VIRsiRNAdb

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

10 hits were found for GAAUACGCUGUGUUUACAU (7 guide strand hits and 3 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_178452

LRRC50

451

469

u

g

A

U

A

C

G

C

U

G

U

a

U

U

U

A

C

A

c

47

4

9

false

<90%

2394

NM_001001671

MAP3K15

4081

4099

a

A

u

U

c

C

G

C

U

G

U

G

U

U

U

A

C

A

U

26

3

14

bc

false

<90%

4697

NM_001007023

DIO2

3853

3871

c

c

A

U

A

g

G

C

U

G

U

G

U

U

U

A

C

A

U

23

3

13

bc

false

<90%

6129

NM_000793

DIO2

4119

4137

c

c

A

U

A

g

G

C

U

G

U

G

U

U

U

A

C

A

U

23

3

13

bc

false

<90%

6395

NM_013989

DIO2

4427

4445

c

c

A

U

A

g

G

C

U

G

U

G

U

U

U

A

C

A

U

23

3

13

bc

false

<90%

6703

NM_020809

ARHGAP20

3169

3187

G

A

A

c

A

C

u

C

U

G

U

G

U

U

U

A

C

A

c

-8

3

11

bc

false

<90%

6207

XR_018805

LOC650618

130

148

G

A

A

U

g

C

a

C

U

G

U

G

U

U

U

A

C

A

U

-17

2

12

bc

false

<90%

1075

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_002568

PABPC1

1933

1951

A

U

G

U

c

A

A

C

A

C

A

G

C

G

U

g

U

U

g

17

3

10

c

false

<90%

2869

NM_007222

ZHX1

3617

3635

A

U

G

U

A

A

A

a

A

C

A

G

C

c

U

A

U

U

u

13

3

7

c

false

<90%

4937

NM_001017926

ZHX1

3712

3730

A

U

G

U

A

A

A

a

A

C

A

G

C

c

U

A

U

U

u

13

3

7

c

false

<90%

5032

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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)
Motif found in guide strand

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