Automatic recommendation
Not OK - siRNA is not specific
42 hits were found for CAUGCAGGCAAGAGAAGCC (13 guide strand hits and 29 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_199175 | C21orf123 | 439 | 457 | C | c | U | G | C | A | G | G | C | A | A | G | A | G | A | A | G | a | g | 80 | 3 | 15 | ac | false | <90% | 2341 | ||
NM_015609 | C1orf144 | 442 | 460 | a | A | U | G | C | A | G | G | C | A | A | G | A | a | A | A | G | a | u | 70 | 4 | 12 | c | false | <90% | 1700 | ||
XM_929034 | LOC646074 | 1558 | 1576 | g | A | U | G | C | A | G | G | C | A | u | G | A | G | A | A | G | a | a | 29 | 4 | 9 | c | false | <90% | 2459 | ||
NM_015492 | C15orf39 | 1533 | 1551 | g | c | U | G | C | A | G | G | a | A | A | G | A | G | A | A | G | C | u | 21 | 4 | 9 | bc | false | <90% | 3775 | ||
NM_001025197 | CHI3L2 | 1182 | 1200 | C | A | a | G | C | A | G | u | C | A | A | G | A | G | A | A | G | C | C | 18 | 2 | 11 | bc | false | <90% | 1456 | ||
NM_004000 | CHI3L2 | 1212 | 1230 | C | A | a | G | C | A | G | u | C | A | A | G | A | G | A | A | G | C | C | 18 | 2 | 11 | bc | false | <90% | 1486 | ||
NM_001025199 | CHI3L2 | 1242 | 1260 | C | A | a | G | C | A | G | u | C | A | A | G | A | G | A | A | G | C | C | 18 | 2 | 11 | bc | false | <90% | 1516 | ||
NM_006058 | TNIP1 | 2131 | 2149 | g | g | a | G | a | A | G | G | C | A | A | G | A | G | A | A | G | C | C | 15 | 4 | 14 | bc | false | <90% | 3268 | ||
NM_133644 | GTPBP3 | 928 | 946 | a | A | U | G | C | g | G | G | C | A | A | G | A | G | c | A | G | C | C | 9 | 3 | 8 | c | false | <90% | 1960 | ||
NM_032620 | GTPBP3 | 817 | 835 | a | A | U | G | C | g | G | G | C | A | A | G | A | G | c | A | G | C | C | 9 | 3 | 8 | c | false | <90% | 2545 | ||
XM_929368 | LOC646442 | 294 | 312 | g | A | U | G | C | A | G | c | C | A | A | a | A | G | A | A | G | C | C | 2 | 3 | 7 | false | <90% | 774 | |||
NM_001901 | CTGF | 886 | 904 | C | c | U | G | C | A | G | G | C | u | A | G | A | G | A | A | G | C | a | 0 | 3 | 8 | bc | false | <90% | 2358 | ||
NM_152505 | C21orf13 | 392 | 410 | g | c | a | G | C | A | u | G | C | A | A | G | A | G | A | A | G | C | C | 0 | 4 | 12 | bc | false | <90% | 2364 |
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_001139 | ALOX12B | 176 | 194 | G | G | C | U | U | C | U | C | U | U | G | C | C | U | G | C | c | U | u | 71 | 2 | 16 | ac | false | <90% | 2502 | ||
NM_182589 | HTR3E | 1643 | 1661 | a | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | G | 70 | 3 | 13 | c | false | <90% | 1927 | ||
XM_001133029 | LOC732372 | 357 | 375 | a | G | C | U | U | C | U | C | U | U | G | C | C | U | G | C | c | g | c | 66 | 4 | 15 | ac | false | <90% | 900 | ||
NM_000644 | AGL | 2814 | 2832 | u | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | a | 65 | 4 | 13 | c | false | <90% | 7109 | ||
NM_000643 | AGL | 2874 | 2892 | u | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | a | 65 | 4 | 13 | c | false | <90% | 7169 | ||
NM_000645 | AGL | 2887 | 2905 | u | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | a | 65 | 4 | 13 | c | false | <90% | 7182 | ||
NM_000646 | AGL | 2887 | 2905 | u | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | a | 65 | 4 | 13 | c | false | <90% | 7182 | ||
NM_000642 | AGL | 3076 | 3094 | u | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | a | 65 | 4 | 13 | c | false | <90% | 7371 | ||
NM_000028 | AGL | 3154 | 3172 | u | G | C | U | U | C | U | C | U | U | G | C | C | U | c | C | A | g | a | 65 | 4 | 13 | c | false | <90% | 7449 | ||
NM_006154 | NEDD4 | 3526 | 3544 | c | c | u | U | U | C | U | C | U | U | G | C | C | U | G | C | A | U | a | 62 | 4 | 15 | bc | false | <90% | 5760 | ||
NM_198400 | NEDD4 | 4785 | 4803 | c | c | u | U | U | C | U | C | U | U | G | C | C | U | G | C | A | U | a | 62 | 4 | 15 | bc | false | <90% | 7019 | ||
NM_145246 | C10orf4 | 1468 | 1486 | a | u | C | U | U | C | U | C | U | U | G | C | C | U | u | C | A | U | u | 56 | 4 | 12 | c | false | <90% | 2400 | ||
NM_032182 | KIAA0157 | 1780 | 1798 | a | c | C | U | U | C | U | C | U | U | G | u | C | U | G | C | A | U | G | 52 | 3 | 9 | false | <90% | 2965 | |||
NM_001025197 | CHI3L2 | 569 | 587 | G | G | C | U | U | C | U | C | U | U | G | a | C | U | G | C | g | g | G | 40 | 3 | 11 | false | <90% | 1456 | |||
NM_004000 | CHI3L2 | 599 | 617 | G | G | C | U | U | C | U | C | U | U | G | a | C | U | G | C | g | g | G | 40 | 3 | 11 | false | <90% | 1486 | |||
NM_001025199 | CHI3L2 | 629 | 647 | G | G | C | U | U | C | U | C | U | U | G | a | C | U | G | C | g | g | G | 40 | 3 | 11 | false | <90% | 1516 | |||
NM_023016 | ANKRD57 | 1059 | 1077 | G | G | C | U | U | C | a | C | U | U | G | C | C | U | G | C | A | c | u | 26 | 3 | 10 | c | false | <90% | 4681 | ||
NM_172028 | ABTB1 | 1622 | 1640 | G | G | C | U | U | C | U | C | U | U | c | C | C | U | c | C | A | U | G | 14 | 2 | 10 | c | false | <90% | 1974 | ||
NM_172027 | ABTB1 | 1657 | 1675 | G | G | C | U | U | C | U | C | U | U | c | C | C | U | c | C | A | U | G | 14 | 2 | 10 | c | false | <90% | 1989 | ||
NM_032548 | ABTB1 | 1668 | 1686 | G | G | C | U | U | C | U | C | U | U | c | C | C | U | c | C | A | U | G | 14 | 2 | 10 | c | false | <90% | 2020 | ||
XM_940758 | TMEM76 | 4467 | 4485 | G | G | C | U | U | C | U | C | c | U | G | C | C | U | c | C | A | U | c | 10 | 3 | 8 | c | false | <90% | 5868 | ||
XM_372038 | TMEM76 | 4551 | 4569 | G | G | C | U | U | C | U | C | c | U | G | C | C | U | c | C | A | U | c | 10 | 3 | 8 | c | false | <90% | 5952 | ||
NM_173362 | RFESD | 1076 | 1094 | c | a | u | U | U | C | U | C | U | U | c | C | C | U | G | C | A | U | G | 5 | 4 | 8 | c | false | <90% | 2711 | ||
NM_018018 | SLC38A4 | 1045 | 1063 | a | u | u | U | U | C | U | C | U | U | a | C | C | U | G | C | A | U | G | 5 | 4 | 8 | c | false | <90% | 3961 | ||
NM_001042734 | SEC24B | 2574 | 2592 | u | G | C | U | U | C | U | C | U | a | G | C | u | U | G | C | A | U | G | 4 | 3 | 8 | false | <90% | 4544 | |||
NM_006323 | SEC24B | 2679 | 2697 | u | G | C | U | U | C | U | C | U | a | G | C | u | U | G | C | A | U | G | 4 | 3 | 8 | false | <90% | 4649 | |||
NM_175733 | SYT9 | 2656 | 2674 | G | G | C | U | U | C | U | C | U | g | G | C | C | U | G | a | A | U | G | -8 | 2 | 9 | c | false | <90% | 3975 | ||
NM_005294 | GPR21 | 351 | 369 | G | G | C | U | U | C | U | C | U | g | G | C | C | U | G | u | A | U | c | -13 | 3 | 9 | c | false | <90% | 1050 | ||
NM_001002034 | FAM109B | 856 | 874 | u | G | C | U | U | C | U | C | U | a | c | C | C | U | G | C | A | U | G | -46 | 3 | 8 | c | false | <90% | 2369 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2087
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