VIRsiRNAdb

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

11 hits were found for CGCUAGCACUCUGGUAUCA (7 guide strand hits and 4 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

XM_001133760

ZNF519

6179

6197

a

a

C

U

A

G

C

A

C

U

C

U

G

u

U

A

U

C

c

62

4

11

c

false

<90%

6497

NM_175728

IL5RA

1203

1221

a

G

C

a

A

G

C

A

C

U

C

U

G

c

U

A

U

C

A

41

3

9

c

false

<90%

1626

NM_175725

IL5RA

1271

1289

a

G

C

a

A

G

C

A

C

U

C

U

G

c

U

A

U

C

A

41

3

9

c

false

<90%

1694

NM_175727

IL5RA

1203

1221

a

G

C

a

A

G

C

A

C

U

C

U

G

c

U

A

U

C

A

41

3

9

c

false

<90%

1956

NM_175724

IL5RA

1271

1289

a

G

C

a

A

G

C

A

C

U

C

U

G

c

U

A

U

C

A

41

3

9

c

false

<90%

2024

NM_175726

IL5RA

1203

1221

a

G

C

a

A

G

C

A

C

U

C

U

G

c

U

A

U

C

A

41

3

9

c

false

<90%

2299

NM_000564

IL5RA

1271

1289

a

G

C

a

A

G

C

A

C

U

C

U

G

c

U

A

U

C

A

41

3

9

c

false

<90%

2367

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_181507

HPS5

293

311

U

G

A

U

A

C

C

A

G

A

G

U

c

C

U

A

c

a

G

63

3

12

false

<90%

4880

NM_024771

NAT11

989

1007

g

G

A

g

A

C

C

A

G

A

G

U

G

C

U

A

G

a

a

53

4

13

c

false

<90%

3303

XR_015734

LOC728773

797

815

a

G

A

U

A

C

C

A

G

g

G

U

G

C

U

A

a

C

G

-8

3

8

c

false

<90%

2033

XR_015420

LOC730694

797

815

a

G

A

U

A

C

C

A

G

g

G

U

G

C

U

A

a

C

G

-8

3

8

c

false

<90%

2033

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3 prime UTR Seed matches

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

3 prime seed match details

Accession

Gene name

Hits to this gene

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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