Automatic recommendation
Not OK - siRNA is not specific
52 hits were found for CAUGGACGAGGACGGGGAA (41 guide strand hits and 11 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_926011 | LOC642515 | 297 | 315 | C | c | U | G | G | A | C | G | A | G | G | A | C | G | G | G | G | c | g | 80 | 3 | 15 | ac | false | <90% | 867 | ||
XM_938306 | LOC642515 | 297 | 315 | C | c | U | G | G | A | C | G | A | G | G | A | C | G | G | G | G | c | g | 80 | 3 | 15 | ac | false | <90% | 867 | ||
XM_939079 | LOC649993 | 46 | 64 | C | g | g | G | G | A | C | G | A | G | G | A | C | G | G | G | G | A | A | 69 | 2 | 16 | bc | false | <90% | 453 | ||
XM_001132472 | LOC730111 | 12 | 30 | g | g | a | G | G | A | C | G | A | G | G | A | C | G | G | G | G | A | A | 67 | 3 | 16 | bc | false | <90% | 828 | ||
XM_001126827 | LOC730696 | 12 | 30 | g | g | a | G | G | A | C | G | A | G | G | A | C | G | G | G | G | A | A | 67 | 3 | 16 | bc | false | <90% | 828 | ||
NM_030918 | SNX27 | 19 | 37 | g | g | c | G | G | A | C | G | A | G | G | A | C | G | G | G | G | A | A | 67 | 3 | 16 | bc | false | <90% | 7085 | ||
NM_005477 | HCN4 | 641 | 659 | C | A | U | G | G | A | C | G | A | G | G | A | a | G | a | G | G | A | c | 59 | 3 | 12 | false | <90% | 5065 | |||
NM_033212 | CCDC102A | 1827 | 1845 | C | c | U | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | c | 58 | 3 | 12 | c | false | <90% | 2461 | ||
NM_031954 | KCTD10 | 940 | 958 | C | c | U | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | g | 58 | 3 | 12 | c | false | <90% | 4057 | ||
NM_148921 | EPN2 | 2435 | 2453 | C | u | U | G | G | A | C | G | A | G | G | A | C | G | u | G | G | A | g | 58 | 3 | 12 | c | false | <90% | 4643 | ||
NM_014964 | EPN2 | 2606 | 2624 | C | u | U | G | G | A | C | G | A | G | G | A | C | G | u | G | G | A | g | 58 | 3 | 12 | c | false | <90% | 4814 | ||
NM_033393 | KIAA1727 | 3560 | 3578 | C | u | g | G | G | A | C | G | A | G | G | A | u | G | G | G | G | A | A | 58 | 3 | 9 | false | <90% | 6480 | |||
NM_152238 | SNX7 | 11 | 29 | u | c | U | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | c | 56 | 4 | 12 | c | false | <90% | 1585 | ||
NM_015976 | SNX7 | 216 | 234 | u | c | U | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | c | 56 | 4 | 12 | c | false | <90% | 1798 | ||
NM_016172 | UBAC1 | 767 | 785 | g | c | U | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | u | 56 | 4 | 12 | c | false | <90% | 1877 | ||
NM_020782 | KLHDC5 | 344 | 362 | g | g | U | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | g | 56 | 4 | 12 | c | false | <90% | 6477 | ||
NM_001004439 | ITGA11 | 2208 | 2226 | C | c | U | G | G | A | C | G | A | G | G | g | C | G | G | G | G | A | c | 49 | 3 | 9 | false | <90% | 5035 | |||
NM_024927 | PLEKHH3 | 490 | 508 | C | g | a | G | G | A | C | G | A | G | G | A | C | G | a | G | G | A | A | 44 | 3 | 11 | c | false | <90% | 2994 | ||
XM_001132117 | LOC732181 | 46 | 64 | C | g | a | G | G | A | C | G | A | G | G | A | C | G | G | c | G | A | A | 42 | 3 | 12 | c | false | <90% | 483 | ||
XR_015234 | LOC440015 | 46 | 64 | C | g | a | G | G | A | C | G | A | G | G | A | C | G | G | c | G | A | A | 42 | 3 | 12 | c | false | <90% | 1255 | ||
NM_153464 | ILF3 | 1385 | 1403 | a | A | U | G | G | A | g | G | A | G | G | A | C | G | G | G | G | A | g | 26 | 3 | 11 | bc | false | <90% | 3234 | ||
NM_004516 | ILF3 | 1385 | 1403 | a | A | U | G | G | A | g | G | A | G | G | A | C | G | G | G | G | A | g | 26 | 3 | 11 | bc | false | <90% | 3677 | ||
NM_012218 | ILF3 | 1385 | 1403 | a | A | U | G | G | A | g | G | A | G | G | A | C | G | G | G | G | A | g | 26 | 3 | 11 | bc | false | <90% | 6058 | ||
XM_001131137 | LOC729729 | 849 | 867 | C | A | U | G | G | A | C | c | A | G | G | A | a | G | G | G | G | A | g | 22 | 3 | 7 | false | <90% | 1284 | |||
XM_001131001 | LOC731838 | 849 | 867 | C | A | U | G | G | A | C | c | A | G | G | A | a | G | G | G | G | A | g | 22 | 3 | 7 | false | <90% | 1284 | |||
NM_005105 | RBM8A | 77 | 95 | C | A | U | G | G | A | u | G | A | G | G | A | u | G | G | G | G | A | c | 18 | 3 | 6 | false | <90% | 2787 | |||
XR_019492 | LOC652316 | 46 | 64 | C | g | g | G | G | A | C | G | g | G | G | A | C | G | G | G | G | A | A | 8 | 3 | 10 | bc | false | <90% | 1270 | ||
NM_012447 | STAG3 | 3680 | 3698 | u | A | U | G | G | A | a | G | A | G | G | A | C | G | a | G | G | A | A | 6 | 3 | 7 | c | false | <90% | 4285 | ||
XM_001129295 | LOC728731 | 1500 | 1518 | g | g | g | G | G | A | C | G | g | G | G | A | C | G | G | G | G | A | A | 6 | 4 | 10 | bc | false | <90% | 4572 | ||
NM_015347 | RIMBP2 | 2432 | 2450 | C | A | U | G | G | A | g | G | A | G | G | A | C | G | a | G | G | A | g | 4 | 3 | 7 | c | false | <90% | 6335 | ||
NM_178043 | LARP2 | 588 | 606 | a | g | a | G | G | c | C | G | A | G | G | A | C | G | G | G | G | A | A | 3 | 4 | 13 | bc | false | <90% | 1819 | ||
NM_032239 | LARP2 | 588 | 606 | a | g | a | G | G | c | C | G | A | G | G | A | C | G | G | G | G | A | A | 3 | 4 | 13 | bc | false | <90% | 2718 | ||
NM_018078 | LARP2 | 588 | 606 | a | g | a | G | G | c | C | G | A | G | G | A | C | G | G | G | G | A | A | 3 | 4 | 13 | bc | false | <90% | 3979 | ||
NM_152629 | GLIS3 | 1187 | 1205 | C | c | U | G | G | A | C | G | A | c | G | A | C | G | G | G | G | A | g | 0 | 3 | 8 | bc | false | <90% | 6672 | ||
NM_001042413 | GLIS3 | 2171 | 2189 | C | c | U | G | G | A | C | G | A | c | G | A | C | G | G | G | G | A | g | 0 | 3 | 8 | bc | false | <90% | 7656 | ||
NM_017455 | NPTN | 44 | 62 | g | c | a | G | G | A | g | G | A | G | G | A | C | G | G | G | G | A | A | 0 | 4 | 12 | bc | false | <90% | 2109 | ||
NM_012428 | NPTN | 44 | 62 | g | c | a | G | G | A | g | G | A | G | G | A | C | G | G | G | G | A | A | 0 | 4 | 12 | bc | false | <90% | 2457 | ||
NM_003378 | VGF | 1435 | 1453 | g | g | a | G | G | A | g | G | A | G | G | A | C | G | G | G | G | A | A | 0 | 4 | 12 | bc | false | <90% | 2545 | ||
NM_032221 | CHD6 | 2666 | 2684 | g | A | U | G | G | g | C | G | A | G | u | A | C | G | G | G | G | A | A | -26 | 3 | 8 | c | false | <90% | 10389 | ||
NM_199326 | PPP2R3B | 571 | 589 | C | A | U | G | G | A | C | c | u | G | G | A | C | G | G | G | G | A | c | -27 | 3 | 9 | bc | false | <90% | 1244 | ||
NM_013239 | PPP2R3B | 1398 | 1416 | C | A | U | G | G | A | C | c | u | G | G | A | C | G | G | G | G | A | c | -27 | 3 | 9 | bc | false | <90% | 2071 |
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_032626 | RBBP6 | 802 | 820 | U | U | C | C | C | C | G | U | C | C | U | C | G | U | C | C | u | c | c | 68 | 3 | 16 | ac | false | <90% | 1780 | ||
NM_018703 | RBBP6 | 802 | 820 | U | U | C | C | C | C | G | U | C | C | U | C | G | U | C | C | u | c | c | 68 | 3 | 16 | ac | false | <90% | 6751 | ||
NM_006910 | RBBP6 | 802 | 820 | U | U | C | C | C | C | G | U | C | C | U | C | G | U | C | C | u | c | c | 68 | 3 | 16 | ac | false | <90% | 6853 | ||
NM_152288 | TMEM142C | 1989 | 2007 | c | U | C | C | C | C | G | U | C | C | U | g | G | U | C | C | A | g | G | 61 | 3 | 10 | false | <90% | 2239 | |||
NM_002973 | ATXN2 | 796 | 814 | U | U | C | g | C | C | G | U | C | C | U | C | G | U | C | C | u | c | G | 37 | 3 | 12 | c | false | <90% | 4702 | ||
NM_178831 | GATS | 931 | 949 | U | U | C | C | u | C | G | U | C | C | U | C | u | U | C | C | A | U | a | 33 | 3 | 7 | false | <90% | 3493 | |||
NM_170775 | KCNN2 | 1072 | 1090 | g | U | C | C | C | g | G | U | C | C | U | C | G | U | C | C | A | g | G | 32 | 3 | 11 | c | false | <90% | 1457 | ||
NM_021614 | KCNN2 | 2130 | 2148 | g | U | C | C | C | g | G | U | C | C | U | C | G | U | C | C | A | g | G | 32 | 3 | 11 | c | false | <90% | 2515 | ||
NM_133456 | SHROOM1 | 203 | 221 | c | U | C | C | C | C | G | g | C | C | U | C | G | U | C | C | A | c | u | 28 | 4 | 9 | c | false | <90% | 3190 | ||
XM_001125756 | LOC727788 | 1785 | 1803 | U | U | C | C | C | C | G | g | C | C | U | C | c | U | C | C | A | U | c | 22 | 3 | 7 | false | <90% | 3331 | |||
NM_002479 | MYOG | 1101 | 1119 | a | U | C | C | C | C | u | U | C | C | U | C | a | U | C | C | A | U | G | 21 | 3 | 6 | false | <90% | 1744 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1612
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