VIRsiRNAdb

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

4 hits were found for CCGCGAAGUGAUCCAUGUA (0 guide strand hits and 4 sense strand hits.)

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

XM_001134223

PKD1L3

5642

5660

U

A

C

A

U

G

G

A

U

C

A

C

U

U

g

G

u

u

a

44

4

14

c

false

<90%

5742

XM_001133467

PKD1L3

5642

5660

U

A

C

A

U

G

G

A

U

C

A

C

U

U

g

G

u

u

a

44

4

14

c

false

<90%

5742

XM_938267

LOC649201

1084

1102

U

A

C

A

U

G

G

A

U

g

A

C

c

U

C

G

C

G

G

6

2

9

false

<90%

1818

XM_001127211

LOC649201

1084

1102

U

A

C

A

U

G

G

A

U

g

A

C

c

U

C

G

C

G

G

6

2

9

false

<90%

1818

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 83
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_018941	CLN8	2
NM_015537	NELF	1
NM_002653	PITX1	1
XM_001132645	ODZ3	1
XM_931600	ODZ3	1
NM_001080477	ODZ3	1
XM_940722	ODZ3	1
NM_005392	PHF2	1
NM_004907	IER2	1
NM_014850	SRGAP3	1
NM_001033117	SRGAP3	1
NM_003317	TITF1	1
NM_001079668	TITF1	1
NM_004302	ACVR1B	1
NM_005599	NHLH2	1
NM_001111061		1
NM_174919	LOC201175	1
NM_004558	NRTN	1
XM_936809	LOC342918	1
XM_292779	LOC342918	1
NM_024884	L2HGDH	1
XM_001130170	LOC729275	1
XM_001127723	LOC730878	1
NM_001953	ECGF1	1
NM_005737	ARL4C	1
NM_005811	GDF11	1
NM_015073	SIPA1L3	1
NM_023067	FOXL2	1
NM_022094	CIDEC	1
NM_025078	PQLC1	1
NM_014867	KBTBD11	1
NM_182811	PLCG1	1
NM_002660	PLCG1	1
NM_032854	CORO6	1
XM_001127668	LOC728119	1
XM_001131429	LOC731118	1
XM_379636	C9orf122	1
XM_940165	C9orf122	1
NM_203382	AMACR	1
NM_172247	CSF2RA	1
NM_172249	CSF2RA	1
NM_001005463	EBF3	1
NM_001003760	KLHL31	1
XM_940362	LOC645984	1
XM_928946	LOC645984	1
NM_003867	FGF17	1
NM_052917	GALNT13	1
NM_130848	C5orf20	1
NM_015321	CRTC1	1
NM_001098482		1
NM_022049	GPR88	1
NM_016358	IRX4	1
NM_001089	ABCA3	1
NM_020851	ISLR2	1
NM_145285	NKX2-3	1
NM_001013640	LOC388503	1
XM_946032	LOC644852	1
XM_934218	LOC644852	1
NM_001002762	DNAJB12	1
NM_017626	DNAJB12	1
NM_001715	BLK	1
NM_015124	DIP	1
NM_020971	SPTBN4	1
NM_015116	LRCH1	1
XM_001126981	LOC730733	1
NM_017723	C9orf167	1
NM_002088	GRIK5	1
NM_001102	ACTN1	1
NM_003281	TNNI1	1
NM_014247		1
NM_001497	B4GALT1	1
XM_001133211	LOC729003	1
XM_001133556	LOC729135	1
NM_018840	C20orf24	1
NM_006322	TUBGCP3	1
NM_201628	FLJ43806	1
NM_018243	SEPT11	1
XM_001126700	LOC728147	1
XM_001126645	LOC730638	1
NM_024662	NAT10	1
XM_001132907	LOC730202	1
XM_001131136	LOC731887	1
NM_001077619	LOC137886	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