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 GACGCACCUUGGGAGAGGU (6 guide strand hits and 10 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_002227

JAK1

2007

2025

c

g

a

G

C

A

C

C

U

U

G

G

G

A

G

A

G

G

c

62

4

15

bc

false

<90%

5053

NM_014851

KLHL21

2178

2196

u

u

C

c

C

A

C

C

U

U

G

G

G

A

G

A

G

G

a

44

4

14

bc

false

<90%

4502

NM_020205

OTUD7B

3760

3778

a

g

u

G

C

A

C

C

U

U

G

G

G

A

G

g

G

G

U

40

4

12

c

false

<90%

6413

NM_152657

GGN

1031

1049

c

u

C

G

C

c

C

C

U

U

G

G

G

A

G

A

G

G

U

23

3

13

bc

false

<90%

2168

NM_000384

APOB

2458

2476

u

c

C

G

C

A

u

C

U

U

G

G

G

A

G

A

G

G

a

15

4

11

bc

false

<90%

14121

NM_001012454

LOC346653

1120

1138

a

A

g

u

g

A

C

C

U

U

G

G

G

A

G

A

G

G

U

-9

4

14

bc

false

<90%

1199

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_199248

CACNB1

1193

1211

A

C

C

U

C

U

C

C

C

A

A

G

G

U

a

C

u

U

C

51

2

14

c

false

<90%

1700

NM_199247

CACNB1

1328

1346

A

C

C

U

C

U

C

C

C

A

A

G

G

U

a

C

u

U

C

51

2

14

c

false

<90%

1847

NM_000723

CACNB1

1193

1211

A

C

C

U

C

U

C

C

C

A

A

G

G

U

a

C

u

U

C

51

2

14

c

false

<90%

3687

NM_000185

SERPIND1

1982

2000

A

C

C

U

C

U

C

C

C

A

A

G

G

a

G

g

G

U

a

49

3

13

c

false

<90%

2237

NR_003130

HSP90B3P

638

656

A

C

C

U

C

a

C

C

C

A

A

G

G

g

G

C

G

U

g

12

3

7

c

false

<90%

8768

NM_033225

CSMD1

3678

3696

A

C

C

U

C

U

g

C

C

A

A

G

G

U

G

u

G

U

g

2

3

8

c

false

<90%

11820

NM_052900

CSMD3

3543

3561

A

C

C

U

C

U

g

C

C

A

A

G

G

U

G

u

G

U

g

2

3

8

c

false

<90%

12643

NM_198124

CSMD3

3747

3765

A

C

C

U

C

U

g

C

C

A

A

G

G

U

G

u

G

U

g

2

3

8

c

false

<90%

13042

NM_198123

CSMD3

3855

3873

A

C

C

U

C

U

g

C

C

A

A

G

G

U

G

u

G

U

g

2

3

8

c

false

<90%

13150

NM_152363

ANKRD41

1514

1532

g

C

C

U

g

c

C

C

C

A

A

G

G

U

G

C

G

U

C

-16

3

13

bc

false

<90%

2893

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 269
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_153818	PEX10	2
NM_002617	PEX10	2
NM_001626	AKT2	2
NM_003576	STK24	1
NM_001032296	STK24	1
NM_005638	SYBL1	1
NM_024910	ZNF767	1
XM_001132771	FAM116A	1
NM_152678	FAM116A	1
NM_145297	ZNF626	1
NM_001099270		1
NM_014473	DIMT1L	1
NM_021224	ZNF462	1
NM_015056	RRP1B	1
XM_001133679	LOC729264	1
XM_001133677	LOC729264	1
NM_001099687		1
XM_001133686	LOC729355	1
NM_016212	TP53TG3	1
NM_001083591	CUGBP2	1
NM_001025077	CUGBP2	1
NM_006561	CUGBP2	1
NM_001025076	CUGBP2	1
XM_037557	KIAA0984	1
XM_939476	KIAA0984	1
NM_001098784		1
NM_000983	RPL22	1
NM_032607	CREB3L3	1
NM_181337	KAAG1	1
NM_006912	RIT1	1
NM_001004358	FGFRL1	1
NM_021923	FGFRL1	1
NM_001004356	FGFRL1	1
NM_205843	NFIC	1
NM_005597	NFIC	1
NM_004431	EPHA2	1
NM_033133	CNP	1
NM_002737	PRKCA	1
NM_133448	TMEM132D	1
NM_001099678		1
NM_152307	C14orf172	1
NM_178835	LOC152485	1
NM_002068	GNA15	1
NM_020768	KCTD16	1
NM_006454	MXD4	1
NM_032287	LDOC1L	1
NM_004852	ONECUT2	1
NM_001012727	AGPAT2	1
NM_006412	AGPAT2	1
NM_020700		1
NM_000757	CSF1	1
NM_172211	CSF1	1
NM_014117	C16orf72	1
NM_022725	FANCF	1
NM_022458	LMBR1	1
NM_000172	GNAT1	1
NM_144499	GNAT1	1
XM_001134414	C1orf133	1
XM_001134416	C1orf133	1
XM_001134417	C1orf133	1
XM_001134415	C1orf133	1
NM_013382	POMT2	1
NM_000033	ABCD1	1
NM_004893	H2AFY	1
NM_138610	H2AFY	1
NM_138609	H2AFY	1
NM_001040158	H2AFY	1
NM_001718	BMP6	1
NM_018306	TMEM40	1
NM_017566	KLHDC4	1
NM_198560	LHFPL4	1
NM_002911	UPF1	1
NM_003247	THBS2	1
NM_001941	DSC3	1
NM_024423	DSC3	1
NM_020378	NAT14	1
NM_181489	ZNF445	1
NM_005231	CTTN	1
NM_138565	CTTN	1
XM_942780	SYNPO2	1
NM_021008	DEAF1	1
XM_001129197	DEAF1	1
NM_018717	MAML3	1
NM_139246	C9orf97	1
NM_006037	HDAC4	1
NM_052906	LRRC62	1
NM_021943	ZFAND3	1
NM_014634	PPM1F	1
NM_001024843	TNRC6B	1
NM_015088	TNRC6B	1
NM_032034	SLC4A11	1
NM_005822	DSCR1L1	1
NM_153022	C12orf59	1
NM_001100624		1
NM_024607	PPP1R3B	1
NM_003764	STX11	1
NM_003151	STAT4	1
NM_172208	TAPBP	1
NM_001101372		1
NM_024605	ARHGAP10	1
NM_005566	LDHA	1
NM_198461	LONRF2	1
NM_024022	TMPRSS3	1
NM_032404	TMPRSS3	1
NM_032401	TMPRSS3	1
NM_014299	BRD4	1
NM_014507	MCAT	1
NM_018403	DCP1A	1
NM_020747	ZNF608	1
NM_003742	ABCB11	1
NM_000778	CYP4A11	1
NM_001002814	RAB11FIP1	1
NM_002019	FLT1	1
NM_033261	IDI2	1
NM_032737	LMNB2	1
NM_014770	CENTG1	1
NM_013227	ACAN	1
NM_001135	ACAN	1
NM_012193	FZD4	1
NM_024537	CARS2	1
NM_018941	CLN8	1
NM_014643		1
NM_020630	RET	1
NM_001003891	PCQAP	1
NM_015889	PCQAP	1
NM_181671	PITPNC1	1
NM_001006641	SLC25A25	1
NM_001006642	SLC25A25	1
NM_052901	SLC25A25	1
NM_001006643	SLC25A25	1
NM_017723	C9orf167	1
XM_938725	LOC151234	1
XM_930027	LOC151234	1
NM_001008895	CUL4A	1
NM_003589	CUL4A	1
NM_014587	SOX8	1
NM_015381	FAM19A5	1
NM_001082967	FAM19A5	1
NM_006795	EHD1	1
NM_014601	EHD2	1
NM_173482	CCDC105	1
XM_945302	LOC652225	1
XM_934407	LOC647131	1
XM_495918	FLJ13224	1
XM_938169	FLJ13224	1
NM_020134	DPYSL5	1
NM_001846	COL4A2	1
NM_198850	PHLDB3	1
XM_928224	LOC653583	1
XM_001131797	LOC732075	1
NM_001004439	ITGA11	1
NM_018027	FRMD4A	1
NM_007118	TRIO	1
NM_007011	ABHD2	1
NM_152924	ABHD2	1
NM_014943	ZHX2	1
NM_023110	FGFR1	1
NM_023106	FGFR1	1
NM_015850	FGFR1	1
NM_023111	FGFR1	1
NM_023105	FGFR1	1
NM_001754	RUNX1	1
NM_001001890	RUNX1	1
NM_024738	C12orf49	1
NM_145173	DIRAS1	1
NM_015313	ARHGEF12	1
NM_004571	PKNOX1	1
NM_145253	FAM100A	1
NM_001104925		1
NM_018257	PCMTD2	1
NM_001003656	PPP2R2D	1
NM_018461	PPP2R2D	1
NM_001044	SLC6A3	1
NM_024742	ARMC5	1
NM_130844	WWOX	1
XM_001132325	LOC730081	1
XM_001127777	LOC730934	1
NM_004145	MYO9B	1
NM_145159	JAG2	1
NM_002226	JAG2	1
NM_032982	CASP2	1
NM_032983	CASP2	1
NM_003221	TFAP2B	1
NM_174983	C19orf28	1
XM_931359	LOC338758	1
XM_944677	LOC338758	1
NM_001535	PRMT2	1
NM_206962	PRMT2	1
NM_004630	SF1	1
NM_018641	CHST12	1
NM_002653	PITX1	1
NM_001012994		1
NM_005829	AP3S2	1
NM_001097620		1
NM_207127	PAOX	1
NM_015259	ICOSLG	1
NM_001040001	MLLT4	1
NM_024735	FBXO31	1
NM_001025092	MBP	1
NM_002385	MBP	1
NM_001025081	MBP	1
NM_001025090	MBP	1
NM_001025101	MBP	1
XM_939259	ZNF469	1
XM_001125745	ZNF469	1
NM_001039802	CDC42	1
NM_001791	CDC42	1
NM_001089595		1
NM_080764	SUHW2	1
NM_145060	C18orf24	1
NM_001039535	C18orf24	1
NM_018390	PLCXD1	1
NM_020896	OSBPL5	1
NM_145638	OSBPL5	1
NM_198240	CLIP1	1
NM_002956	CLIP1	1
NM_022112	P53AIP1	1
NM_002243	KCNJ15	1
NM_170736	KCNJ15	1
NM_170737	KCNJ15	1
NM_032508	TMEM185A	1
NM_000303	PMM2	1
NM_025040	ZNF614	1
NM_000332	ATXN1	1
NM_004821	HAND1	1
NM_001102371		1
NM_024955	FOXRED2	1
NM_000301	PLG	1
NM_001005463	EBF3	1
NM_015365	AMMECR1	1
NM_001025580	AMMECR1	1
NM_001299	CNN1	1
NM_000788	DCK	1
NM_020651	PELI1	1
NM_153611	CYBASC3	1
NM_003045	SLC7A1	1
NM_002357	MXD1	1
NM_022557	GH2	1
NM_022644	CSH2	1
NM_022640	CSH1	1
NM_001039570	KREMEN1	1
NM_001039571	KREMEN1	1
NM_015570	AUTS2	1
NM_173344	ST3GAL1	1
NM_003033	ST3GAL1	1
NM_006038	SPATA2	1
NM_198055	MZF1	1
NM_003422	MZF1	1
NM_014649	SAFB2	1
XM_941352	LOC255275	1
XM_171855	LOC255275	1
NM_001098484		1
NM_003759	SLC4A4	1
XM_930505	LOC645676	1
XM_941520	LOC645676	1
NM_001001938	C9orf47	1
NM_001319	CSNK1G2	1
NM_021168	RAB40C	1
NM_021924	MUPCDH	1
NM_031264	MUPCDH	1
NM_198901	SRI	1
NM_003130	SRI	1
NM_199169	TMEPAI	1
NM_199170	TMEPAI	1
NM_199171	TMEPAI	1
NM_020182	TMEPAI	1
NM_005585	SMAD6	1
NM_018961	UBASH3A	1
NM_001001895	UBASH3A	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