Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
41 hits were found for AAGCCUCCAAGCUGUGCCU (24 guide strand hits and 17 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_012291 | ESPL1 | 5815 | 5833 | c | A | G | C | C | U | C | C | A | A | G | C | a | c | U | G | C | C | U | 68 | 3 | 11 | false | <90% | 6641 | |||
NM_000261 | MYOC | 1539 | 1557 | A | A | G | C | C | U | C | C | A | A | G | C | U | G | U | a | C | a | g | 66 | 3 | 15 | c | false | <90% | 2061 | ||
NM_002845 | PTPRM | 2004 | 2022 | c | A | G | C | C | U | C | C | A | A | G | C | U | G | c | G | C | a | g | 65 | 4 | 13 | c | false | <90% | 5065 | ||
NM_001015054 | MPG | 718 | 736 | g | c | c | C | C | U | C | C | A | A | G | C | U | G | U | G | C | C | a | 62 | 4 | 15 | bc | false | <90% | 1055 | ||
NM_001015052 | MPG | 775 | 793 | g | c | c | C | C | U | C | C | A | A | G | C | U | G | U | G | C | C | a | 62 | 4 | 15 | bc | false | <90% | 1112 | ||
NM_002434 | MPG | 968 | 986 | g | c | c | C | C | U | C | C | A | A | G | C | U | G | U | G | C | C | a | 62 | 4 | 15 | bc | false | <90% | 1305 | ||
XM_001126273 | LOC727773 | 2398 | 2416 | c | u | c | C | C | U | C | C | A | A | G | C | g | G | U | G | C | C | U | 56 | 4 | 9 | false | <90% | 5198 | |||
NM_032329 | ING5 | 2398 | 2416 | c | u | c | C | C | U | C | C | A | A | G | C | g | G | U | G | C | C | U | 56 | 4 | 9 | false | <90% | 5233 | |||
XM_941026 | ING5 | 2649 | 2667 | c | u | c | C | C | U | C | C | A | A | G | C | g | G | U | G | C | C | U | 56 | 4 | 9 | false | <90% | 5449 | |||
XM_001131562 | LOC729862 | 316 | 334 | A | A | G | C | C | U | C | C | A | A | G | C | U | a | U | G | a | u | U | 54 | 3 | 13 | c | false | <90% | 390 | ||
XM_001126066 | LOC730497 | 1588 | 1606 | A | A | G | C | C | U | C | C | A | A | G | C | U | a | U | G | a | u | U | 54 | 3 | 13 | c | false | <90% | 1996 | ||
NM_003162 | STRN | 400 | 418 | A | A | G | C | C | U | C | C | A | A | G | C | U | a | U | G | a | u | U | 54 | 3 | 13 | c | false | <90% | 3479 | ||
NM_021601 | CD79A | 203 | 221 | A | g | u | C | C | U | C | C | A | A | G | C | U | c | U | G | C | C | U | 49 | 3 | 10 | c | false | <90% | 1144 | ||
NM_001783 | CD79A | 203 | 221 | A | g | u | C | C | U | C | C | A | A | G | C | U | c | U | G | C | C | U | 49 | 3 | 10 | c | false | <90% | 1258 | ||
XM_940310 | LOC651186 | 1496 | 1514 | u | A | G | C | C | U | a | C | A | A | G | C | U | G | U | G | C | C | a | 26 | 3 | 11 | bc | false | <90% | 2073 | ||
NM_080752 | ZSWIM3 | 1717 | 1735 | u | A | G | C | C | U | a | C | A | A | G | C | U | G | U | G | C | C | a | 26 | 3 | 11 | bc | false | <90% | 2789 | ||
NR_002711 | CLK2P | 790 | 808 | u | g | G | C | C | U | C | C | c | A | G | C | U | G | U | G | C | C | a | 21 | 4 | 9 | bc | false | <90% | 1665 | ||
NM_144604 | NHN1 | 1620 | 1638 | A | A | G | C | C | g | C | C | A | A | G | C | U | G | a | G | C | C | a | 7 | 3 | 8 | c | false | <90% | 3572 | ||
NM_006133 | DAGLA | 2532 | 2550 | c | A | G | C | C | U | C | C | A | c | G | C | U | G | U | G | C | u | g | 7 | 4 | 8 | c | false | <90% | 5756 | ||
NM_175849 | DNMT3B | 1937 | 1955 | A | A | G | C | C | c | C | C | A | A | G | C | U | G | U | a | C | C | c | 5 | 3 | 9 | c | false | <90% | 4104 | ||
NM_175850 | DNMT3B | 1916 | 1934 | A | A | G | C | C | c | C | C | A | A | G | C | U | G | U | a | C | C | c | 5 | 3 | 9 | c | false | <90% | 4267 | ||
NM_175848 | DNMT3B | 1937 | 1955 | A | A | G | C | C | c | C | C | A | A | G | C | U | G | U | a | C | C | c | 5 | 3 | 9 | c | false | <90% | 4293 | ||
NM_006892 | DNMT3B | 1997 | 2015 | A | A | G | C | C | c | C | C | A | A | G | C | U | G | U | a | C | C | c | 5 | 3 | 9 | c | false | <90% | 4353 | ||
NM_018344 | SLC29A3 | 373 | 391 | u | g | c | C | C | U | C | C | A | u | G | C | U | G | U | G | C | C | U | -15 | 4 | 9 | bc | false | <90% | 2243 |
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_000435 | NOTCH3 | 6486 | 6504 | u | G | G | C | A | C | A | G | C | U | U | G | G | u | G | G | C | c | c | 70 | 4 | 12 | c | false | <90% | 8089 | ||
NR_003110 | CCT6AP1 | 1141 | 1159 | A | G | G | C | A | C | A | G | C | U | U | G | G | A | G | u | C | c | a | 66 | 3 | 15 | c | false | <90% | 1783 | ||
XR_019061 | LOC651806 | 1295 | 1313 | g | G | G | C | A | C | A | G | C | U | U | G | G | A | G | u | C | c | a | 64 | 4 | 14 | c | false | <90% | 1596 | ||
XR_016472 | LOC391739 | 1295 | 1313 | g | G | G | C | A | C | A | G | C | U | U | G | G | A | G | u | C | c | a | 64 | 4 | 14 | c | false | <90% | 1596 | ||
NM_001009186 | CCT6A | 1324 | 1342 | g | G | G | C | A | C | A | G | C | U | U | G | G | A | G | u | C | c | a | 64 | 4 | 14 | c | false | <90% | 2547 | ||
NM_001762 | CCT6A | 1459 | 1477 | g | G | G | C | A | C | A | G | C | U | U | G | G | A | G | u | C | c | a | 64 | 4 | 14 | c | false | <90% | 2682 | ||
XM_001133696 | LOC731680 | 231 | 249 | A | G | G | C | A | C | A | G | C | U | U | G | c | A | G | a | C | U | g | 58 | 3 | 12 | false | <90% | 916 | |||
XM_001129241 | LOC439949 | 965 | 983 | A | G | u | C | A | C | A | G | C | U | U | G | G | A | G | G | a | a | a | 49 | 4 | 13 | c | false | <90% | 1402 | ||
XM_001128367 | LOC439949 | 965 | 983 | A | G | u | C | A | C | A | G | C | U | U | G | G | A | G | G | a | a | a | 49 | 4 | 13 | c | false | <90% | 1403 | ||
NM_194293 | CMYA1 | 1864 | 1882 | u | G | G | C | A | C | A | G | C | U | c | G | G | u | G | G | C | U | U | 17 | 3 | 9 | c | false | <90% | 6451 | ||
NM_004254 | SLC22A8 | 1005 | 1023 | A | G | G | C | u | C | A | G | C | U | U | G | G | A | G | G | a | g | c | 17 | 4 | 11 | c | false | <90% | 2207 | ||
XM_001125843 | LOC727804 | 1613 | 1631 | A | G | c | C | A | C | g | G | C | U | U | G | G | A | G | G | C | U | g | 9 | 3 | 11 | bc | false | <90% | 2060 | ||
XM_001131467 | LOC731976 | 1615 | 1633 | A | G | c | C | A | C | g | G | C | U | U | G | G | A | G | G | C | U | g | 9 | 3 | 11 | bc | false | <90% | 2062 | ||
XM_001132665 | LOC728803 | 636 | 654 | A | G | G | C | A | C | g | G | C | U | U | G | G | u | G | G | C | U | g | 9 | 3 | 6 | c | false | <90% | 2645 | ||
XM_001134353 | LOC732318 | 636 | 654 | A | G | G | C | A | C | g | G | C | U | U | G | G | u | G | G | C | U | g | 9 | 3 | 6 | c | false | <90% | 2645 | ||
XM_945050 | LOC643624 | 728 | 746 | A | G | G | C | c | C | A | G | C | U | g | G | G | A | G | G | C | U | c | -17 | 3 | 7 | c | false | <90% | 1047 | ||
NM_024798 | SNX22 | 299 | 317 | c | G | G | C | A | g | g | G | C | U | U | G | G | A | G | G | C | U | U | -31 | 3 | 12 | bc | false | <90% | 3614 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2033
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