Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
32 hits were found for CAAAUACUUUGUCACCAAA (20 guide strand hits and 12 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_030650 | KIAA1715 | 4185 | 4203 | u | A | A | A | U | A | C | U | U | U | G | U | u | g | C | C | A | A | A | 68 | 3 | 11 | false | <90% | 5765 | |||
NM_006818 | MLLT11 | 389 | 407 | a | A | A | A | U | A | C | U | U | U | G | U | a | A | C | C | u | A | A | 64 | 3 | 11 | false | <90% | 2180 | |||
NM_080645 | COL12A1 | 7442 | 7460 | a | A | A | A | U | A | C | U | U | U | G | U | u | A | a | C | A | A | A | 62 | 3 | 11 | false | <90% | 8087 | |||
NM_004370 | COL12A1 | 10934 | 10952 | a | A | A | A | U | A | C | U | U | U | G | U | u | A | a | C | A | A | A | 62 | 3 | 11 | false | <90% | 11579 | |||
NM_001010898 | SLC6A17 | 2026 | 2044 | a | A | A | c | U | A | C | U | U | U | G | U | C | A | C | C | A | u | g | 53 | 4 | 13 | c | false | <90% | 6420 | ||
NM_005191 | CD80 | 2700 | 2718 | C | A | g | A | U | A | C | U | U | U | G | U | C | A | g | C | A | A | u | 50 | 3 | 11 | c | false | <90% | 2757 | ||
XM_030729 | FAM22F | 1566 | 1584 | g | g | A | A | g | A | C | U | U | U | G | U | C | A | C | C | A | A | g | 30 | 4 | 13 | bc | false | <90% | 2756 | ||
NM_001045477 | FAM22G | 2020 | 2038 | g | g | A | A | g | A | C | U | U | U | G | U | C | A | C | C | A | A | g | 30 | 4 | 13 | bc | false | <90% | 4888 | ||
NM_003728 | UNC5C | 2791 | 2809 | g | A | A | u | U | A | C | U | U | U | G | c | C | A | C | C | A | A | A | 27 | 3 | 7 | false | <90% | 3646 | |||
NM_170744 | UNC5B | 3085 | 3103 | g | A | A | u | U | A | C | U | U | U | G | c | C | A | C | C | A | A | A | 27 | 3 | 7 | false | <90% | 3935 | |||
NM_001459 | FLT3LG | 402 | 420 | g | A | u | A | c | A | C | U | U | U | G | U | C | A | C | C | A | A | A | 26 | 3 | 14 | bc | false | <90% | 1056 | ||
NM_033118 | MYLK2 | 1539 | 1557 | C | A | A | A | g | A | C | U | U | U | G | U | C | u | C | C | A | A | c | 24 | 3 | 8 | c | false | <90% | 2683 | ||
NM_001015045 | FAM13A1 | 3480 | 3498 | C | A | A | A | g | A | C | U | U | U | G | U | C | A | C | a | A | A | A | 22 | 2 | 10 | c | false | <90% | 4919 | ||
NM_014883 | FAM13A1 | 4419 | 4437 | C | A | A | A | g | A | C | U | U | U | G | U | C | A | C | a | A | A | A | 22 | 2 | 10 | c | false | <90% | 5858 | ||
NM_022726 | ELOVL4 | 2743 | 2761 | u | A | A | A | U | A | C | U | U | U | u | U | C | c | C | C | A | A | A | 17 | 3 | 9 | c | false | <90% | 2992 | ||
XM_001129617 | LOC729189 | 933 | 951 | a | A | A | A | U | A | u | U | U | U | G | U | C | u | C | C | A | A | A | 12 | 3 | 6 | c | false | <90% | 1577 | ||
XM_001128342 | LOC728744 | 1010 | 1028 | a | A | A | A | U | A | u | U | U | U | G | U | C | u | C | C | A | A | A | 12 | 3 | 6 | c | false | <90% | 1654 | ||
XM_001133554 | LOC729127 | 1424 | 1442 | a | A | A | A | U | A | u | U | U | U | G | U | C | u | C | C | A | A | A | 12 | 3 | 6 | c | false | <90% | 2068 | ||
NM_182833 | GDPD4 | 105 | 123 | C | A | A | A | U | g | C | U | U | U | G | U | C | A | C | C | u | u | c | 5 | 4 | 10 | c | false | <90% | 2545 | ||
NM_016612 | SLC25A37 | 1122 | 1140 | C | A | A | g | U | A | C | U | U | U | c | U | C | A | C | C | A | A | g | -3 | 3 | 7 | c | false | <90% | 1865 |
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_004190 | LIPF | 841 | 859 | U | U | U | G | G | U | G | A | C | A | A | A | a | U | A | U | U | c | u | 81 | 3 | 12 | false | <90% | 1497 | |||
NM_001031710 | KLHL7 | 2064 | 2082 | U | U | U | G | G | U | G | A | C | A | A | A | G | U | u | U | U | g | G | 72 | 2 | 14 | c | false | <90% | 3137 | ||
NM_018846 | KLHL7 | 2204 | 2222 | U | U | U | G | G | U | G | A | C | A | A | A | G | U | u | U | U | g | G | 72 | 2 | 14 | c | false | <90% | 3140 | ||
NM_020698 | TMCC3 | 3452 | 3470 | U | U | U | G | G | U | G | A | u | A | A | A | G | U | A | U | U | U | u | 34 | 2 | 9 | bc | false | <90% | 4727 | ||
NM_000566 | FCGR1A | 2026 | 2044 | U | U | U | G | G | a | G | A | C | A | A | A | a | U | A | U | U | U | u | 21 | 3 | 6 | false | <90% | 2230 | |||
NM_000235 | LIPA | 850 | 868 | U | U | U | G | G | a | G | A | C | A | A | A | G | a | A | U | U | U | c | 12 | 3 | 7 | c | false | <90% | 2654 | ||
NM_002015 | FOXO1A | 4490 | 4508 | c | U | U | G | G | U | G | c | C | A | A | A | G | U | A | c | U | U | G | 9 | 3 | 7 | c | false | <90% | 5738 | ||
NM_003496 | TRRAP | 1109 | 1127 | g | U | U | G | G | U | G | A | C | u | A | A | G | U | A | U | U | c | u | 7 | 4 | 8 | c | false | <90% | 12563 | ||
NM_001039618 | CREBZF | 4591 | 4609 | g | U | U | G | G | U | a | A | C | A | A | A | G | U | A | a | U | U | G | 5 | 3 | 8 | c | false | <90% | 7304 | ||
NM_004086 | COCH | 930 | 948 | U | U | U | G | G | U | G | u | C | A | A | u | G | U | A | U | U | U | a | 0 | 3 | 7 | false | <90% | 2534 | |||
NM_001547 | IFIT2 | 178 | 196 | U | U | U | G | a | a | G | A | C | A | A | A | G | U | A | U | U | U | u | -19 | 3 | 12 | bc | false | <90% | 3058 | ||
NM_000527 | LDLR | 1933 | 1951 | U | U | U | G | a | g | G | A | C | A | A | A | G | U | A | U | U | U | u | -19 | 3 | 12 | bc | false | <90% | 5175 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1888
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