Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
27 hits were found for CCUAUAACAUCAAAUUCAA (11 guide strand hits and 16 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_015954 | DERA | 1370 | 1388 | u | u | g | A | U | A | A | C | A | U | C | A | A | A | U | U | C | u | A | 64 | 4 | 14 | c | false | <90% | 1741 | ||
| NM_020466 | LYRM2 | 4939 | 4957 | g | a | a | A | U | A | A | C | A | U | C | A | A | A | U | U | C | A | g | 62 | 4 | 15 | bc | false | <90% | 5371 | ||
| NM_006258 | PRKG1 | 1800 | 1818 | C | C | U | A | U | A | A | C | A | U | C | A | u | A | U | U | g | A | g | 61 | 3 | 12 | false | <90% | 3740 | |||
| NM_004336 | BUB1 | 603 | 621 | a | u | g | A | U | A | A | C | A | U | C | A | A | A | a | U | C | A | A | 42 | 4 | 11 | c | false | <90% | 3486 | ||
| XM_001133468 | LOC729280 | 400 | 418 | u | C | c | c | U | A | A | C | A | U | C | A | A | A | U | U | C | A | A | 41 | 3 | 15 | bc | false | <90% | 897 | ||
| XM_001133470 | LOC729280 | 487 | 505 | u | C | c | c | U | A | A | C | A | U | C | A | A | A | U | U | C | A | A | 41 | 3 | 15 | bc | false | <90% | 984 | ||
| XM_001128623 | LOC728849 | 2017 | 2035 | C | C | U | g | U | A | A | C | A | U | C | u | A | A | U | U | C | A | g | 24 | 3 | 7 | false | <90% | 10120 | |||
| NM_138270 | ATRX | 2132 | 2150 | C | C | U | g | U | A | A | C | A | U | C | u | A | A | U | U | C | A | g | 24 | 3 | 7 | false | <90% | 11088 | |||
| NM_000489 | ATRX | 2246 | 2264 | C | C | U | g | U | A | A | C | A | U | C | u | A | A | U | U | C | A | g | 24 | 3 | 7 | false | <90% | 11202 | |||
| NM_004863 | SPTLC2 | 4039 | 4057 | C | C | U | A | U | A | A | a | A | U | C | A | A | A | U | a | C | A | u | 6 | 3 | 7 | c | false | <90% | 7250 | ||
| NM_016282 | AK3 | 550 | 568 | u | C | U | A | U | A | A | C | A | U | u | g | A | A | U | U | C | A | A | 2 | 3 | 9 | false | <90% | 2642 | |||
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 | |||||||||||||
| NR_003365 | SUGT1L1 | 3385 | 3403 | c | U | G | A | A | U | U | U | G | A | U | G | U | U | A | U | A | c | a | 90 | 3 | 16 | ac | false | <90% | 4202 | ||
| NM_005369 | MCF2 | 1331 | 1349 | a | U | G | A | A | U | U | U | G | A | U | G | U | a | A | U | A | u | u | 70 | 4 | 12 | c | false | <90% | 3652 | ||
| NM_199436 | SPAST | 1141 | 1159 | U | U | a | A | A | U | U | U | G | A | U | G | a | U | A | U | A | G | c | 65 | 3 | 9 | false | <90% | 5125 | |||
| NM_014946 | SPAST | 1237 | 1255 | U | U | a | A | A | U | U | U | G | A | U | G | a | U | A | U | A | G | c | 65 | 3 | 9 | false | <90% | 5221 | |||
| NM_004857 | AKAP5 | 2331 | 2349 | g | U | G | A | A | U | U | U | G | A | U | G | U | U | A | c | A | a | a | 64 | 4 | 14 | c | false | <90% | 2601 | ||
| NM_022894 | PAPOLG | 704 | 722 | U | U | G | A | A | U | U | U | G | A | U | G | g | U | A | U | u | G | a | 61 | 3 | 12 | false | <90% | 4252 | |||
| NM_032141 | CCDC55 | 2223 | 2241 | a | g | G | A | A | U | U | U | G | A | U | G | U | U | A | c | A | G | u | 55 | 4 | 13 | c | false | <90% | 2542 | ||
| NM_030799 | YIPF5 | 2990 | 3008 | U | U | G | c | A | U | U | U | G | A | U | G | U | U | c | U | A | G | a | 33 | 3 | 10 | c | false | <90% | 3126 | ||
| NM_000297 | PKD2 | 3819 | 3837 | c | U | G | A | A | U | U | U | a | A | U | G | U | U | A | U | A | a | c | 30 | 4 | 8 | c | false | <90% | 5073 | ||
| XM_379203 | LOC348801 | 553 | 571 | a | c | G | A | A | U | U | U | G | A | g | G | U | U | A | U | A | G | G | 25 | 3 | 8 | c | false | <90% | 2233 | ||
| XM_931908 | LOC348801 | 553 | 571 | a | c | G | A | A | U | U | U | G | A | g | G | U | U | A | U | A | G | G | 25 | 3 | 8 | c | false | <90% | 2272 | ||
| XM_943217 | LOC348801 | 553 | 571 | a | c | G | A | A | U | U | U | G | A | g | G | U | U | A | U | A | G | G | 25 | 3 | 8 | c | false | <90% | 2279 | ||
| XR_018539 | LOC649050 | 1330 | 1348 | U | U | a | A | A | a | U | U | G | A | U | G | U | U | A | U | A | G | c | 12 | 3 | 12 | bc | false | <90% | 1408 | ||
| XR_015169 | LOC727941 | 1633 | 1651 | U | U | a | A | A | a | U | U | G | A | U | G | U | U | A | U | A | G | c | 12 | 3 | 12 | bc | false | <90% | 1711 | ||
| NM_018017 | C10orf118 | 5124 | 5142 | U | U | G | A | A | U | U | a | G | A | U | G | U | U | A | U | c | c | c | 6 | 4 | 8 | c | false | <90% | 6277 | ||
| NM_002581 | PAPPA | 8639 | 8657 | g | U | c | A | A | U | U | U | G | u | U | G | U | U | A | U | A | G | G | -4 | 3 | 9 | bc | false | <90% | 11025 | ||
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1459
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