VIRsiRNAdb

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

14 hits were found for GCGAUAGAGCAGGGCCCCG (5 guide strand hits and 9 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_001040630

NCALD

192

210

G

C

G

g

U

A

G

A

G

C

A

G

G

G

a

C

C

C

c

33

3

10

c

false

<90%

3826

NM_014738

KIAA0195

4774

4792

a

a

G

A

U

g

G

A

G

C

A

G

G

G

C

C

C

C

c

18

4

12

bc

false

<90%

5001

NM_003660

PPFIA3

208

226

G

C

G

A

c

A

G

A

G

C

c

G

G

G

C

C

C

C

G

-12

2

8

c

false

<90%

4733

NM_033150

COL2A1

3656

3674

c

C

G

A

g

A

G

A

G

a

A

G

G

G

C

C

C

C

G

-36

3

9

bc

false

<90%

4880

NM_001844

COL2A1

3863

3881

c

C

G

A

g

A

G

A

G

a

A

G

G

G

C

C

C

C

G

-36

3

9

bc

false

<90%

5087

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_007046

EMILIN1

3009

3027

C

G

G

G

G

C

C

C

U

G

C

U

C

U

A

U

g

G

g

71

2

16

ac

false

<90%

3431

NM_003501

ACOX3

1879

1897

C

G

c

G

G

C

C

C

U

G

C

U

C

U

A

c

C

G

a

49

3

12

c

false

<90%

2415

NM_000794

DRD1

64

82

C

G

G

G

G

C

C

C

U

G

C

U

C

U

g

U

a

G

g

46

3

14

c

false

<90%

3373

NM_003492

TMEM187

811

829

C

a

u

G

G

C

C

C

U

G

C

U

C

U

A

U

g

G

C

45

3

13

c

false

<90%

1682

NM_199141

CARM1

194

212

C

G

G

G

G

C

C

C

U

G

C

g

C

U

A

c

C

G

u

35

3

11

false

<90%

2968

NM_145200

CABP4

413

431

C

G

G

G

c

C

C

C

U

G

C

U

C

a

A

U

C

G

a

24

3

8

c

false

<90%

1466

XM_001127678

LOC730900

928

946

g

G

G

G

u

C

C

C

U

G

C

U

C

U

A

c

C

G

C

20

3

10

c

false

<90%

954

XM_001127730

LOC728547

928

946

g

G

G

G

u

C

C

C

U

G

C

U

C

U

A

c

C

G

C

20

3

10

c

false

<90%

954

NM_206895

UNQ830

323

341

u

G

G

G

G

C

C

C

g

G

C

g

C

U

A

U

C

G

C

4

3

7

false

<90%

480

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 121
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_017596	KIF21B	1
NM_005385	NKTR	1
NM_016474	C3orf19	1
NM_152380	TBX15	1
NM_024745	SHCBP1	1
NM_015987	HEBP1	1
XM_943830	LOC643194	1
XM_931396	LOC643194	1
NM_152557	ZNF746	1
NM_020960	GPR107	1
NM_001098536		1
NM_003481	USP5	1
NM_004823	KCNK6	1
NM_020536	CSRP2BP	1
NM_177926	CSRP2BP	1
NM_001004302	ZNF783	1
NM_007264	ADMR	1
NM_001101396		1
NM_002336	LRP6	1
NM_001047605	KIR3DX1	1
NM_006731	FCMD	1
NM_001079802	FCMD	1
NM_018319	TDP1	1
NM_001008744	TDP1	1
NM_025104	DBF4B	1
NM_000696	ALDH9A1	1
NM_013952	PAX8	1
NM_013953	PAX8	1
NM_013951	PAX8	1
NM_003466	PAX8	1
NM_013992	PAX8	1
NM_021913	AXL	1
NM_001699	AXL	1
NM_021830	PEO1	1
NM_001420	ELAVL3	1
NM_032281	ELAVL3	1
NM_014766	SCRN1	1
NM_001759	CCND2	1
NM_173484	KLF17	1
NM_031442	TMEM47	1
NM_001013622	FAM53A	1
XM_001133565	LOC731440	1
NM_005226	EDG3	1
NM_006080	SEMA3A	1
NM_000164	GIPR	1
NM_018662	DISC1	1
NM_001012957	DISC1	1
NM_022832	USP46	1
NM_022648	TNS1	1
NM_015016		1
NM_181291	WDR20	1
NM_175609	ARFGAP1	1
NM_018209	ARFGAP1	1
NM_016441	CRIM1	1
NM_199282	ARHGAP27	1
NM_006180	NTRK2	1
NM_001018064	NTRK2	1
NM_000252	MTM1	1
NM_007175	ERLIN2	1
NM_020806	GPHN	1
NM_001024218	GPHN	1
NM_001083913	C10orf26	1
NM_017787	C10orf26	1
NM_178586	PPP2R5C	1
NM_002719	PPP2R5C	1
NM_014344	FJX1	1
NM_021143	ZNF20	1
NM_001102371		1
NM_024955	FOXRED2	1
NM_014910	ZNF507	1
NM_201262	DNAJC12	1
NM_032105	PPP1R12B	1
NM_002481	PPP1R12B	1
NM_173658	ZNF660	1
NM_001005212	OR9Q1	1
NM_014325	CORO1C	1
XM_001125791	LOC642788	1
XM_001127886	LOC728100	1
XM_001132421	LOC388312	1
NM_153025	C16orf55	1
NM_032682	FOXP1	1
NM_024627	C22orf29	1
NM_198182	GRHL1	1
NM_014552	GRHL1	1
NM_005098	MSC	1
NM_198075	LRRC56	1
XM_001128447	LOC728775	1
XM_001127270	LOC730801	1
NM_001081573	GAB3	1
NM_080612	GAB3	1
NM_024616	C3orf52	1
NM_001030010	ALDH3B1	1
NM_000694	ALDH3B1	1
NM_030650	KIAA1715	1
NM_053053	TADA1L	1
NM_001754	RUNX1	1
NM_001001890	RUNX1	1
NM_148960	CLDN19	1
NM_004783	TAOK2	1
NM_001004342	TRIM67	1
NM_153645	NUP50	1
NM_007172	NUP50	1
NM_145013	C11orf45	1
NM_001100626		1
NM_006459	ERLIN1	1
NM_032778	MINA	1
NM_153182	MINA	1
NM_001042533	MINA	1
NM_005578	LPP	1
NM_019851	FGF20	1
NM_014777	KIAA0133	1
NM_004098	EMX2	1
NM_002688	SEPT5	1
NM_004798	KIF3B	1
NM_001102592		1
NM_144584	C1orf59	1
NM_198256	E2F6	1
NM_001011720	XKR9	1
NM_002547	OPHN1	1
NM_020297	ABCC9	1
NM_182503	DEADC1	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