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 CGGCAUACAGCUUCAACUG (7 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_013296

GPSM2

1818

1836

u

G

c

C

A

U

A

C

A

G

C

U

U

C

A

A

C

a

a

70

4

14

c

false

<90%

2806

NM_147686

TRAF3IP2

207

225

u

u

G

C

A

U

A

C

A

G

C

U

U

C

c

A

C

U

u

56

4

12

c

false

<90%

2514

NM_001079812

DIAPH1

4028

4046

u

c

a

C

A

U

A

C

A

G

C

U

U

C

A

g

C

U

G

40

4

12

c

false

<90%

5718

NM_005219

DIAPH1

4055

4073

u

c

a

C

A

U

A

C

A

G

C

U

U

C

A

g

C

U

G

40

4

12

c

false

<90%

5745

XM_942129

C3orf41

1572

1590

u

G

G

C

A

c

A

C

A

G

C

U

g

C

A

A

C

U

G

24

3

6

false

<90%

2628

XM_001133294

LOC729085

1572

1590

u

G

G

C

A

c

A

C

A

G

C

U

g

C

A

A

C

U

G

24

3

6

false

<90%

2628

NR_002723

GABPAP

55930

55948

C

G

G

C

A

g

A

C

A

c

C

U

U

C

A

A

C

U

u

-51

3

8

bc

false

<90%

194142

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_173830

C6orf182

684

702

C

A

G

a

U

G

A

A

G

C

U

G

U

A

U

G

C

a

a

55

3

13

c

false

<90%

2530

NM_001083535

C6orf182

1069

1087

C

A

G

a

U

G

A

A

G

C

U

G

U

A

U

G

C

a

a

55

3

13

c

false

<90%

2915

NM_017654

SAMD9

3450

3468

C

A

G

U

U

G

A

A

G

C

U

G

U

A

U

u

g

C

u

45

3

15

c

false

<90%

6853

NM_000807

GABRA2

695

713

C

A

G

U

U

c

A

A

G

C

U

G

a

A

U

G

C

C

c

21

3

6

false

<90%

2189

NR_003501

EARS2

390

408

C

g

G

U

U

G

g

A

G

C

U

G

U

A

U

G

C

C

c

17

3

11

bc

false

<90%

3886

NM_001083614

EARS2

390

408

C

g

G

U

U

G

g

A

G

C

U

G

U

A

U

G

C

C

c

17

3

11

bc

false

<90%

3979

NM_000433

NCF2

595

613

C

A

G

U

U

c

A

A

G

C

U

G

U

u

U

G

C

C

u

12

3

7

c

false

<90%

2406

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 163
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_004869	VPS4B	1
NM_153619	SEMA6D	1
NM_153618	SEMA6D	1
NM_153616	SEMA6D	1
NM_153617	SEMA6D	1
NM_020858	SEMA6D	1
NM_004100	EYA4	1
NM_172105	EYA4	1
NM_172103	EYA4	1
XM_929034	LOC646074	1
XM_001129328	LOC728418	1
NM_001079535	CPEB1	1
NM_001079534	CPEB1	1
NM_030594	CPEB1	1
NM_001079533	CPEB1	1
NM_001040613	TMEM70	1
NM_016224	SNX9	1
NM_001025266	LOC285382	1
NM_016424	CROP	1
NM_006107	CROP	1
NM_001037131	CENTG2	1
NM_014914	CENTG2	1
NM_145321	OSBPL3	1
NM_145320	OSBPL3	1
NM_145322	OSBPL3	1
NM_015550	OSBPL3	1
NM_003658	BARX2	1
NM_183419	RNF19	1
NM_015435	RNF19	1
NM_015717	CD207	1
XM_001134153	ELSPBP1	1
XM_001134152	ELSPBP1	1
NM_022142	ELSPBP1	1
NM_001080523	ARRDC5	1
XM_940152	LOC645432	1
NM_024830	AYTL2	1
NM_003902	FUBP1	1
NM_006798	UGT2A1	1
NM_022438	MAL	1
NM_022439	MAL	1
NM_022440	MAL	1
NM_002371	MAL	1
NM_182606	TMPRSS11A	1
NM_006129	BMP1	1
NM_005044	PRKX	1
NM_032012	C9orf5	1
NM_001099734		1
NM_004588	SCN2B	1
NM_003576	STK24	1
NM_001032296	STK24	1
NM_006818	MLLT11	1
NM_000990	RPL27A	1
NM_032787	GPR128	1
NM_015074	KIF1B	1
NM_001042417	RUFY2	1
NM_014746	RNF144	1
NM_015367	BCL2L13	1
NM_001274	CHEK1	1
NM_014614	PSME4	1
XM_933646	LOC646484	1
XM_943429	LOC646484	1
NM_014726	TBKBP1	1
NM_012256	ZNF212	1
XM_001131384	LOC646522	1
XM_933676	LOC646522	1
NM_001018100	Gcom1	1
NM_152451	Gcom1	1
NM_207037	TCF12	1
NM_003205	TCF12	1
NM_207040	TCF12	1
NM_207036	TCF12	1
NM_207038	TCF12	1
NM_001102658		1
NM_001077497	PRR3	1
NM_025263	PRR3	1
NM_212503	PCTK3	1
NM_002596	PCTK3	1
NM_212502	PCTK3	1
NM_020740	ANKFY1	1
NM_052882	ZIM3	1
NM_017637	BNC2	1
NM_001003674	C18orf1	1
NM_181483	C18orf1	1
NM_181481	C18orf1	1
NM_001003675	C18orf1	1
NM_004338	C18orf1	1
NM_003015	SFRP5	1
NM_001001974	PLEKHA1	1
NM_021622	PLEKHA1	1
XM_934619	LOC284577	1
XM_945015	LOC284577	1
NM_001010891	MTX3	1
NM_001098798		1
NM_001098797		1
NM_001098796		1
NM_032883	TOX2	1
NM_207436	FLJ42957	1
NM_001300	KLF6	1
NM_018708	FEM1A	1
NM_002163	IRF8	1
NM_016032	ZDHHC9	1
NM_001008222	ZDHHC9	1
NM_198183	UBE2L6	1
NM_004223	UBE2L6	1
NM_178550	C1orf110	1
NM_014316	CARHSP1	1
NM_001042476	CARHSP1	1
NM_012292	HMHA1	1
NM_003190	TAPBP	1
NM_018719	CDCA7L	1
NM_001097620		1
XM_940314	NLF2	1
NM_207316	UNQ846	1
NM_000334	SCN4A	1
NM_019607	C8orf44	1
NM_001018065	NTRK2	1
NM_001018066	NTRK2	1
NM_004838	HOMER3	1
NM_001518	GTF2I	1
NM_032999	GTF2I	1
NM_033000	GTF2I	1
NM_033001	GTF2I	1
XM_001133646	LOC732437	1
NM_024665	TBL1XR1	1
NM_003298	NR2C2	1
NM_002340	LSS	1
NM_006052	DSCR3	1
NM_199229	RPE	1
NM_031366	COL4A3	1
NM_000091	COL4A3	1
NM_031365	COL4A3	1
NM_031362	COL4A3	1
NM_001002247	ANAPC11	1
NM_001002248	ANAPC11	1
NM_016476	ANAPC11	1
NM_001002249	ANAPC11	1
NM_001002245	ANAPC11	1
NM_001002246	ANAPC11	1
NM_001002244	ANAPC11	1
XM_001133283	LOC728919	1
XM_001133292	LOC728919	1
XM_001133288	LOC728919	1
XM_001133297	LOC728919	1
NM_173699	MAGEB18	1
NM_032091	PCDHGA11	1
NM_015351		1
NM_145006	SUSD3	1
NM_033426	KIAA1737	1
NM_004854	CHST10	1
NM_020714	ZNF490	1
NM_032599	NYD-SP18	1
NM_015059	TLN2	1
NM_013336	SEC61A1	1
NM_003670	BHLHB2	1
NM_173598	KSR2	1
NM_005036	PPARA	1
NM_001001928	PPARA	1
NM_017623	CNNM3	1
NM_199078	CNNM3	1
XM_944838	LOC285733	1
XM_379432	LOC285733	1
NM_021961	TEAD1	1
NM_020921	NIN	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