Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
58 hits were found for AUGAAGAGCAGGACAAAAG (36 guide strand hits and 22 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_033044 | MACF1 | 4171 | 4189 | A | U | G | A | A | G | A | G | C | A | G | G | A | a | A | A | A | g | c | 72 | 3 | 13 | c | false | <90% | 19271 | ||
NM_001042723 | RYR1 | 11940 | 11958 | u | U | G | A | A | G | A | G | C | A | G | G | g | C | A | A | g | A | G | 64 | 3 | 11 | false | <90% | 15376 | |||
NM_000540 | RYR1 | 11955 | 11973 | u | U | G | A | A | G | A | G | C | A | G | G | g | C | A | A | g | A | G | 64 | 3 | 11 | false | <90% | 15391 | |||
XR_018256 | LOC643067 | 828 | 846 | u | g | G | A | A | G | A | G | C | A | G | G | A | a | A | A | A | A | a | 62 | 4 | 11 | c | false | <90% | 1184 | ||
XR_016316 | LOC643067 | 828 | 846 | u | g | G | A | A | G | A | G | C | A | G | G | A | a | A | A | A | A | a | 62 | 4 | 11 | c | false | <90% | 1184 | ||
NM_014711 | CP110 | 2415 | 2433 | u | a | G | A | A | G | A | G | C | A | G | G | A | g | A | A | A | A | u | 62 | 4 | 11 | c | false | <90% | 5488 | ||
NM_023921 | TAS2R10 | 361 | 379 | u | U | G | A | A | G | A | G | C | A | G | a | A | C | A | A | A | u | a | 56 | 4 | 10 | false | <90% | 924 | |||
NM_139157 | ST5 | 378 | 396 | c | c | G | A | A | G | A | G | C | A | G | G | A | C | g | A | A | A | a | 56 | 4 | 12 | c | false | <90% | 3039 | ||
NM_213618 | ST5 | 1710 | 1728 | c | c | G | A | A | G | A | G | C | A | G | G | A | C | g | A | A | A | a | 56 | 4 | 12 | c | false | <90% | 4371 | ||
NM_005418 | ST5 | 1910 | 1928 | c | c | G | A | A | G | A | G | C | A | G | G | A | C | g | A | A | A | a | 56 | 4 | 12 | c | false | <90% | 4571 | ||
NM_080836 | STK35 | 1468 | 1486 | c | a | G | A | A | G | A | G | C | A | G | G | A | C | A | c | A | A | u | 55 | 4 | 13 | c | false | <90% | 6033 | ||
XR_016308 | LOC139516 | 404 | 422 | c | U | G | A | A | G | A | G | C | A | G | G | A | g | A | A | g | A | G | 54 | 3 | 12 | c | false | <90% | 2766 | ||
XR_018410 | LOC139516 | 404 | 422 | c | U | G | A | A | G | A | G | C | A | G | G | A | g | A | A | g | A | G | 54 | 3 | 12 | c | false | <90% | 2766 | ||
NM_012288 | TRAM2 | 4291 | 4309 | A | c | c | A | A | G | A | G | C | A | G | G | A | g | A | A | A | A | G | 49 | 3 | 10 | c | false | <90% | 7065 | ||
NR_003135 | CEP170L | 1487 | 1505 | u | a | c | A | A | G | A | G | C | A | G | G | A | C | c | A | A | A | G | 42 | 4 | 11 | c | false | <90% | 90477 | ||
NM_182664 | RASSF5 | 1098 | 1116 | A | a | G | A | g | G | A | G | C | A | G | G | A | C | A | A | A | A | u | 32 | 3 | 13 | bc | false | <90% | 3521 | ||
NM_182665 | RASSF5 | 1108 | 1126 | A | a | G | A | g | G | A | G | C | A | G | G | A | C | A | A | A | A | u | 32 | 3 | 13 | bc | false | <90% | 3531 | ||
NM_182663 | RASSF5 | 1214 | 1232 | A | a | G | A | g | G | A | G | C | A | G | G | A | C | A | A | A | A | u | 32 | 3 | 13 | bc | false | <90% | 3637 | ||
NM_012234 | RYBP | 338 | 356 | u | U | G | A | A | a | A | G | C | A | G | G | A | C | A | A | A | g | a | 27 | 4 | 11 | c | false | <90% | 4562 | ||
NM_001001344 | ATP2B3 | 4031 | 4049 | A | g | G | A | A | G | A | G | g | A | G | G | A | C | A | A | A | A | a | 23 | 3 | 9 | bc | false | <90% | 6438 | ||
NM_021949 | ATP2B3 | 4185 | 4203 | A | g | G | A | A | G | A | G | g | A | G | G | A | C | A | A | A | A | a | 23 | 3 | 9 | bc | false | <90% | 6592 | ||
NM_144698 | ANKRD35 | 1850 | 1868 | A | U | G | A | A | G | A | G | a | A | G | G | A | g | A | A | A | A | G | 20 | 2 | 8 | c | false | <90% | 3363 | ||
NM_001083617 | RB1CC1 | 4475 | 4493 | u | U | G | A | A | G | A | G | C | A | a | G | A | a | A | A | A | A | G | 17 | 3 | 9 | c | false | <90% | 6661 | ||
NM_014781 | RB1CC1 | 4475 | 4493 | u | U | G | A | A | G | A | G | C | A | a | G | A | a | A | A | A | A | G | 17 | 3 | 9 | c | false | <90% | 6670 | ||
NM_015382 | HECTD1 | 3657 | 3675 | A | U | u | A | A | G | A | G | a | A | G | G | A | C | A | A | A | A | u | 15 | 3 | 9 | bc | false | <90% | 9134 | ||
NM_000329 | RPE65 | 1530 | 1548 | c | c | c | A | g | G | A | G | C | A | G | G | A | C | A | A | A | A | G | 15 | 4 | 14 | bc | false | <90% | 2608 | ||
NM_172210 | CSF1 | 569 | 587 | A | U | G | A | A | G | A | G | C | A | u | G | A | C | A | A | g | g | c | 7 | 4 | 10 | c | false | <90% | 1519 | ||
NM_172211 | CSF1 | 569 | 587 | A | U | G | A | A | G | A | G | C | A | u | G | A | C | A | A | g | g | c | 7 | 4 | 10 | c | false | <90% | 1855 | ||
NM_172212 | CSF1 | 569 | 587 | A | U | G | A | A | G | A | G | C | A | u | G | A | C | A | A | g | g | c | 7 | 4 | 10 | c | false | <90% | 2545 | ||
NM_000757 | CSF1 | 569 | 587 | A | U | G | A | A | G | A | G | C | A | u | G | A | C | A | A | g | g | c | 7 | 4 | 10 | c | false | <90% | 2749 | ||
NM_007214 | SEC63 | 1693 | 1711 | A | a | c | A | A | G | A | a | C | A | G | G | A | C | A | A | A | A | G | 6 | 3 | 11 | bc | false | <90% | 3850 | ||
NM_020130 | C8orf4 | 313 | 331 | u | U | G | A | A | G | A | a | g | A | G | G | A | C | A | A | A | A | G | -24 | 3 | 10 | bc | false | <90% | 1833 | ||
NM_031271 | TEX15 | 1550 | 1568 | A | U | G | A | A | a | A | G | g | A | G | G | A | C | A | A | A | A | a | -28 | 3 | 9 | bc | false | <90% | 10155 | ||
NM_001008541 | MXI1 | 2582 | 2600 | A | U | G | A | A | a | A | a | C | A | G | G | A | C | A | A | A | A | c | -30 | 3 | 10 | bc | false | <90% | 3047 | ||
NM_005962 | MXI1 | 2807 | 2825 | A | U | G | A | A | a | A | a | C | A | G | G | A | C | A | A | A | A | c | -30 | 3 | 10 | bc | false | <90% | 3272 | ||
NM_130439 | MXI1 | 3005 | 3023 | A | U | G | A | A | a | A | a | C | A | G | G | A | C | A | A | A | A | c | -30 | 3 | 10 | bc | false | <90% | 3470 |
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_172244 | SGCD | 632 | 650 | u | c | U | U | U | G | U | C | C | U | G | C | U | C | c | U | C | A | U | 61 | 3 | 12 | c | false | <90% | 1576 | ||
NM_000337 | SGCD | 632 | 650 | u | c | U | U | U | G | U | C | C | U | G | C | U | C | c | U | C | A | U | 61 | 3 | 12 | c | false | <90% | 8052 | ||
NM_182983 | HPN | 343 | 361 | g | U | U | c | U | G | U | C | C | U | G | C | U | C | U | U | C | c | U | 58 | 3 | 13 | c | false | <90% | 2363 | ||
NM_178176 | MOGAT3 | 300 | 318 | u | c | U | U | U | G | U | C | C | U | c | C | U | C | U | U | C | A | c | 20 | 4 | 8 | c | false | <90% | 1420 | ||
NM_031922 | REPS1 | 1607 | 1625 | g | U | U | U | U | G | U | g | C | U | G | C | U | u | U | U | C | A | U | 16 | 3 | 6 | c | false | <90% | 3565 | ||
NM_153616 | SEMA6D | 4262 | 4280 | a | U | U | U | U | G | U | g | C | U | G | C | U | a | U | U | C | A | U | 16 | 3 | 6 | c | false | <90% | 5884 | ||
NM_153619 | SEMA6D | 4297 | 4315 | a | U | U | U | U | G | U | g | C | U | G | C | U | a | U | U | C | A | U | 16 | 3 | 6 | c | false | <90% | 5919 | ||
NM_020858 | SEMA6D | 4301 | 4319 | a | U | U | U | U | G | U | g | C | U | G | C | U | a | U | U | C | A | U | 16 | 3 | 6 | c | false | <90% | 5923 | ||
NM_153617 | SEMA6D | 4319 | 4337 | a | U | U | U | U | G | U | g | C | U | G | C | U | a | U | U | C | A | U | 16 | 3 | 6 | c | false | <90% | 5941 | ||
NM_153618 | SEMA6D | 4487 | 4505 | a | U | U | U | U | G | U | g | C | U | G | C | U | a | U | U | C | A | U | 16 | 3 | 6 | c | false | <90% | 6109 | ||
XR_019631 | LOC650368 | 53 | 71 | C | U | U | U | U | u | U | C | C | U | G | C | U | C | U | U | u | c | a | 5 | 4 | 10 | c | false | <90% | 728 | ||
NM_052869 | TTYH2 | 1640 | 1658 | C | U | U | U | U | G | c | C | C | U | G | C | U | C | U | c | C | A | c | 2 | 3 | 8 | c | false | <90% | 3278 | ||
NM_032646 | TTYH2 | 1830 | 1848 | C | U | U | U | U | G | c | C | C | U | G | C | U | C | U | c | C | A | c | 2 | 3 | 8 | c | false | <90% | 3468 | ||
NM_016841 | MAPT | 4311 | 4329 | C | U | U | g | U | G | c | C | C | U | G | C | U | C | U | U | C | A | g | -8 | 3 | 11 | bc | false | <90% | 5464 | ||
NM_016834 | MAPT | 4404 | 4422 | C | U | U | g | U | G | c | C | C | U | G | C | U | C | U | U | C | A | g | -8 | 3 | 11 | bc | false | <90% | 5557 | ||
NM_005910 | MAPT | 4578 | 4596 | C | U | U | g | U | G | c | C | C | U | G | C | U | C | U | U | C | A | g | -8 | 3 | 11 | bc | false | <90% | 5731 | ||
NM_016835 | MAPT | 5529 | 5547 | C | U | U | g | U | G | c | C | C | U | G | C | U | C | U | U | C | A | g | -8 | 3 | 11 | bc | false | <90% | 6682 | ||
NM_177437 | TAS2R60 | 753 | 771 | C | U | U | U | U | G | c | C | a | U | G | C | U | C | U | U | C | A | U | -26 | 2 | 10 | bc | false | <90% | 957 | ||
NM_014837 | SMG7 | 5132 | 5150 | C | U | U | U | U | G | U | g | C | U | u | C | U | C | U | U | C | A | g | -28 | 3 | 7 | c | false | <90% | 5648 | ||
NM_201569 | SMG7 | 5160 | 5178 | C | U | U | U | U | G | U | g | C | U | u | C | U | C | U | U | C | A | g | -28 | 3 | 7 | c | false | <90% | 5676 | ||
NM_201568 | SMG7 | 5192 | 5210 | C | U | U | U | U | G | U | g | C | U | u | C | U | C | U | U | C | A | g | -28 | 3 | 7 | c | false | <90% | 5708 | ||
NM_173156 | SMG7 | 5330 | 5348 | C | U | U | U | U | G | U | g | C | U | u | C | U | C | U | U | C | A | g | -28 | 3 | 7 | c | false | <90% | 5846 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 3321
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