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 GACGACCUGGUUACGGAAA (5 guide strand hits and 6 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_022464

SIL1

1127

1145

u

A

C

G

A

C

C

U

G

G

U

c

A

C

G

G

A

g

A

61

3

10

false

<90%

1908

NM_001037633

SIL1

1215

1233

u

A

C

G

A

C

C

U

G

G

U

c

A

C

G

G

A

g

A

61

3

10

false

<90%

1996

NM_004509

SP110

1956

1974

u

u

g

G

A

C

C

U

G

G

U

U

A

a

G

G

A

A

A

47

4

10

c

false

<90%

2359

NM_080424

SP110

2028

2046

u

u

g

G

A

C

C

U

G

G

U

U

A

a

G

G

A

A

A

47

4

10

c

false

<90%

2431

NM_033226

ABCC12

4313

4331

c

A

C

G

u

C

C

U

G

G

U

U

A

u

G

G

A

A

A

27

3

8

c

false

<90%

5168

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_001001654

MED8

260

278

g

U

U

C

C

G

U

A

A

C

C

A

G

G

U

C

a

U

C

74

2

15

ac

false

<90%

1193

NM_001001653

MED8

303

321

g

U

U

C

C

G

U

A

A

C

C

A

G

G

U

C

a

U

C

74

2

15

ac

false

<90%

1236

NM_001001651

MED8

260

278

g

U

U

C

C

G

U

A

A

C

C

A

G

G

U

C

a

U

C

74

2

15

ac

false

<90%

1502

NM_052877

MED8

321

339

g

U

U

C

C

G

U

A

A

C

C

A

G

G

U

C

a

U

C

74

2

15

ac

false

<90%

1563

NM_201542

MED8

303

321

g

U

U

C

C

G

U

A

A

C

C

A

G

G

U

C

a

U

C

74

2

15

ac

false

<90%

2038

NM_152749

ATXN7L4

337

355

U

g

c

C

u

G

U

A

A

C

C

A

G

G

U

C

G

U

C

17

3

14

bc

false

<90%

1530

---

3 prime UTR Seed matches

Hits to same gene : 0
Hits to other genes : 158
View matched accessions

3 prime seed match details

Accession	Gene name	Hits to this gene
NM_021079	NMT1	2
XM_001134250	LOC732053	2
XM_001126849	LOC727900	2
NM_002699	POU3F1	2
NM_006283	TACC1	1
NM_021961	TEAD1	1
NM_001409	MEGF6	1
NM_018431	DOK5	1
NM_152342	CDYL2	1
NM_032476	MRPS6	1
NM_016529	ATP8A2	1
XM_372194	C1orf170	1
XM_936696	C1orf170	1
NM_003787	NOL4	1
NM_022450	RHBDF1	1
NM_015036		1
NM_005955	MTF1	1
NM_003603	SORBS2	1
NM_021069	SORBS2	1
NM_014850	SRGAP3	1
NM_001033117	SRGAP3	1
NM_001010926	HES5	1
NM_014730	KIAA0152	1
XM_209554	LOC285299	1
XM_936463	LOC285299	1
NM_052907	TMEM132B	1
NM_033409	C20orf54	1
XM_942692	MGC5139	1
NM_001080533	MGC5139	1
NM_199141	CARM1	1
NM_016946	F11R	1
NM_138795	ARL8A	1
NM_033512	TSPYL5	1
NM_018284	GBP3	1
NM_001040285	PAPD5	1
NM_001040284	PAPD5	1
NM_022123	NPAS3	1
NM_020698	TMCC3	1
NM_133328	DEDD2	1
NM_003590	CUL3	1
NM_000721	CACNA1E	1
NM_006504	PTPRE	1
NM_130435	PTPRE	1
NM_014474	SMPDL3B	1
NM_001649	SHROOM2	1
NM_182562	FLJ39743	1
NM_002501	NFIX	1
NM_182697	UBE2H	1
NM_003344	UBE2H	1
NM_018224	C7orf44	1
NM_145245	EVI5L	1
NM_013943	CLIC4	1
NM_194286	KIAA1853	1
NM_001105576		1
NM_006330	LYPLA1	1
NM_003421	ZNF37A	1
NM_001007094	ZNF37A	1
NM_001044370	MPPED1	1
NM_005828	WDR68	1
NM_032843	FIBCD1	1
NM_145861	EDARADD	1
NM_080738	EDARADD	1
NM_000606	C8G	1
NM_024310	PLEKHF1	1
NM_014488	RAB30	1
NM_017712	PGPEP1	1
NM_001018003	SORBS3	1
NM_005775	SORBS3	1
NM_001001716	NFKBIB	1
NM_001042631	LOC644096	1
NM_001715	BLK	1
NM_015140	TTLL12	1
NM_152253	CHKB	1
NM_052869	TTYH2	1
NM_032646	TTYH2	1
XM_930750	LOC642366	1
XM_943652	LOC642366	1
NM_018649	H2AFY2	1
NM_001099409		1
NM_015166	MLC1	1
NM_139202	MLC1	1
NM_003120	SPI1	1
NM_001080547	SPI1	1
NM_207360		1
NM_144679	C17orf56	1
XM_001133420	LOC728991	1
NM_021183	RAP2C	1
NM_003241	TGM4	1
NM_022468	MMP25	1
NM_006176	NRGN	1
NM_002999	SDC4	1
XM_497648	LOC441869	1
XM_001126121	LOC441869	1
NM_032575	GLIS2	1
NM_003505	FZD1	1
NM_058192	RPUSD1	1
NM_014732	KIAA0513	1
XM_927238	LOC643988	1
XM_936418	LOC647347	1
NM_002939	RNH1	1
NM_203388	RNH1	1
NM_203386	RNH1	1
NM_203387	RNH1	1
NM_203384	RNH1	1
NM_203383	RNH1	1
NM_203385	RNH1	1
NM_203389	RNH1	1
XM_001134463	BAHCC1	1
NM_001080519	BAHCC1	1
XM_937000	LOC147645	1
XM_085831	LOC147645	1
NM_004170	SLC1A1	1
NM_001013640	LOC388503	1
NM_000662	NAT1	1
XM_001127234	NAT1	1
NM_032682	FOXP1	1
NM_015318	ARHGEF18	1
NM_199459	C10orf71	1
NM_025245	PBX4	1
NM_001148	ANK2	1
NM_020977	ANK2	1
NM_002250	KCNN4	1
NM_001008406	BCAP29	1
NM_001013661	VSIG8	1
NM_002653	PITX1	1
NM_182641	BPTF	1
NM_004459	BPTF	1
NM_198207	LASS1	1
NM_005883	APC2	1
NM_001018111	PODXL	1
NM_005397	PODXL	1
NM_025136	OPA3	1
NM_019625	ABCB9	1
NM_203444	ABCB9	1
NM_019624	ABCB9	1
NM_002738	PRKCB1	1
NM_032800	C1orf198	1
NM_203413	C17orf81	1
NM_017637	BNC2	1
NM_006440	TXNRD2	1
NM_020823		1
NM_031418	TMEM16C	1
NM_024770	METTL8	1
NM_024909	C6orf134	1
NM_139276	STAT3	1
NM_003150	STAT3	1
NM_213662	STAT3	1
NM_001040105	MUC17	1
NM_022067	C14orf133	1
NM_139075	TPCN2	1
NM_015321	CRTC1	1
NM_001098482		1
NM_001076778	FAM107A	1
NM_007177	FAM107A	1
NM_144667	FLJ32894	1
NM_001008712	RBPMS	1
NM_207405	FLJ46481	1
NM_004991	MDS1	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