VIRsiRNAdb

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

47 hits were found for CGAUAGCUGCUUCUUCUUG (6 guide strand hits and 41 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_001039580

MAP9

3654

3672

a

a

A

U

A

G

C

U

G

C

U

U

g

U

U

C

U

U

a

71

4

10

false

<90%

7333

NM_004569

PIGH

1220

1238

a

G

A

U

A

G

C

U

G

C

U

U

u

U

U

a

U

U

G

61

3

11

false

<90%

1439

XR_018098

LOC642241

444

462

C

u

A

a

A

G

C

U

G

C

U

U

C

U

U

C

U

U

u

46

3

14

bc

false

<90%

1670

NM_133268

OSBPL1A

1056

1074

u

G

A

U

A

G

C

U

G

C

c

U

C

U

U

C

U

U

u

31

3

9

c

false

<90%

4096

NM_080597

OSBPL1A

1056

1074

u

G

A

U

A

G

C

U

G

C

c

U

C

U

U

C

U

U

u

31

3

9

c

false

<90%

4165

NM_019605

SERTAD4

1655

1673

a

G

A

U

A

c

C

U

G

C

U

U

C

U

U

C

U

a

u

27

4

11

c

false

<90%

2038

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_001723

DST

2715

2733

g

A

A

G

A

A

G

A

A

G

C

A

G

u

U

A

U

a

G

75

3

12

c

false

<90%

8972

NM_020388

DST

2715

2733

g

A

A

G

A

A

G

A

A

G

C

A

G

u

U

A

U

a

G

75

3

12

c

false

<90%

9348

NM_015548

DST

2715

2733

g

A

A

G

A

A

G

A

A

G

C

A

G

u

U

A

U

a

G

75

3

12

c

false

<90%

16384

NM_183380

DST

4111

4129

g

A

A

G

A

A

G

A

A

G

C

A

G

u

U

A

U

a

G

75

3

12

c

false

<90%

18036

XR_017154

LOC390597

673

691

a

c

c

G

A

A

G

A

A

G

C

A

G

C

U

A

U

g

G

64

4

14

c

false

<90%

2185

XR_019085

LOC390597

673

691

a

c

c

G

A

A

G

A

A

G

C

A

G

C

U

A

U

g

G

64

4

14

c

false

<90%

2185

NM_000662

NAT1

85

103

C

A

g

G

A

A

G

A

A

G

C

A

G

C

a

A

U

C

u

50

3

11

c

false

<90%

1438

NM_002589

PCDH7

804

822

a

A

A

a

A

A

G

A

A

G

C

A

u

C

U

A

U

C

G

50

3

8

false

<90%

4646

NM_032457

PCDH7

804

822

a

A

A

a

A

A

G

A

A

G

C

A

u

C

U

A

U

C

G

50

3

8

false

<90%

4893

NM_032456

PCDH7

804

822

a

A

A

a

A

A

G

A

A

G

C

A

u

C

U

A

U

C

G

50

3

8

false

<90%

4921

XR_016911

LOC645266

1470

1488

C

A

A

G

A

A

G

A

A

G

C

A

G

g

U

c

U

C

c

49

3

13

c

false

<90%

3097

XR_018148

LOC645266

1470

1488

C

A

A

G

A

A

G

A

A

G

C

A

G

g

U

c

U

C

c

49

3

13

c

false

<90%

3097

NM_003913

PRPF4B

1179

1197

C

A

A

G

A

A

G

A

A

G

C

A

G

g

U

c

U

C

c

49

3

13

c

false

<90%

7482

XR_016385

LOC642828

651

669

C

A

A

G

A

A

G

A

A

G

C

A

G

C

U

g

c

g

G

47

3

15

c

false

<90%

928

XM_001127464

ALOX5

1776

1794

C

A

A

G

A

A

G

A

A

G

C

A

G

C

U

g

c

C

a

45

3

15

c

false

<90%

2278

NM_000698

ALOX5

2055

2073

C

A

A

G

A

A

G

A

A

G

C

A

G

C

U

g

c

C

a

45

3

15

c

false

<90%

2568

NM_014601

EHD2

1136

1154

C

A

A

G

A

A

G

A

A

G

C

A

G

C

U

g

a

u

c

42

4

15

c

false

<90%

3517

XM_940948

LOC651731

664

682

C

A

A

G

A

A

G

A

A

G

C

u

G

C

U

A

c

u

G

40

3

11

false

<90%

741

XM_930256

LOC647216

664

682

C

A

A

G

A

A

G

A

A

G

C

u

G

C

U

A

c

u

G

40

3

11

false

<90%

741

NM_015289

VPS39

1472

1490

C

A

A

G

A

A

G

A

A

G

C

u

G

C

U

A

c

a

a

35

4

11

false

<90%

4851

XR_017145

LOC643358

804

822

a

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

U

C

x

31

3

9

c

false

<90%

830

XR_019408

LOC649513

804

822

a

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

U

C

x

31

3

9

c

false

<90%

830

NM_015252

EHBP1

3705

3723

g

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

U

g

a

29

4

9

c

false

<90%

5077

NM_015057

MYCBP2

12890

12908

g

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

U

a

a

29

4

9

c

false

<90%

14735

NM_014367

C3orf28

520

538

a

A

A

G

A

g

G

A

A

G

C

A

G

C

U

A

U

g

a

27

4

11

c

false

<90%

838

XR_019078

LOC651103

230

248

C

A

A

G

A

A

G

A

A

G

C

A

G

C

a

c

c

a

G

23

4

14

c

false

<90%

1272

XR_016597

LOC401767

230

248

C

A

A

G

A

A

G

A

A

G

C

A

G

C

a

c

c

a

G

23

4

14

c

false

<90%

1273

XM_936897

KIAA1109

9500

9518

C

A

g

G

A

A

G

u

A

G

C

A

G

C

U

A

U

C

u

13

3

10

bc

false

<90%

15440

XM_371706

KIAA1109

9635

9653

C

A

g

G

A

A

G

u

A

G

C

A

G

C

U

A

U

C

u

13

3

10

bc

false

<90%

15575

XR_018334

LOC392505

646

664

C

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

c

a

G

12

3

10

c

false

<90%

863

XR_016288

LOC392505

646

664

C

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

c

a

G

12

3

10

c

false

<90%

863

NM_020843

ZNF291

1881

1899

C

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

a

g

G

12

3

10

c

false

<90%

4703

NM_032206

NLRC5

631

649

C

A

A

G

A

A

G

c

A

G

C

A

G

C

U

A

g

a

G

11

3

8

c

false

<90%

6822

NM_014890

FILIP1L

1640

1658

C

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

a

g

u

7

4

10

c

false

<90%

3274

NM_182909

FILIP1L

2577

2595

C

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

a

g

u

7

4

10

c

false

<90%

3962

NM_001042459

FILIP1L

2577

2595

C

A

A

G

A

A

G

A

A

G

a

A

G

C

U

A

a

g

u

7

4

10

c

false

<90%

4211

XM_001126647

MLKL

1325

1343

C

A

A

G

A

A

G

g

A

G

C

A

G

C

U

u

U

C

a

6

3

7

c

false

<90%

1832

NM_173690

C9orf126

813

831

C

A

A

G

A

A

G

u

A

G

C

A

G

C

U

u

U

C

a

6

3

7

c

false

<90%

1968

NM_152649

MLKL

1029

1047

C

A

A

G

A

A

G

g

A

G

C

A

G

C

U

u

U

C

a

6

3

7

c

false

<90%

2496

NM_020802

KIAA1377

2080

2098

C

A

A

a

A

A

G

c

A

G

C

A

G

C

U

A

U

C

a

-3

3

10

bc

false

<90%

7043

NM_020715

PLEKHH1

6508

6526

C

A

A

u

A

A

a

A

A

G

C

A

G

C

U

A

U

C

u

-8

3

11

bc

false

<90%

6540

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 115
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_016536	ZNF571	1
NM_012247	SEPHS1	1
NM_001013622	FAM53A	1
NM_002577	PAK2	1
NM_003955	SOCS3	1
NM_138972	BACE1	1
NM_012104	BACE1	1
NM_138973	BACE1	1
NM_138971	BACE1	1
XM_001133565	LOC731440	1
NM_020148	SPIRE1	1
NM_000320	QDPR	1
NM_017588	WDR5	1
NM_052821	WDR5	1
NM_005226	EDG3	1
NM_006080	SEMA3A	1
NM_019091	PLEKHA3	1
NM_014309	RBM9	1
NM_001082576	RBM9	1
NM_001082577	RBM9	1
NM_001031695	RBM9	1
NM_001082578	RBM9	1
NM_001082579	RBM9	1
NM_001003940	BMF	1
NM_001003943	BMF	1
NM_001003942	BMF	1
NM_033503	BMF	1
NM_002025	AFF2	1
NM_000684	ADRB1	1
NM_024770	METTL8	1
NM_001003398	BICD1	1
NM_001714	BICD1	1
NM_001001974	PLEKHA1	1
NM_021622	PLEKHA1	1
NM_000164	GIPR	1
NM_001030060	SAMD5	1
NM_001693	ATP6V1B2	1
NM_018662	DISC1	1
NM_001012957	DISC1	1
NM_004930	CAPZB	1
NM_139169	TRUB1	1
NM_004171	SLC1A2	1
NM_138700	TRIM40	1
NM_022832	USP46	1
NM_207454	FLJ44815	1
NM_022648	TNS1	1
NM_030918	SNX27	1
NM_022096	ANKRD5	1
NM_198798	ANKRD5	1
NM_015016		1
NM_181291	WDR20	1
NM_203403	C9orf150	1
NM_003747	TNKS	1
NM_002998	SDC2	1
XM_931945	LOC643962	1
XM_943665	LOC643962	1
NM_001001702	FLJ33360	1
NM_133487	RAD51	1
NM_002875	RAD51	1
NM_198506	FLJ44691	1
NM_003006	SELPLG	1
NM_175609	ARFGAP1	1
NM_018209	ARFGAP1	1
NM_016441	CRIM1	1
NM_199282	ARHGAP27	1
NM_022152	TMBIM1	1
NM_005845	ABCC4	1
NM_013449	BAZ2A	1
NM_030920	ANP32E	1
NM_138402	LOC93349	1
NM_007237	SP140	1
NM_005250	FOXL1	1
XM_940609	FLJ25076	1
XM_059689	FLJ25076	1
NM_001171	ABCC6	1
NM_014080	DUOX2	1
NM_007371	BRD3	1
NM_019067	GNL3L	1
NM_006180	NTRK2	1
NM_001018064	NTRK2	1
NM_024942	C10orf88	1
NM_000252	MTM1	1
NM_006291	TNFAIP2	1
NM_017688	BSPRY	1
NM_003410	ZFX	1
NM_002760	PRKY	1
NM_002712	PPP1R7	1
NM_014911	AAK1	1
NM_175875	SIX5	1
NM_199461	NANOS1	1
NM_032121	DKFZp564K142	1
NM_152523	CCNYL1	1
NM_080741	NEU4	1
XM_933646	LOC646484	1
XM_943429	LOC646484	1
NM_173797	PAPD4	1
NM_152667	NANP	1
XM_001134379	LOC732350	1
XM_001128421	LOC728069	1
NM_000870	HTR4	1
NM_001040172	HTR4	1
NM_001040173	HTR4	1
NM_001014431	AKT1	1
NM_001014432	AKT1	1
NM_005163	AKT1	1
NM_024947	PHC3	1
NM_007175	ERLIN2	1
NM_194434	VAPA	1
NM_003574	VAPA	1
NM_005088	CXYorf3	1
NM_012264	C22orf5	1
NM_020806	GPHN	1
NM_001024218	GPHN	1
XM_931281	LOC643072	1
XM_943769	LOC643072	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