Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
39 hits were found for CCUGCUCUUGGACUGCAUG (19 guide strand hits and 20 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_001129280 | LOC729086 | 212 | 230 | g | C | U | G | C | U | C | U | U | G | G | A | g | U | G | C | A | c | a | 79 | 4 | 11 | false | <90% | 2950 | |||
NM_030796 | ECOP | 225 | 243 | g | C | U | G | C | U | C | U | U | G | G | A | g | U | G | C | A | c | a | 79 | 4 | 11 | false | <90% | 2962 | |||
NM_020826 | SYT13 | 2131 | 2149 | C | C | U | G | C | U | C | U | U | G | G | A | C | U | G | a | A | U | u | 68 | 2 | 15 | c | false | <90% | 5108 | ||
NM_207428 | C11orf55 | 55 | 73 | C | C | U | G | C | U | C | U | U | G | G | A | g | U | G | C | u | U | u | 61 | 3 | 12 | false | <90% | 2744 | |||
NM_152795 | HIF3A | 5259 | 5277 | g | C | U | G | C | U | C | c | U | G | G | A | C | U | u | C | A | U | G | 11 | 3 | 6 | c | false | <90% | 5850 | ||
NM_152794 | HIF3A | 5273 | 5291 | g | C | U | G | C | U | C | c | U | G | G | A | C | U | u | C | A | U | G | 11 | 3 | 6 | c | false | <90% | 5864 | ||
NM_022462 | HIF3A | 5317 | 5335 | g | C | U | G | C | U | C | c | U | G | G | A | C | U | u | C | A | U | G | 11 | 3 | 6 | c | false | <90% | 5908 | ||
NM_005995 | TBX10 | 424 | 442 | C | C | U | G | C | U | C | a | U | G | G | A | C | U | u | C | A | U | c | 8 | 3 | 7 | c | false | <90% | 1557 | ||
NM_173647 | RNF149 | 35 | 53 | u | C | U | G | C | U | C | U | U | c | G | A | C | U | G | C | A | c | c | 7 | 4 | 8 | c | false | <90% | 2452 | ||
XM_001131778 | KIAA0368 | 1029 | 1047 | g | C | U | G | C | U | u | U | U | G | G | A | C | U | u | C | A | U | G | 6 | 3 | 7 | c | false | <90% | 7391 | ||
NM_001080398 | KIAA0368 | 1029 | 1047 | g | C | U | G | C | U | u | U | U | G | G | A | C | U | u | C | A | U | G | 6 | 3 | 7 | c | false | <90% | 7391 | ||
NM_001395 | DUSP9 | 179 | 197 | C | C | U | G | C | U | C | c | U | G | G | A | C | U | G | C | c | g | c | 6 | 4 | 8 | c | false | <90% | 2303 | ||
NM_001716 | BLR1 | 495 | 513 | C | C | U | G | C | U | C | c | U | G | G | c | C | U | G | C | A | U | c | 0 | 3 | 7 | false | <90% | 2824 | |||
NM_032966 | BLR1 | 564 | 582 | C | C | U | G | C | U | C | c | U | G | G | c | C | U | G | C | A | U | c | 0 | 3 | 7 | false | <90% | 2893 | |||
NM_015545 | PTCD1 | 992 | 1010 | C | C | U | G | C | U | C | a | U | G | G | g | C | U | G | C | A | U | c | 0 | 3 | 7 | false | <90% | 3079 | |||
NM_005104 | BRD2 | 2836 | 2854 | u | C | U | G | C | a | C | U | U | G | G | c | C | U | G | C | A | U | G | 0 | 3 | 7 | false | <90% | 4693 | |||
NM_000634 | IL8RA | 494 | 512 | C | C | U | G | C | U | g | U | U | G | G | c | C | U | G | C | A | U | c | -5 | 3 | 6 | false | <90% | 2502 | |||
NM_001401 | EDG2 | 2802 | 2820 | C | C | U | G | C | U | u | U | U | G | u | A | C | U | G | C | A | U | G | -27 | 2 | 8 | c | false | <90% | 3104 | ||
NM_057159 | EDG2 | 2880 | 2898 | C | C | U | G | C | U | u | U | U | G | u | A | C | U | G | C | A | U | G | -27 | 2 | 8 | c | false | <90% | 3182 |
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_005382 | NEFM | 970 | 988 | g | c | U | G | C | A | G | U | C | C | A | A | G | A | G | C | A | u | c | 78 | 4 | 15 | ac | false | <90% | 3238 | ||
XM_001130956 | ANKS6 | 2102 | 2120 | u | c | g | G | C | A | G | U | C | C | A | A | G | A | G | C | A | G | u | 62 | 4 | 15 | bc | false | <90% | 3492 | ||
NM_173551 | ANKS6 | 2298 | 2316 | u | c | g | G | C | A | G | U | C | C | A | A | G | A | G | C | A | G | u | 62 | 4 | 15 | bc | false | <90% | 7147 | ||
NM_002474 | MYH11 | 3898 | 3916 | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | c | 62 | 4 | 11 | c | false | <90% | 6882 | ||
NM_001040114 | MYH11 | 3919 | 3937 | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | c | 62 | 4 | 11 | c | false | <90% | 6903 | ||
NM_022844 | MYH11 | 3898 | 3916 | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | c | 62 | 4 | 11 | c | false | <90% | 6921 | ||
NM_001040113 | MYH11 | 3919 | 3937 | g | c | U | G | C | A | G | U | C | C | A | A | G | u | G | C | A | G | c | 62 | 4 | 11 | c | false | <90% | 6942 | ||
NM_020845 | PITPNM2 | 743 | 761 | C | A | U | G | C | A | G | U | C | C | A | A | G | A | u | C | g | a | G | 49 | 3 | 14 | c | false | <90% | 6754 | ||
NM_001009616 | SPANXN5 | 234 | 252 | a | A | U | c | C | A | G | U | C | C | A | A | G | A | G | g | A | G | G | 35 | 3 | 11 | c | false | <90% | 581 | ||
NM_001009614 | SPANXN1 | 234 | 252 | a | A | U | c | C | A | G | U | C | C | A | A | G | A | G | g | A | G | G | 35 | 3 | 11 | c | false | <90% | 613 | ||
NM_001066 | TNFRSF1B | 1637 | 1655 | C | c | U | G | C | A | G | g | C | C | A | A | G | A | G | C | A | G | a | 21 | 3 | 10 | bc | false | <90% | 3682 | ||
NM_016274 | PLEKHO1 | 525 | 543 | C | c | g | G | a | A | G | U | C | C | A | A | G | A | G | C | A | G | G | 17 | 3 | 14 | bc | false | <90% | 1627 | ||
NM_014793 | LCMT2 | 2472 | 2490 | C | A | U | G | C | A | G | U | C | C | g | A | G | A | G | g | A | G | u | 7 | 3 | 10 | c | false | <90% | 2931 | ||
NM_001001420 | SMAD5 | 6166 | 6184 | g | A | U | c | C | A | G | U | C | C | u | A | G | A | G | C | A | G | G | 0 | 3 | 8 | c | false | <90% | 6937 | ||
NM_005903 | SMAD5 | 6241 | 6259 | g | A | U | c | C | A | G | U | C | C | u | A | G | A | G | C | A | G | G | 0 | 3 | 8 | c | false | <90% | 7012 | ||
NM_001001419 | SMAD5 | 6325 | 6343 | g | A | U | c | C | A | G | U | C | C | u | A | G | A | G | C | A | G | G | 0 | 3 | 8 | c | false | <90% | 7096 | ||
NM_152843 | HPS4 | 1931 | 1949 | C | A | U | G | g | A | G | c | C | C | A | A | G | A | G | C | A | G | c | -18 | 3 | 10 | bc | false | <90% | 2950 | ||
NM_152841 | HPS4 | 1498 | 1516 | C | A | U | G | g | A | G | c | C | C | A | A | G | A | G | C | A | G | c | -18 | 3 | 10 | bc | false | <90% | 4069 | ||
NM_022081 | HPS4 | 1968 | 1986 | C | A | U | G | g | A | G | c | C | C | A | A | G | A | G | C | A | G | c | -18 | 3 | 10 | bc | false | <90% | 4539 | ||
NM_207459 | FLJ35767 | 1054 | 1072 | g | A | U | G | C | A | c | c | C | C | A | A | G | A | G | C | A | G | G | -30 | 3 | 11 | bc | false | <90% | 1907 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3235
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