VIRsiRNAdb

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

12 hits were found for UUCGCAGUCCCCAACCUCC (5 guide strand hits and 7 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_003221

TFAP2B

2003

2021

c

U

C

G

C

A

G

U

C

C

C

C

g

c

C

C

U

C

C

68

3

11

false

<90%

5770

NM_014767

SPOCK2

3423

3441

c

U

g

G

C

A

G

U

C

C

C

C

A

g

C

C

U

C

C

58

3

10

c

false

<90%

5316

NM_152403

EGFLAM

197

215

c

U

C

G

C

A

G

c

C

C

C

C

c

A

C

C

U

C

C

25

3

6

false

<90%

3952

NM_144968

RIBC1

885

903

U

g

u

G

C

A

G

a

C

C

C

C

A

A

C

C

U

C

C

6

3

11

bc

false

<90%

1949

NM_139285

GAS2L2

2586

2604

a

g

a

G

C

A

G

c

C

C

C

C

A

A

C

C

U

C

C

4

4

11

bc

false

<90%

3025

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_032025

EIF2A

3666

3684

a

G

A

G

G

U

U

G

G

G

G

A

C

U

u

C

G

u

g

65

4

13

c

false

<90%

3894

NM_004285

H6PD

4153

4171

a

u

A

G

G

U

U

G

G

G

G

A

C

U

G

u

G

A

u

55

4

13

c

false

<90%

9117

NM_145214

TRIM11

1291

1309

G

G

A

G

G

U

U

G

G

G

G

A

C

c

G

C

a

c

c

49

4

13

c

false

<90%

2715

NM_018424

EPB41L4B

928

946

G

G

A

G

c

U

U

G

G

G

G

A

g

U

G

C

G

A

g

33

3

7

false

<90%

3783

NM_019114

EPB41L4B

928

946

G

G

A

G

c

U

U

G

G

G

G

A

g

U

G

C

G

A

g

33

3

7

false

<90%

5578

NM_006339

HMG20B

586

604

c

a

A

G

G

g

U

G

G

G

G

A

C

U

G

C

G

A

u

18

4

12

bc

false

<90%

1584

NM_006677

USP19

2855

2873

G

G

A

G

G

c

U

G

G

G

G

A

C

a

G

C

G

A

g

12

3

7

c

false

<90%

4401

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 328
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_024076	KCTD15	2
NM_000912	OPRK1	2
NM_152371	C1orf93	2
NM_022166	XYLT1	2
XM_001125986	LOC283824	2
NM_001039479	KIAA0317	2
NM_022745	ATPAF1	2
NM_001042546	ATPAF1	2
NM_002073	GNAZ	1
XM_939259	ZNF469	1
XM_001125745	ZNF469	1
NM_020975	RET	1
NM_032229	SLITRK6	1
NM_020960	GPR107	1
XM_928252	LOC645212	1
XM_939117	LOC645212	1
NM_000817	GAD1	1
NM_005188	CBL	1
NM_018403	DCP1A	1
NM_178554	KY	1
NM_001037165	FOXK1	1
NM_001112736		1
NM_054030	MRGPRX2	1
NM_178818	CMTM4	1
NM_181521	CMTM4	1
XM_001132281	LOC728716	1
NM_001932	MPP3	1
NM_033224	PURB	1
NM_020122	KCMF1	1
XM_001133393	KCMF1	1
NM_022777	RABL5	1
NM_133334	WHSC1	1
NM_001040101	D4S234E	1
NM_014392	D4S234E	1
NM_182628	CCDC37	1
NM_017438	SETD4	1
NM_145802	SEPT6	1
NM_145800	SEPT6	1
NM_001042508	LOC653483	1
XM_001125098	LOC730417	1
NM_014926	SLITRK3	1
NM_021634	RXFP1	1
XM_938028	C19orf16	1
NM_207577	MAP6	1
XM_001127146	IL7R	1
NM_003094	SNRPE	1
NM_002639	SERPINB5	1
NM_033131	WNT3A	1
NM_015191	SNF1LK2	1
NM_015409	EP400	1
NM_022062	PKNOX2	1
NM_006861	RAB35	1
NM_015554	GLCE	1
XM_001131577	FLJ36644	1
XM_001126095	FLJ36644	1
NM_080671	KCNE4	1
NM_003128	SPTBN1	1
NM_015568	PPP1R16B	1
NM_014787	DNAJC6	1
NM_173601		1
NM_001099650		1
NM_144638	TMEM42	1
NM_003124	SPR	1
NM_030647	JHDM1D	1
NM_000647	CCR2	1
XM_001133430	LOC729230	1
NM_015289	VPS39	1
NM_014944	CLSTN1	1
NM_001009566	CLSTN1	1
NM_138635	H2AFV	1
NM_001014797	KCNMA1	1
NM_003082	SNAPC1	1
NM_033066	MPP4	1
NM_001029839	C3orf23	1
NM_001029840	C3orf23	1
NM_182485	CPEB2	1
NM_182646	CPEB2	1
NM_005528	DNAJC4	1
NM_004491	GRLF1	1
NM_002382	MAX	1
NM_145113	MAX	1
NM_145112	MAX	1
NM_001031617	COX19	1
NM_005858	AKAP8	1
XM_378661	C17orf51	1
XM_944416	C17orf51	1
NM_014803	ZNF518	1
NM_016021	UBE2J1	1
NM_005940	MMP11	1
NM_001003936	TXNDC8	1
NM_004395	DBN1	1
NM_080881	DBN1	1
NM_005477	HCN4	1
NM_144993		1
NM_003328	TXK	1
NM_020940	KIAA1600	1
NM_053042	KIAA1729	1
NM_000555	DCX	1
NM_178152	DCX	1
NM_178153	DCX	1
NM_178151	DCX	1
NM_014876	JOSD1	1
NM_001025356	TMEM16F	1
NM_000545	TCF1	1
XM_001129997	NTSR2	1
NM_012344	NTSR2	1
NM_001001549	GRB10	1
NM_001001555	GRB10	1
NM_001001550	GRB10	1
NM_005311	GRB10	1
NM_172169	CAMK2G	1
NM_001222	CAMK2G	1
NM_172173	CAMK2G	1
NM_172171	CAMK2G	1
NM_172170	CAMK2G	1
NM_052846	EMILIN3	1
NM_003045	SLC7A1	1
NM_003681	PDXK	1
NM_004852	ONECUT2	1
NM_014653	WSCD2	1
NM_000455	STK11	1
NM_024522	FAM77C	1
XM_001129946	LOC730396	1
XM_001130706	LOC729583	1
XM_001131223	LOC730405	1
XM_001131133	LOC731885	1
NM_032039	ITFG3	1
NM_181458	PAX3	1
NM_181461	PAX3	1
NM_004614	TK2	1
NM_024749	VASH2	1
NM_003189	TAL1	1
NM_033446	FAM125B	1
NM_153345	TMEM139	1
NM_001419	ELAVL1	1
NM_006315	PCGF3	1
NM_006176	NRGN	1
NM_001100170		1
NM_001100169		1
NM_006839	IMMT	1
NM_000368	TSC1	1
XM_001133521	MGC51338	1
XM_001132564	LOC728882	1
XM_001133525	LOC731501	1
NM_001362	DIO3	1
NM_153334	SCARF2	1
NM_182895	SCARF2	1
XM_001133211	LOC729003	1
XM_001133556	LOC729135	1
NM_203329	CD59	1
NM_203331	CD59	1
NM_203330	CD59	1
NM_000611	CD59	1
XM_926158	LOC642443	1
XM_936495	LOC647346	1
NM_004898	CLOCK	1
NM_152722	HEPACAM	1
XM_946142	SHANK3	1
NM_001080420	SHANK3	1
NM_014418	TCL6	1
NM_012468	TCL6	1
NM_144599	NIPA1	1
NM_033012	TNFSF11	1
NM_003701	TNFSF11	1
NM_019117	KLHL4	1
NM_001098816		1
NM_201520	SLC25A35	1
NM_170665	ATP2A2	1
NM_003592	CUL1	1
NM_145285	NKX2-3	1
NM_015891	CDC40	1
NM_001043318	C14orf43	1
NM_194278	C14orf43	1
NM_004481	GALNT2	1
NM_001010903	DKFZp779B1540	1
NM_016073	HDGFRP3	1
NM_001018058	TFEC	1
NM_012252	TFEC	1
NM_000330	RS1	1
NM_181654	CPLX4	1
NM_015035	ZHX3	1
NM_001017370	LOC387921	1
NM_001012754	LOC387921	1
NM_017972	C14orf118	1
NM_017926	C14orf118	1
NM_001083962		1
NM_003199	TCF4	1
NM_006753	SURF6	1
NM_031200	CCR9	1
NM_006641	CCR9	1
NM_001008408	RBM33	1
NM_053043	PRR8	1
NM_052862	RCSD1	1
NM_005934	MLLT1	1
XM_001131982	LOC731109	1
NM_007084	SOX21	1
NM_015481	ZNF385	1
NM_000206	IL2RG	1
NM_021945	C6orf85	1
NM_015170	SULF1	1
NM_001348	DAPK3	1
NM_001005502	CPM	1
NM_198320	CPM	1
NM_001874	CPM	1
NM_001093772		1
NM_000222	KIT	1
NM_145274	TMEM99	1
NM_003023	SH3BP2	1
NM_001013624	LOC201181	1
NM_001029861	NANOS2	1
NM_001527	HDAC2	1
NM_198571	FLJ39237	1
NM_003505	FZD1	1
NM_005883	APC2	1
NM_001040402	DCUN1D4	1
NM_015115	DCUN1D4	1
NM_004454	ETV5	1
XM_001134164	ETV5	1
NM_052918	SORCS1	1
NM_001013031	SORCS1	1
XM_001131384	LOC646522	1
XM_933676	LOC646522	1
NM_012184	FOXD4L1	1
NM_001099279		1
NM_199244	FOXD4L4	1
NM_199358	FOXD4L3	1
NM_001085476		1
NM_199135	FOXD4L2	1
NM_207305	FOXD4	1
NM_000461	THRB	1
NM_015086	DDN	1
NM_001080395	AATK	1
NM_001715	BLK	1
NM_005337	NCKAP1L	1
NM_014293	NPTXR	1
NM_006266	RALGDS	1
NM_001042368	RALGDS	1
NM_018073	TRIM68	1
NM_005032	PLS3	1
NM_024071	ZFYVE21	1
NM_183230	IKZF3	1
NM_183229	IKZF3	1
NM_183231	IKZF3	1
NM_183228	IKZF3	1
NM_183232	IKZF3	1
NM_012481	IKZF3	1
NM_000831	GRIK3	1
XM_001125933	LOC727737	1
NM_006454	MXD4	1
NM_178520	TMEM105	1
NM_003910	BUD31	1
NM_005829	AP3S2	1
NM_002942	ROBO2	1
NM_004865	TBPL1	1
NM_152834	TMEM18	1
XM_930505	LOC645676	1
XM_941520	LOC645676	1
NM_001102421		1
NM_001102420		1
NM_006007	ZFAND5	1
NM_138434	C7orf29	1
NM_003808	TNFSF13	1
NM_172088	TNFSF13	1
NM_172087	TNFSF13	1
NM_172089	TNFSF12-TNFSF13	1
NM_145175	FAM84A	1
NM_017705	PAQR5	1
NM_001104554		1
NM_002428	MMP15	1
NM_004455	EXTL1	1
NM_006933	SLC5A3	1
NM_015266	SLC9A8	1
NM_001259	CDK6	1
NM_001012994		1
NM_004438	EPHA4	1
NM_004730	ETF1	1
NM_023112	OTUB2	1
NM_207406	CCDC4	1
NM_004982	KCNJ8	1
NM_001089591		1
NM_173156	SMG7	1
NM_201569	SMG7	1
NM_201568	SMG7	1
NM_153757	NAP1L5	1
NM_018955	UBB	1
NM_015855	WIT1	1
NM_005197	CHES1	1
NM_001085471		1
NM_001040214	TCBA1	1
NM_018075	TMEM16K	1
NM_001017930	WDR42B	1
NM_153367	C10orf56	1
NM_004088	DNTT	1
NM_001017520	DNTT	1
NM_001497	B4GALT1	1
NM_022479	WBSCR17	1
XM_939663	KIAA1553	1
NM_001080450	KIAA1553	1
NM_020836	KIAA1446	1
NM_006777	ZBTB33	1
NM_024820	DENND1A	1
NM_032521	PARD6B	1
NM_017758	ALKBH5	1
NM_032861	SERAC1	1
NM_133330	WHSC1	1
NM_001042424	WHSC1	1
NM_133331	WHSC1	1
NM_133335	WHSC1	1
NM_207303	ATRNL1	1
NM_007232	HRH3	1
NM_001032280	TFAP2A	1
NM_003220	TFAP2A	1
NM_001042425	TFAP2A	1
NM_019089	HES2	1
NM_194293	CMYA1	1
NM_001103170		1
NM_001103169		1
NM_001101676		1
NM_014112	TRPS1	1
NM_153712	TTL	1
NM_148893		1
NM_139135	ARID1A	1
NM_006015	ARID1A	1
NM_181836	TMED7	1
NM_018945	PDE7B	1
NM_002182	IL1RAP	1
NM_025224	ZBTB46	1
NM_014157	CCDC113	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).

---

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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