Automatic recommendation
Not OK - siRNA is not specific
35 hits were found for GACAAAUGCAGAUGCUGGC (24 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 | |||||||||||||
NM_002420 | TRPM1 | 2504 | 2522 | u | g | C | A | A | A | U | G | C | A | G | A | U | G | C | U | G | G | C | 86 | 2 | 17 | abc | false | <90% | 5428 | ||
NM_173078 | SLITRK4 | 421 | 439 | G | A | C | A | A | A | U | G | C | A | G | A | U | u | C | U | G | a | C | 77 | 2 | 13 | c | false | <90% | 3383 | ||
NM_015507 | EGFL6 | 472 | 490 | a | A | C | A | A | A | U | G | C | A | G | A | U | G | C | U | u | u | C | 71 | 3 | 15 | ac | false | <90% | 2398 | ||
NM_003839 | TNFRSF11A | 537 | 555 | G | A | C | A | A | A | U | G | C | A | G | A | c | c | C | U | G | G | a | 65 | 3 | 12 | false | <90% | 3133 | |||
NM_021933 | IIP45 | 1265 | 1283 | c | A | C | c | A | A | U | G | C | A | G | A | U | G | C | U | G | c | C | 58 | 3 | 13 | c | false | <90% | 1588 | ||
NM_024702 | ZNF750 | 2580 | 2598 | u | A | C | A | A | A | U | G | C | A | G | c | U | G | C | U | G | c | u | 56 | 4 | 10 | false | <90% | 3218 | |||
NM_019891 | ERO1LB | 1382 | 1400 | G | A | C | A | A | A | U | G | C | A | G | A | U | u | a | U | G | G | g | 50 | 3 | 13 | c | false | <90% | 2977 | ||
NM_020403 | PCDH9 | 2475 | 2493 | G | A | C | A | g | A | U | G | C | A | G | A | U | G | C | U | G | G | a | 43 | 2 | 13 | bc | false | <90% | 6127 | ||
NM_203487 | PCDH9 | 2475 | 2493 | G | A | C | A | g | A | U | G | C | A | G | A | U | G | C | U | G | G | a | 43 | 2 | 13 | bc | false | <90% | 6229 | ||
NM_145025 | C6orf199 | 723 | 741 | c | c | g | A | A | A | U | G | C | A | G | A | U | G | g | U | G | G | C | 42 | 4 | 11 | c | false | <90% | 2583 | ||
NM_133478 | SLC4A5 | 5412 | 5430 | G | A | C | A | A | A | U | G | C | A | G | g | U | G | C | U | u | u | C | 40 | 3 | 11 | false | <90% | 6364 | |||
NM_001797 | CDH11 | 1613 | 1631 | a | g | a | A | A | A | U | G | C | A | G | c | U | G | C | U | G | G | C | 33 | 4 | 8 | false | <90% | 3654 | |||
XM_943270 | LOC647628 | 11 | 29 | a | c | C | A | g | A | U | G | C | A | G | A | U | G | C | U | G | G | u | 30 | 4 | 13 | bc | false | <90% | 644 | ||
XM_931034 | LOC642394 | 11 | 29 | a | c | C | A | g | A | U | G | C | A | G | A | U | G | C | U | G | G | u | 30 | 4 | 13 | bc | false | <90% | 644 | ||
NM_017639 | DCHS2 | 7347 | 7365 | c | u | C | A | g | A | U | G | C | A | G | A | U | G | C | U | G | G | u | 30 | 4 | 13 | bc | false | <90% | 8751 | ||
NM_021035 | ZNFX1 | 3942 | 3960 | G | A | a | A | c | A | U | G | C | A | G | A | U | G | C | U | G | G | C | 28 | 2 | 14 | bc | false | <90% | 7371 | ||
NM_170662 | CBLB | 841 | 859 | c | A | C | A | A | A | a | G | C | A | G | A | U | G | C | U | G | c | u | 24 | 4 | 10 | c | false | <90% | 3976 | ||
NM_144633 | KCNH8 | 4869 | 4887 | G | g | C | A | A | A | U | u | C | A | G | A | U | G | C | U | G | G | g | 21 | 3 | 10 | bc | false | <90% | 5106 | ||
XR_015884 | LOC729157 | 137 | 155 | G | A | C | A | A | A | U | c | C | A | G | A | U | G | C | U | a | a | g | 6 | 4 | 8 | c | false | <90% | 1500 | ||
XR_015862 | LOC731415 | 137 | 155 | G | A | C | A | A | A | U | c | C | A | G | A | U | G | C | U | a | a | g | 6 | 4 | 8 | c | false | <90% | 1500 | ||
NM_023003 | TM6SF1 | 844 | 862 | c | u | a | A | A | A | U | u | C | A | G | A | U | G | C | U | G | G | C | 4 | 4 | 11 | bc | false | <90% | 1440 | ||
NM_001356 | DDX3X | 2015 | 2033 | a | g | g | A | A | A | U | a | C | A | G | A | U | G | C | U | G | G | C | 4 | 4 | 11 | bc | false | <90% | 5433 | ||
XR_018698 | LOC392479 | 1052 | 1070 | a | g | g | A | A | c | U | G | C | A | G | A | U | G | C | U | G | G | C | 3 | 4 | 13 | bc | false | <90% | 1643 | ||
NM_004433 | ELF3 | 1264 | 1282 | c | A | C | A | g | u | U | G | C | A | G | A | U | G | C | U | G | G | C | -16 | 3 | 13 | bc | false | <90% | 5036 |
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_030767 | AKNA | 3479 | 3497 | c | C | C | A | G | C | A | U | C | U | G | C | c | U | U | U | G | a | C | 84 | 3 | 11 | false | <90% | 5385 | |||
XR_018132 | LOC391552 | 824 | 842 | G | C | C | A | G | C | A | U | C | U | G | C | A | U | U | a | G | c | a | 66 | 3 | 15 | c | false | <90% | 2443 | ||
XR_016313 | LOC391552 | 824 | 842 | G | C | C | A | G | C | A | U | C | U | G | C | A | U | U | a | G | c | a | 66 | 3 | 15 | c | false | <90% | 2443 | ||
XR_018142 | LOC647502 | 1454 | 1472 | G | C | C | A | G | C | A | U | C | U | G | C | A | U | U | a | G | c | a | 66 | 3 | 15 | c | false | <90% | 3074 | ||
NM_018046 | AGGF1 | 878 | 896 | G | C | C | A | G | C | A | U | C | U | G | C | A | U | U | a | G | c | a | 66 | 3 | 15 | c | false | <90% | 4480 | ||
XM_001133717 | LOC731881 | 76 | 94 | a | C | C | A | G | C | A | U | C | U | G | C | A | U | c | U | G | a | u | 65 | 4 | 13 | c | false | <90% | 306 | ||
NM_006962 | ZNF182 | 352 | 370 | a | C | C | A | G | C | A | U | C | U | G | C | A | U | c | U | G | g | u | 65 | 4 | 13 | c | false | <90% | 3598 | ||
NM_017610 | RNF111 | 2175 | 2193 | u | g | g | A | G | C | A | U | C | U | G | C | A | U | U | U | G | a | C | 64 | 4 | 14 | c | false | <90% | 5556 | ||
NM_002763 | PROX1 | 356 | 374 | G | a | C | A | G | C | A | U | C | U | G | C | A | U | U | U | u | U | u | 60 | 3 | 14 | ac | false | <90% | 3088 | ||
NM_152420 | C9orf41 | 598 | 616 | G | C | C | A | G | C | A | U | C | U | a | C | A | U | U | U | G | a | C | 36 | 2 | 10 | c | false | <90% | 2219 | ||
NM_025015 | HSPA12A | 3365 | 3383 | a | C | C | A | G | a | A | U | C | U | G | C | A | U | U | U | G | U | a | 29 | 3 | 12 | bc | false | <90% | 5739 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1954
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