Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
42 hits were found for ACCAAAAGAAACACCAUCC (18 guide strand hits and 24 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_182496 | CCDC38 | 616 | 634 | A | C | C | A | A | A | A | G | A | A | A | C | A | C | a | A | U | C | a | 70 | 2 | 14 | c | false | <90% | 1953 | ||
XR_019222 | LOC648859 | 694 | 712 | A | a | g | A | A | A | A | G | A | A | A | C | A | C | C | A | U | u | C | 66 | 3 | 14 | c | false | <90% | 1169 | ||
NM_012479 | YWHAG | 3431 | 3449 | A | g | C | A | A | A | A | G | A | A | A | C | A | C | C | A | g | u | g | 57 | 4 | 14 | ac | false | <90% | 3747 | ||
NM_207046 | ENSA | 857 | 875 | g | a | u | A | A | A | A | G | A | A | A | C | u | C | C | A | U | C | C | 56 | 4 | 9 | false | <90% | 1116 | |||
NM_207045 | ENSA | 905 | 923 | g | a | u | A | A | A | A | G | A | A | A | C | u | C | C | A | U | C | C | 56 | 4 | 9 | false | <90% | 1164 | |||
NM_004436 | ENSA | 993 | 1011 | g | a | u | A | A | A | A | G | A | A | A | C | u | C | C | A | U | C | C | 56 | 4 | 9 | false | <90% | 1252 | |||
NM_207042 | ENSA | 1041 | 1059 | g | a | u | A | A | A | A | G | A | A | A | C | u | C | C | A | U | C | C | 56 | 4 | 9 | false | <90% | 1300 | |||
NM_014641 | MDC1 | 2888 | 2906 | A | C | C | A | A | A | A | G | A | A | A | C | A | g | C | A | g | a | g | 49 | 4 | 13 | c | false | <90% | 7385 | ||
NM_032385 | C5orf4 | 811 | 829 | u | C | C | A | c | A | A | G | A | A | A | C | A | C | C | A | U | g | a | 38 | 4 | 12 | c | false | <90% | 3817 | ||
NM_153456 | HS6ST3 | 1015 | 1033 | A | g | u | g | A | A | A | G | A | A | A | C | A | C | C | A | U | C | C | 32 | 3 | 15 | bc | false | <90% | 7817 | ||
NM_002661 | PLCG2 | 618 | 636 | A | C | C | A | g | A | A | G | A | A | A | C | A | g | C | A | U | C | a | 24 | 3 | 8 | c | false | <90% | 4263 | ||
NM_031288 | ZNHIT4 | 185 | 203 | A | C | a | A | g | A | A | G | A | A | A | C | A | C | C | A | U | C | a | 23 | 3 | 13 | bc | false | <90% | 1217 | ||
XR_016132 | LOC642661 | 754 | 772 | u | C | C | A | A | A | A | G | A | u | A | C | A | C | C | A | U | g | C | 12 | 3 | 8 | c | false | <90% | 2413 | ||
NM_153264 | FLJ35880 | 1408 | 1426 | A | C | C | A | A | A | u | G | A | A | A | C | A | u | C | A | U | C | u | 9 | 3 | 6 | c | false | <90% | 2691 | ||
NM_173054 | RELN | 9721 | 9739 | u | g | g | A | A | A | A | G | A | A | u | C | A | C | C | A | U | C | C | 5 | 4 | 8 | c | false | <90% | 11558 | ||
NM_005045 | RELN | 9721 | 9739 | u | g | g | A | A | A | A | G | A | A | u | C | A | C | C | A | U | C | C | 5 | 4 | 8 | c | false | <90% | 11564 | ||
NM_033191 | KRTAP9-4 | 506 | 524 | c | C | C | A | A | g | A | G | A | A | c | C | A | C | C | A | U | C | C | -26 | 3 | 8 | c | false | <90% | 990 | ||
NM_031961 | KRTAP9-2 | 539 | 557 | u | C | C | A | A | g | A | G | A | A | c | C | A | C | C | A | U | C | C | -26 | 3 | 8 | c | false | <90% | 1042 |
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 | |||||||||||||
XR_018218 | LOC642590 | 1563 | 1581 | u | G | A | U | G | G | U | G | U | U | U | C | U | U | U | U | c | c | c | 66 | 4 | 15 | ac | false | <90% | 1670 | ||
XR_016251 | LOC642590 | 1563 | 1581 | u | G | A | U | G | G | U | G | U | U | U | C | U | U | U | U | c | c | c | 66 | 4 | 15 | ac | false | <90% | 1670 | ||
NM_003347 | UBE2L3 | 793 | 811 | G | a | A | U | G | G | U | G | U | U | U | C | U | U | U | U | c | u | U | 62 | 3 | 14 | ac | false | <90% | 2907 | ||
NM_198157 | UBE2L3 | 902 | 920 | G | a | A | U | G | G | U | G | U | U | U | C | U | U | U | U | c | u | U | 62 | 3 | 14 | ac | false | <90% | 3016 | ||
NM_006154 | NEDD4 | 5527 | 5545 | a | a | A | U | G | G | U | G | U | U | U | g | U | U | U | U | G | G | g | 47 | 4 | 9 | false | <90% | 5760 | |||
NM_198400 | NEDD4 | 6786 | 6804 | a | a | A | U | G | G | U | G | U | U | U | g | U | U | U | U | G | G | g | 47 | 4 | 9 | false | <90% | 7019 | |||
NM_014879 | P2RY14 | 876 | 894 | G | G | A | U | u | G | U | G | U | U | U | C | U | U | U | U | G | u | U | 45 | 2 | 12 | c | false | <90% | 2504 | ||
NM_001081455 | P2RY14 | 1066 | 1084 | G | G | A | U | u | G | U | G | U | U | U | C | U | U | U | U | G | u | U | 45 | 2 | 12 | c | false | <90% | 2694 | ||
NM_001010924 | C10orf38 | 914 | 932 | a | c | A | c | G | G | U | G | U | U | U | C | U | U | U | U | G | G | c | 44 | 4 | 14 | bc | false | <90% | 3964 | ||
NM_014729 | TOX | 99 | 117 | G | G | A | a | G | G | U | G | U | U | U | C | U | U | U | U | a | c | U | 37 | 3 | 12 | c | false | <90% | 4131 | ||
XR_019652 | LOC392435 | 445 | 463 | a | G | A | a | G | G | U | G | U | U | U | a | U | U | U | U | G | G | U | 27 | 3 | 7 | false | <90% | 1145 | |||
XR_017125 | LOC392435 | 445 | 463 | a | G | A | a | G | G | U | G | U | U | U | a | U | U | U | U | G | G | U | 27 | 3 | 7 | false | <90% | 1145 | |||
NM_006080 | SEMA3A | 4517 | 4535 | a | u | A | U | G | G | U | G | U | U | g | C | U | U | U | U | G | G | a | 20 | 4 | 8 | c | false | <90% | 5672 | ||
NM_199478 | PLP1 | 237 | 255 | G | G | A | U | u | G | U | G | U | U | U | C | U | U | U | g | G | G | g | 17 | 3 | 10 | c | false | <90% | 2933 | ||
NM_000533 | PLP1 | 237 | 255 | G | G | A | U | u | G | U | G | U | U | U | C | U | U | U | g | G | G | g | 17 | 3 | 10 | c | false | <90% | 3038 | ||
NM_005901 | SMAD2 | 4758 | 4776 | G | c | A | U | G | G | g | G | U | U | U | C | U | U | U | U | G | G | a | 17 | 3 | 11 | bc | false | <90% | 10384 | ||
NM_001003652 | SMAD2 | 4905 | 4923 | G | c | A | U | G | G | g | G | U | U | U | C | U | U | U | U | G | G | a | 17 | 3 | 11 | bc | false | <90% | 10531 | ||
NM_052937 | PCMTD1 | 2326 | 2344 | u | u | u | U | u | G | U | G | U | U | U | C | U | U | U | U | G | G | U | 15 | 4 | 14 | bc | false | <90% | 3967 | ||
NM_006390 | IPO8 | 3975 | 3993 | G | G | g | U | G | G | U | a | U | U | U | C | U | U | U | U | G | G | g | 13 | 3 | 10 | bc | false | <90% | 5178 | ||
NM_001009959 | KIAA1189 | 1419 | 1437 | u | u | c | U | G | G | U | a | U | U | U | C | U | U | U | U | G | G | U | 4 | 4 | 11 | bc | false | <90% | 3722 | ||
NM_020711 | KIAA1189 | 1487 | 1505 | u | u | c | U | G | G | U | a | U | U | U | C | U | U | U | U | G | G | U | 4 | 4 | 11 | bc | false | <90% | 3790 | ||
NM_004999 | MYO6 | 2357 | 2375 | G | G | A | U | G | G | U | G | U | c | U | g | U | U | U | U | G | G | a | -21 | 3 | 9 | false | <90% | 8662 | |||
NM_002485 | NBN | 392 | 410 | G | G | A | U | G | G | U | a | U | U | a | C | U | U | U | U | G | G | a | -28 | 3 | 7 | c | false | <90% | 4639 | ||
NM_001024688 | NBN | 442 | 460 | G | G | A | U | G | G | U | a | U | U | a | C | U | U | U | U | G | G | a | -28 | 3 | 7 | c | false | <90% | 4689 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3386
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