Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
36 hits were found for GCCUUCACAUUCAGACCUC (15 guide strand hits and 21 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_001039886 | ZNF808 | 278 | 296 | u | a | C | U | U | C | A | C | A | U | U | C | A | c | A | C | C | U | C | 67 | 3 | 11 | c | false | <90% | 1158 | ||
NM_001008801 | ZNF468 | 2770 | 2788 | u | a | C | U | U | C | A | C | A | U | U | C | A | c | A | C | C | U | C | 67 | 3 | 11 | c | false | <90% | 3935 | ||
NM_199132 | ZNF468 | 2888 | 2906 | u | a | C | U | U | C | A | C | A | U | U | C | A | c | A | C | C | U | C | 67 | 3 | 11 | c | false | <90% | 4053 | ||
NM_006969 | ZNF28 | 3508 | 3526 | u | a | C | U | U | C | A | C | A | U | U | C | A | c | A | C | C | U | C | 67 | 3 | 11 | c | false | <90% | 4675 | ||
NM_023016 | ANKRD57 | 1696 | 1714 | c | C | C | U | U | C | A | C | A | U | U | g | A | G | A | C | C | a | a | 56 | 4 | 10 | false | <90% | 4681 | |||
NM_001040185 | ZNF765 | 3435 | 3453 | u | a | a | U | U | C | A | C | A | U | U | C | A | c | A | C | C | U | C | 47 | 4 | 10 | c | false | <90% | 4577 | ||
NM_005478 | INSL5 | 11 | 29 | a | g | a | U | U | C | A | C | A | U | U | C | A | G | u | C | C | U | C | 42 | 4 | 11 | c | false | <90% | 715 | ||
NM_020645 | NRIP3 | 929 | 947 | u | C | C | U | U | C | c | C | A | U | U | C | A | G | A | C | C | U | C | 31 | 2 | 12 | bc | false | <90% | 1508 | ||
XM_001134449 | KBTBD9 | 20 | 38 | G | C | C | U | U | u | A | C | A | U | U | C | A | G | A | C | a | g | g | 5 | 4 | 10 | c | false | <90% | 5047 | ||
NM_199078 | CNNM3 | 2328 | 2346 | a | u | a | U | U | C | A | g | A | U | U | C | A | G | A | C | C | U | C | 4 | 4 | 11 | bc | false | <90% | 4772 | ||
NM_017623 | CNNM3 | 2472 | 2490 | a | u | a | U | U | C | A | g | A | U | U | C | A | G | A | C | C | U | C | 4 | 4 | 11 | bc | false | <90% | 4916 | ||
NM_001962 | EFNA5 | 1414 | 1432 | G | C | C | U | U | C | u | C | A | U | U | C | A | G | A | a | C | U | g | 2 | 3 | 8 | c | false | <90% | 1574 | ||
XR_016203 | LOC441938 | 593 | 611 | c | C | C | c | U | g | A | C | A | U | U | C | A | G | A | C | C | U | C | -2 | 3 | 13 | bc | false | <90% | 2070 | ||
XM_936372 | LMTK3 | 435 | 453 | G | C | C | U | U | C | A | C | A | c | U | C | A | G | A | C | a | U | g | -11 | 3 | 9 | c | false | <90% | 4972 | ||
NM_001080434 | LMTK3 | 435 | 453 | G | C | C | U | U | C | A | C | A | c | U | C | A | G | A | C | a | U | g | -11 | 3 | 9 | c | false | <90% | 4972 |
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_152433 | KBTBD3 | 1885 | 1903 | c | A | G | G | U | C | U | G | A | A | U | G | g | G | A | A | G | a | a | 79 | 4 | 11 | false | <90% | 3774 | |||
NM_198439 | KBTBD3 | 2087 | 2105 | c | A | G | G | U | C | U | G | A | A | U | G | g | G | A | A | G | a | a | 79 | 4 | 11 | false | <90% | 3976 | |||
NM_207122 | EXT2 | 2506 | 2524 | G | A | G | G | U | C | U | G | A | A | U | G | U | G | A | g | G | c | u | 66 | 3 | 15 | c | false | <90% | 3651 | ||
NM_000401 | EXT2 | 2659 | 2677 | G | A | G | G | U | C | U | G | A | A | U | G | U | G | A | g | G | c | u | 66 | 3 | 15 | c | false | <90% | 3804 | ||
NM_015087 | SPG20 | 4443 | 4461 | a | g | u | G | U | C | U | G | A | A | U | G | U | G | A | A | G | u | C | 64 | 4 | 14 | c | false | <90% | 4838 | ||
NM_005459 | GUCA1C | 153 | 171 | a | A | G | G | U | C | U | G | A | A | U | c | a | G | A | A | G | G | C | 53 | 3 | 10 | false | <90% | 860 | |||
NM_152630 | FAM46D | 2197 | 2215 | c | A | G | c | U | C | U | G | A | A | U | G | U | G | A | A | a | G | C | 37 | 3 | 12 | c | false | <90% | 3027 | ||
NM_001942 | DSG1 | 2270 | 2288 | G | A | G | G | U | C | U | G | A | A | U | a | U | G | A | A | u | u | u | 35 | 4 | 11 | false | <90% | 5447 | |||
NM_006434 | SORBS1 | 48 | 66 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 5402 | ||
NM_001034957 | SORBS1 | 48 | 66 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 5570 | ||
NM_024991 | SORBS1 | 229 | 247 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 5874 | ||
NM_015385 | SORBS1 | 229 | 247 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 5979 | ||
NM_001034956 | SORBS1 | 48 | 66 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 6065 | ||
NM_001034955 | SORBS1 | 48 | 66 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 6803 | ||
NM_001034954 | SORBS1 | 48 | 66 | G | A | G | u | U | C | U | G | A | A | U | G | U | G | A | u | G | G | u | 32 | 3 | 11 | c | false | <90% | 7226 | ||
NM_004654 | USP9Y | 6138 | 6156 | u | A | G | G | U | a | U | G | A | A | U | G | U | G | A | A | G | a | a | 27 | 4 | 11 | c | false | <90% | 10048 | ||
NM_152259 | C15orf42 | 1756 | 1774 | c | A | a | G | g | C | U | G | A | A | U | G | U | G | A | A | G | G | C | 26 | 3 | 14 | bc | false | <90% | 6688 | ||
NM_012405 | ICMT | 2184 | 2202 | G | A | a | G | U | g | U | G | A | A | U | G | U | G | A | A | G | G | C | 17 | 2 | 13 | bc | false | <90% | 4815 | ||
NM_014141 | CNTNAP2 | 1167 | 1185 | G | A | c | G | U | C | U | G | A | A | a | G | U | G | A | A | G | G | a | 14 | 3 | 7 | c | false | <90% | 9890 | ||
NM_080617 | CBLN4 | 445 | 463 | G | A | G | G | U | g | U | G | A | A | U | G | U | G | A | g | G | G | u | 5 | 3 | 9 | c | false | <90% | 2573 | ||
NM_015120 | ALMS1 | 7278 | 7296 | G | A | G | G | U | C | U | G | A | A | c | c | U | G | A | A | G | G | g | 0 | 3 | 10 | false | <90% | 12928 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2361
View matched accessions
3 prime seed match details
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 |
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