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 ACGAACUUGGAGCAGUCCG (2 guide strand hits and 15 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_018167

BTBD7

36

54

g

g

G

A

A

C

c

U

G

G

A

G

C

A

G

U

C

C

c

15

4

11

bc

false

<90%

2568

NM_001002860

BTBD7

36

54

g

g

G

A

A

C

c

U

G

G

A

G

C

A

G

U

C

C

c

15

4

11

bc

false

<90%

8448

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_001083605

PTCH1

1268

1286

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

7658

NM_001083604

PTCH1

1285

1303

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

7675

NM_001083606

PTCH1

1367

1385

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

7757

NM_001083607

PTCH1

1441

1459

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

7831

NM_001083603

PTCH1

1521

1539

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

7911

NM_000264

PTCH1

1567

1585

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

7957

NM_001083602

PTCH1

1675

1693

g

G

G

A

C

U

G

C

U

C

C

A

A

G

U

c

C

c

a

64

4

14

c

false

<90%

8065

NM_033226

ABCC12

3548

3566

C

G

G

A

C

U

G

C

U

C

C

A

A

G

U

g

u

G

U

50

2

15

c

false

<90%

5168

NM_032482

DOT1L

2117

2135

u

G

G

A

C

U

G

C

a

C

C

A

A

G

U

U

C

u

c

30

4

8

c

false

<90%

4889

NM_153603

COG7

190

208

u

G

G

A

C

U

u

C

U

C

C

A

A

G

U

U

C

c

U

29

3

10

c

false

<90%

2792

NM_173157

NR4A1

1309

1327

u

G

G

A

C

U

a

C

U

C

C

A

A

G

U

U

C

c

a

24

4

10

c

false

<90%

2549

NM_002135

NR4A1

1459

1477

u

G

G

A

C

U

a

C

U

C

C

A

A

G

U

U

C

c

a

24

4

10

c

false

<90%

2699

XM_001125744

LOC92154

1142

1160

C

G

G

A

C

U

G

g

U

C

C

A

A

G

g

U

C

G

g

8

3

7

c

false

<90%

2852

NM_138383

ABBA-1

1387

1405

C

G

G

A

C

U

G

g

U

C

C

A

A

G

g

U

C

G

g

8

3

7

c

false

<90%

4977

NM_178841

RNF166

452

470

C

c

a

A

C

U

G

C

c

C

C

A

A

G

U

U

C

G

U

8

3

10

bc

false

<90%

1895

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 247
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_024569	MPZL1	2
NM_003953	MPZL1	2
NM_015207		2
NM_032873	STS-1	2
NM_152594	SPRED1	1
NM_198392	TCF21	1
NM_198480	ZNF615	1
NM_032291	SGIP1	1
NM_014720	SLK	1
NM_025149	FLJ20920	1
NM_020803	KLHL8	1
XM_001129103	LOC729029	1
XM_001128912	LOC731238	1
NM_022780	RMND5A	1
NM_206933	USH2A	1
NM_014289	CAPN6	1
NM_022149	MAGEF1	1
NM_014911	AAK1	1
NM_021912	GABRB3	1
NM_000814	GABRB3	1
NM_001896	CSNK2A2	1
NM_198973	MKNK1	1
NM_138718	SLC26A8	1
NM_052961	SLC26A8	1
NM_003200	TCF3	1
NM_001257	CDH13	1
NM_203463	LASS6	1
NM_022901	LRRC19	1
NM_012397	SERPINB13	1
NM_000217	KCNA1	1
NM_012290	TLK1	1
XM_001130398	LOC731666	1
XM_001131009	LOC729680	1
NM_001362	DIO3	1
NM_002092	GRSF1	1
NM_001098477		1
NM_005737	ARL4C	1
NM_176081	TRDMT1	1
NM_004412	TRDMT1	1
NM_176083	TRDMT1	1
NM_018124	RFWD3	1
NM_172375	KCNH5	1
NM_001005473	PLCXD3	1
NM_005329	HAS3	1
NM_015227	POFUT2	1
NM_014344	FJX1	1
XM_946265	FHAD1	1
XM_934889	FHAD1	1
NM_001439	EXTL2	1
NM_001033025	EXTL2	1
NM_016410	CHMP5	1
NM_001049	SSTR1	1
NM_006547	IGF2BP3	1
NM_001001420	SMAD5	1
NM_001001419	SMAD5	1
NM_005903	SMAD5	1
NM_015173	TBC1D1	1
NM_022458	LMBR1	1
NM_207172	NPSR1	1
NM_198194	STOM	1
NM_004099	STOM	1
XM_001131068	LOC729696	1
XM_001129643	LOC731435	1
NM_020762	SRGAP1	1
NM_007067	MYST2	1
NM_020853	KIAA1467	1
NM_017723	C9orf167	1
NM_139008	HFE	1
NM_139003	HFE	1
NM_139010	HFE	1
NM_139011	HFE	1
NM_139009	HFE	1
NM_000410	HFE	1
NM_139004	HFE	1
NM_139007	HFE	1
NM_139006	HFE	1
NM_001102608		1
NM_005494	DNAJB6	1
XM_941810	LOC284023	1
XM_929835	LOC284023	1
NM_003347	UBE2L3	1
NM_198157	UBE2L3	1
NM_003983	SLC7A6	1
NM_001076785	SLC7A6	1
NM_033064	ATCAY	1
NM_003247	THBS2	1
NM_207577	MAP6	1
NM_004285	H6PD	1
NM_005284	GPR6	1
NM_024751	GSTCD	1
NM_014734	KIAA0247	1
NM_005065	SEL1L	1
XM_001131577	FLJ36644	1
XM_001126095	FLJ36644	1
XM_943323	LOC646719	1
XM_933842	LOC646719	1
NM_025185		1
NM_016538	SIRT7	1
NM_203411	TMEM88	1
NM_016235	GPRC5B	1
NM_006379	SEMA3C	1
NM_003296	CRISP2	1
NM_002865	RAB2A	1
NM_014817	KIAA0644	1
NM_016028	SUV420H1	1
NM_024630	ZDHHC14	1
NM_153746	ZDHHC14	1
NM_015565	ZNF294	1
NM_001031835	PHKB	1
NM_000293	PHKB	1
NM_006237	POU4F1	1
NM_031844	HNRPU	1
NM_004501	HNRPU	1
NM_198066	GNPNAT1	1
NM_024870	DEPDC2	1
NM_003655	CBX4	1
NM_177535	MAGED4	1
NM_177537	MAGED4	1
NM_001098800		1
NM_030801	MAGED4	1
NM_004055	CAPN5	1
NM_001040059	CD68	1
NM_001251	CD68	1
NM_001007271	DUSP13	1
NM_020993	BCL7A	1
NM_001024808	BCL7A	1
NM_053064	GNG2	1
NM_002073	GNAZ	1
NM_134269	SMTN	1
NM_014901	RNF44	1
NM_182573	LYPD5	1
NM_001031749	LYPD5	1
NM_032866	CGNL1	1
NM_018268	WDR41	1
NM_015446	AHCTF1	1
XM_001126456	AHCTF1	1
NM_014916	LMTK2	1
NM_016018	PHF20L1	1
XM_934287	LOC144817	1
XM_945225	LOC144817	1
NM_003107	SOX4	1
NM_000527	LDLR	1
NM_016823	CRK	1
NM_005206	CRK	1
XM_934166	LOC653441	1
NM_004426	PHC1	1
NM_002859	PXN	1
NM_001498	GCLC	1
NM_025113	C13orf18	1
XM_936833	LOC644196	1
XM_927389	LOC644196	1
NM_144963	FAM91A1	1
NM_007137	ZNF81	1
NM_001098475		1
NM_012215	MGEA5	1
NM_001014283	DCUN1D2	1
NM_022748	TNS3	1
NM_004697	PRPF4	1
NM_133477	SYNPO2	1
XM_942776	SYNPO2	1
XM_936336	SYNPO2	1
NM_002336	LRP6	1
NM_001105	ACVR1	1
XM_292785	LOC342865	1
XM_939057	LOC342865	1
NM_006055	LANCL1	1
NM_002072	GNAQ	1
NM_177454	KIAA1946	1
NM_172239	REXO1L1	1
NM_004725	BUB3	1
NM_032300	TCHP	1
NM_001012993	C9orf152	1
NM_016545	IER5	1
XM_371369	MIA3	1
XM_943876	MIA3	1
XM_943869	MIA3	1
XM_943873	MIA3	1
XM_496436	MIA3	1
XM_932541	MIA3	1
XM_932548	MIA3	1
NM_198551	MIA3	1
NM_012194		1
NM_014743	KIAA0232	1
NM_001100590		1
NM_001449	FHL1	1
NM_153048	FYN	1
NM_002037	FYN	1
NM_153047	FYN	1
NM_130848	C5orf20	1
NM_005789	PSME3	1
NM_176863	PSME3	1
NM_000147	FUCA1	1
NM_015042	ZNF609	1
NM_012184	FOXD4L1	1
NM_207305	FOXD4	1
NM_199358	FOXD4L3	1
NM_001085476		1
NM_199135	FOXD4L2	1
NM_001099279		1
NM_199244	FOXD4L4	1
NM_201555	FHL2	1
NM_001450	FHL2	1
NM_201557	FHL2	1
NM_001039492	FHL2	1
NM_001104647		1
NM_018155	SLC25A36	1
NM_003480	MFAP5	1
NM_021960	MCL1	1
NM_182763	MCL1	1
XM_370636	LOC387787	1
XM_945912	LOC650826	1
NM_001523	HAS1	1
NM_004566	PFKFB3	1
NM_173683	XKR6	1
NM_003679	KMO	1
XM_929496	LOC646561	1
NM_207362	MGC42367	1
NM_001098819		1
NM_001098818		1
NM_000923	PDE4C	1
NM_182493	MLCK	1
NM_001098638		1
NM_138468	ICA1L	1
NM_017628	KIAA1546	1
NM_002190	IL17A	1
NM_018323	PI4K2B	1
NM_000880	IL7	1
XM_927661	LOC644538	1
XM_939025	LOC644538	1
NM_020943	KIAA1604	1
NM_172071	RC3H1	1
NM_005602	CLDN11	1
NM_022965	FGFR3	1
NM_000142	FGFR3	1
XM_944363	SIRPB2	1
NM_032808	LINGO1	1
NM_005130	FGFBP1	1
NM_004283	RAB3D	1
NM_000223	KRT12	1
NM_019613	WDR45L	1
NM_016248	AKAP11	1
NM_005694	COX17	1
NM_053045	MGC14327	1
NM_004504	HRB	1
NM_006910	RBBP6	1
NM_018703	RBBP6	1
NM_003221	TFAP2B	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