Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
28 hits were found for UUUGGAGCUGAUGCCGUAG (18 guide strand hits and 10 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_144780 | DEGS1 | 514 | 532 | c | U | U | G | G | A | G | C | U | G | A | U | G | g | C | G | U | c | G | 75 | 3 | 12 | c | false | <90% | 1681 | ||
NM_003676 | DEGS1 | 514 | 532 | c | U | U | G | G | A | G | C | U | G | A | U | G | g | C | G | U | c | G | 75 | 3 | 12 | c | false | <90% | 2058 | ||
NM_005570 | LMAN1 | 372 | 390 | a | U | U | G | G | A | G | C | U | G | A | U | G | g | C | c | U | A | G | 52 | 3 | 12 | c | false | <90% | 2764 | ||
NM_031472 | TRPT1 | 362 | 380 | g | U | U | G | G | A | G | C | U | G | A | U | G | C | C | c | c | u | G | 45 | 4 | 14 | c | false | <90% | 883 | ||
NM_001033678 | TRPT1 | 505 | 523 | g | U | U | G | G | A | G | C | U | G | A | U | G | C | C | c | c | u | G | 45 | 4 | 14 | c | false | <90% | 962 | ||
NM_152910 | DGKH | 1633 | 1651 | g | U | U | G | u | A | G | C | U | G | A | U | G | C | C | G | U | g | G | 43 | 3 | 12 | c | false | <90% | 4117 | ||
NM_178009 | DGKH | 1633 | 1651 | g | U | U | G | u | A | G | C | U | G | A | U | G | C | C | G | U | g | G | 43 | 3 | 12 | c | false | <90% | 4248 | ||
NM_025161 | C17orf70 | 927 | 945 | U | U | U | G | G | A | G | C | U | G | A | U | G | C | C | a | c | c | c | 42 | 4 | 15 | c | false | <90% | 3843 | ||
NM_020853 | KIAA1467 | 656 | 674 | U | U | U | G | G | A | G | C | U | G | A | U | G | C | C | a | g | g | a | 42 | 4 | 15 | c | false | <90% | 4725 | ||
NM_025080 | ASRGL1 | 2031 | 2049 | a | g | a | G | G | A | G | C | U | G | A | U | G | C | u | G | U | A | G | 42 | 4 | 11 | c | false | <90% | 2347 | ||
NM_001083926 | ASRGL1 | 2108 | 2126 | a | g | a | G | G | A | G | C | U | G | A | U | G | C | u | G | U | A | G | 42 | 4 | 11 | c | false | <90% | 2424 | ||
NM_024689 | CXorf36 | 1590 | 1608 | g | c | a | G | G | A | G | C | U | G | A | U | G | C | u | G | U | A | G | 42 | 4 | 11 | c | false | <90% | 2502 | ||
NM_004985 | KRAS | 206 | 224 | g | U | U | G | G | A | G | C | U | G | g | U | G | g | C | G | U | A | G | 17 | 3 | 9 | c | false | <90% | 5312 | ||
NM_033360 | KRAS | 206 | 224 | g | U | U | G | G | A | G | C | U | G | g | U | G | g | C | G | U | A | G | 17 | 3 | 9 | c | false | <90% | 5436 | ||
NM_199454 | PRDM16 | 3632 | 3650 | U | U | U | G | G | A | G | C | c | G | A | U | G | C | C | G | a | c | u | 8 | 4 | 8 | c | false | <90% | 8669 | ||
NM_022114 | PRDM16 | 3632 | 3650 | U | U | U | G | G | A | G | C | c | G | A | U | G | C | C | G | a | c | u | 8 | 4 | 8 | c | false | <90% | 8726 | ||
NM_017448 | LDHC | 134 | 152 | g | U | U | G | G | A | a | C | U | G | g | U | G | C | C | G | U | A | G | -29 | 3 | 8 | c | false | <90% | 1171 | ||
NM_002301 | LDHC | 241 | 259 | g | U | U | G | G | A | a | C | U | G | g | U | G | C | C | G | U | A | G | -29 | 3 | 8 | c | false | <90% | 1278 |
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_144992 | MGC26733 | 3948 | 3966 | C | c | A | C | G | G | C | A | U | C | A | G | C | U | C | C | c | A | u | 60 | 3 | 14 | ac | false | <90% | 4765 | ||
NM_145648 | SLC15A4 | 206 | 224 | C | U | A | C | G | G | C | A | U | C | A | c | g | U | C | C | A | A | c | 50 | 3 | 11 | false | <90% | 2802 | |||
NM_017842 | FLJ20489 | 137 | 155 | C | U | c | C | G | G | C | A | U | C | A | G | C | U | C | C | g | u | g | 49 | 4 | 13 | c | false | <90% | 1950 | ||
NM_000125 | ESR1 | 402 | 420 | C | U | A | C | u | G | C | A | U | C | A | G | a | U | C | C | A | A | g | 33 | 3 | 7 | false | <90% | 6456 | |||
NM_138424 | KIF12 | 1991 | 2009 | g | a | g | a | G | G | C | A | U | C | A | G | C | U | C | C | A | A | A | 30 | 4 | 15 | bc | false | <90% | 2024 | ||
NM_198591 | BSG | 586 | 604 | C | a | A | C | G | G | C | A | c | C | A | G | C | U | C | C | A | A | g | 23 | 3 | 9 | bc | false | <90% | 1609 | ||
NM_198589 | BSG | 653 | 671 | C | a | A | C | G | G | C | A | c | C | A | G | C | U | C | C | A | A | g | 23 | 3 | 9 | bc | false | <90% | 1676 | ||
NM_198590 | BSG | 743 | 761 | C | a | A | C | G | G | C | A | c | C | A | G | C | U | C | C | A | A | g | 23 | 3 | 9 | bc | false | <90% | 1766 | ||
NM_001728 | BSG | 1001 | 1019 | C | a | A | C | G | G | C | A | c | C | A | G | C | U | C | C | A | A | g | 23 | 3 | 9 | bc | false | <90% | 2024 | ||
NM_031911 | C1QTNF7 | 10 | 28 | C | U | A | C | a | G | C | A | U | g | A | G | C | U | C | C | A | A | g | -39 | 3 | 8 | bc | false | <90% | 3954 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3376
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