSHR	1
NM_012306	FAIM2	1
NM_022918	TMEM135	1
NM_198207	LASS1	1
NM_001097636		1
NM_001097634		1
NM_001097635		1
NM_001490	GCNT1	1
NM_001097633		1
NM_183380	DST	1
NM_015548	DST	1
NM_001730	KLF5	1
NM_016436	PHF20	1
NM_015206	KIAA1024	1
NM_020697	KCNS2	1
NM_001006657	WDR35	1
NM_020779	WDR35	1
NM_016221	DCTN4	1
NM_015537	NELF	1
NM_152758	YTHDF3	1
NM_018265	C1orf106	1
NM_006026	H1FX	1
NM_000411	HLCS	1
NM_000529	MC2R	1
NM_031461	CRISPLD1	1
NM_000824	GLRB	1
NM_177967	UBAC2	1
NM_024900	PHF17	1
NM_006546	IGF2BP1	1
NM_006335	TIMM17A	1
NM_182705	FAM101B	1
XM_001126665	FAM101B	1
XM_001131891	LOC732115	1
NM_052936	ATG4A	1
NM_178270	ATG4A	1
NM_003740	KCNK5	1
NM_022766	CERK	1
NM_001080519	BAHCC1	1
XM_001134463	BAHCC1	1
NM_178439	GMCL1	1
NM_001003686	PMS2L3	1
NM_001033087	C20orf133	1
NM_080676	C20orf133	1
NM_003610	RAE1	1
NM_001015885	RAE1	1
NM_001664	RHOA	1
NM_177550	SLC13A5	1
NM_130807	MOBKL2A	1
NM_013382	POMT2	1
NM_004334	BST1	1
NM_133334	WHSC1	1
NM_001001790		1
NM_017958	PLEKHB2	1
NM_001100623		1
NM_001031739	ASB9	1
NM_024087	ASB9	1
NM_173602	DIP2B	1
NM_001077490	GNAS	1
NM_016592	GNAS	1
XM_291020	LOC339809	1
XM_936940	LOC339809	1
NM_198128	RNF138	1
NM_016271	RNF138	1
NM_007197	FZD10	1
NM_144767	AKAP13	1
NM_006738	AKAP13	1
NM_007200	AKAP13	1
NM_014630	ZNF592	1
NM_004586	RPS6KA3	1
NM_006791	MORF4L1	1
NM_206839	MORF4L1	1
XM_001126961	LOC730295	1
NM_006524	ZNF138	1
XM_001129007	LOC731265	1
NM_182492	LRP5L	1
NM_020245	TULP4	1
NM_001007466	TULP4	1
NM_001975	ENO2	1
NM_181489	ZNF445	1
NM_016631	C21orf66	1
NM_016376	ANKFY1	1
NM_182551	LYCAT	1
NM_001002257	LYCAT	1
NM_015373	CBY1	1
NM_001002880	CBY1	1
NM_001018053	PFKFB2	1
NM_180991	SLCO4C1	1
NM_018569	C4orf16	1
XM_001133837	LOC732099	1
XM_001133987	LOC729681	1
NM_030755	TXNDC1	1
NM_015038		1
XM_934118	LOC653489	1
XM_934115	LOC653489	1
NM_018036	C14orf103	1
NM_017730	QRICH1	1
NM_198880	QRICH1	1
NM_033285	TP53INP1	1
NM_145303	LOC202459	1
NM_181354	OXR1	1
NM_201397	GPX1	1
NM_152409	C5orf24	1
NM_001042437	ST3GAL5	1
NM_003896	ST3GAL5	1
NM_001011553	SEPT7	1
NM_001788	SEPT7	1
NM_003800	RNGTT	1
NM_001414	EIF2B1	1
NM_006372	SYNCRIP	1
NM_005813	PRKD3	1
NM_006306	SMC1A	1
NM_139277	KLK7	1
NM_005046	KLK7	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