Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
39 hits were found for GCAUUGAACAUGAGCAGCA (15 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_014517 | UBP1 | 1376 | 1394 | c | a | g | U | U | G | A | A | C | A | U | G | A | G | C | A | G | a | A | 64 | 4 | 14 | c | false | <90% | 4158 | ||
NM_020247 | CABC1 | 1304 | 1322 | G | u | g | U | U | G | A | A | C | A | U | G | A | G | C | A | a | C | A | 45 | 3 | 13 | c | false | <90% | 2932 | ||
NM_020768 | KCTD16 | 1752 | 1770 | G | a | A | U | c | G | A | A | C | A | U | G | A | G | C | A | G | C | A | 37 | 2 | 14 | bc | false | <90% | 5246 | ||
NM_012090 | MACF1 | 11760 | 11778 | c | C | A | U | U | G | A | u | C | A | U | G | A | G | C | A | G | C | u | 30 | 3 | 10 | bc | false | <90% | 17821 | ||
NM_033044 | MACF1 | 13192 | 13210 | c | C | A | U | U | G | A | u | C | A | U | G | A | G | C | A | G | C | u | 30 | 3 | 10 | bc | false | <90% | 19271 | ||
NM_001080404 | LOC729747 | 293 | 311 | a | C | A | U | U | G | A | A | g | A | U | G | A | G | C | A | c | C | A | 14 | 3 | 7 | c | false | <90% | 1737 | ||
XM_001126568 | LOC730617 | 293 | 311 | a | C | A | U | U | G | A | A | g | A | U | G | A | G | C | A | c | C | A | 14 | 3 | 7 | c | false | <90% | 1737 | ||
XM_001126500 | ZNF440 | 287 | 305 | a | C | A | U | U | G | A | A | u | A | U | G | A | G | C | A | c | C | A | 14 | 3 | 7 | c | false | <90% | 2833 | ||
XM_001131146 | ZNF440 | 693 | 711 | a | C | A | U | U | G | A | A | u | A | U | G | A | G | C | A | c | C | A | 14 | 3 | 7 | c | false | <90% | 3533 | ||
NM_001684 | ATP2B4 | 1432 | 1450 | G | C | A | U | U | G | A | A | C | A | g | G | A | G | C | A | a | a | A | 12 | 3 | 10 | c | false | <90% | 8733 | ||
NM_001001396 | ATP2B4 | 1432 | 1450 | G | C | A | U | U | G | A | A | C | A | g | G | A | G | C | A | a | a | A | 12 | 3 | 10 | c | false | <90% | 8911 | ||
NM_145041 | TMEM106A | 2757 | 2775 | a | a | g | U | U | u | A | A | C | A | U | G | A | G | C | A | G | C | A | 3 | 4 | 13 | bc | false | <90% | 2795 | ||
XM_001133074 | LOC728772 | 2759 | 2777 | a | a | g | U | U | u | A | A | C | A | U | G | A | G | C | A | G | C | A | 3 | 4 | 13 | bc | false | <90% | 3268 | ||
XM_001133059 | LOC728772 | 2778 | 2796 | a | a | g | U | U | u | A | A | C | A | U | G | A | G | C | A | G | C | A | 3 | 4 | 13 | bc | false | <90% | 3287 | ||
XM_001133066 | LOC728772 | 3061 | 3079 | a | a | g | U | U | u | A | A | C | A | U | G | A | G | C | A | G | C | A | 3 | 4 | 13 | bc | false | <90% | 3570 |
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 | |||||||||||||
XM_001130075 | LAMA1 | 5437 | 5455 | U | G | C | U | G | C | U | C | A | U | G | g | U | C | A | A | U | G | C | 66 | 1 | 11 | false | <90% | 9304 | |||
NM_005559 | LAMA1 | 5437 | 5455 | U | G | C | U | G | C | U | C | A | U | G | g | U | C | A | A | U | G | C | 66 | 1 | 11 | false | <90% | 9530 | |||
XR_019485 | LOC341315 | 1406 | 1424 | U | G | C | U | G | C | U | C | A | U | G | U | a | C | A | A | g | G | u | 61 | 3 | 12 | false | <90% | 1838 | |||
XR_017616 | LOC341315 | 1406 | 1424 | U | G | C | U | G | C | U | C | A | U | G | U | a | C | A | A | g | G | u | 61 | 3 | 12 | false | <90% | 1838 | |||
NM_198941 | SERINC3 | 474 | 492 | c | u | C | U | G | C | U | C | A | U | G | U | U | C | A | A | a | G | u | 58 | 4 | 14 | ac | false | <90% | 1744 | ||
NM_006811 | SERINC3 | 474 | 492 | c | u | C | U | G | C | U | C | A | U | G | U | U | C | A | A | a | G | u | 58 | 4 | 14 | ac | false | <90% | 2592 | ||
NM_002616 | PER1 | 3581 | 3599 | g | G | C | U | G | C | U | C | A | U | G | g | c | C | A | A | U | G | C | 53 | 3 | 10 | false | <90% | 4656 | |||
NR_000034 | TMEM185B | 710 | 728 | U | G | C | U | G | C | U | C | A | U | G | U | U | C | g | A | a | G | u | 46 | 3 | 14 | c | false | <90% | 2131 | ||
NM_031993 | PCDHGA1 | 781 | 799 | a | G | C | U | G | C | U | C | A | U | G | g | U | a | A | A | U | G | C | 44 | 3 | 10 | false | <90% | 2472 | |||
NM_018912 | PCDHGA1 | 781 | 799 | a | G | C | U | G | C | U | C | A | U | G | g | U | a | A | A | U | G | C | 44 | 3 | 10 | false | <90% | 4602 | |||
NM_139247 | ADCY4 | 887 | 905 | U | G | g | U | G | C | U | C | A | U | G | c | U | C | A | A | U | G | a | 41 | 3 | 8 | false | <90% | 3320 | |||
NM_006598 | SLC12A7 | 545 | 563 | U | G | C | U | G | C | a | C | A | U | G | U | a | C | A | A | U | G | C | 23 | 2 | 6 | false | <90% | 5316 | |||
NM_003589 | CUL4A | 1742 | 1760 | U | G | C | U | c | C | U | C | A | U | G | U | U | C | A | A | c | G | a | 20 | 3 | 11 | c | false | <90% | 3735 | ||
NM_001008895 | CUL4A | 1804 | 1822 | U | G | C | U | c | C | U | C | A | U | G | U | U | C | A | A | c | G | a | 20 | 3 | 11 | c | false | <90% | 3797 | ||
NM_000023 | SGCA | 1089 | 1107 | c | c | C | U | G | C | c | C | A | U | G | U | U | C | A | A | U | G | u | 15 | 4 | 11 | bc | false | <90% | 1404 | ||
XM_001133708 | LOC729738 | 106 | 124 | U | G | C | U | G | g | U | C | A | U | G | U | U | C | A | A | a | G | C | 13 | 2 | 10 | c | false | <90% | 810 | ||
NM_001079872 | CUL4B | 2525 | 2543 | U | G | C | U | G | C | U | a | A | U | G | U | U | u | A | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 5198 | ||
NM_003588 | CUL4B | 2692 | 2710 | U | G | C | U | G | C | U | a | A | U | G | U | U | u | A | A | U | G | a | 13 | 3 | 7 | c | false | <90% | 5365 | ||
NM_001034024 | DMAP1 | 1159 | 1177 | U | G | g | U | G | C | a | C | A | U | G | U | U | C | A | A | U | G | a | 9 | 3 | 11 | bc | false | <90% | 1563 | ||
NM_001034023 | DMAP1 | 1199 | 1217 | U | G | g | U | G | C | a | C | A | U | G | U | U | C | A | A | U | G | a | 9 | 3 | 11 | bc | false | <90% | 1603 | ||
NM_019100 | DMAP1 | 1380 | 1398 | U | G | g | U | G | C | a | C | A | U | G | U | U | C | A | A | U | G | a | 9 | 3 | 11 | bc | false | <90% | 1784 | ||
NM_000350 | ABCA4 | 5568 | 5586 | c | G | C | U | G | C | U | C | A | g | G | U | U | C | A | A | c | G | C | -8 | 3 | 8 | c | false | <90% | 7326 | ||
NM_001014842 | TM9SF1 | 1334 | 1352 | U | G | C | U | G | g | g | C | A | U | G | U | U | C | A | A | U | G | u | -34 | 3 | 11 | bc | false | <90% | 2124 | ||
NM_006405 | TM9SF1 | 1334 | 1352 | U | G | C | U | G | g | g | C | A | U | G | U | U | C | A | A | U | G | u | -34 | 3 | 11 | bc | false | <90% | 2449 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1534
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