Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
45 hits were found for CUCCUGGAACAAUGGAACC (22 guide strand hits and 23 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_198158 | MITF | 820 | 838 | g | c | g | C | U | G | G | A | A | C | A | A | g | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 4472 | |||
NM_000248 | MITF | 838 | 856 | g | c | g | C | U | G | G | A | A | C | A | A | g | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 4490 | |||
NM_198178 | MITF | 945 | 963 | g | c | g | C | U | G | G | A | A | C | A | A | g | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 4597 | |||
NM_198177 | MITF | 972 | 990 | g | c | g | C | U | G | G | A | A | C | A | A | g | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 4624 | |||
NM_006722 | MITF | 1048 | 1066 | g | c | g | C | U | G | G | A | A | C | A | A | g | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 4700 | |||
NM_198159 | MITF | 1136 | 1154 | g | c | g | C | U | G | G | A | A | C | A | A | g | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 4788 | |||
NM_001018058 | TFEC | 619 | 637 | g | c | g | C | U | G | G | A | A | C | A | A | a | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 6544 | |||
NM_012252 | TFEC | 706 | 724 | g | c | g | C | U | G | G | A | A | C | A | A | a | G | G | A | A | C | C | 56 | 4 | 9 | false | <90% | 6631 | |||
XM_001129348 | LOC731359 | 327 | 345 | C | U | g | C | U | G | G | A | A | C | A | A | U | G | G | A | g | g | C | 54 | 3 | 13 | c | false | <90% | 687 | ||
NM_001038702 | CDC42SE2 | 2542 | 2560 | C | U | C | C | U | G | G | A | A | C | A | A | U | a | G | u | A | C | g | 49 | 3 | 13 | c | false | <90% | 3498 | ||
NM_020240 | CDC42SE2 | 2711 | 2729 | C | U | C | C | U | G | G | A | A | C | A | A | U | a | G | u | A | C | g | 49 | 3 | 13 | c | false | <90% | 3667 | ||
XM_938237 | LOC649168 | 183 | 201 | C | U | C | C | U | G | G | A | A | C | A | A | U | G | a | c | A | a | u | 41 | 4 | 14 | c | false | <90% | 252 | ||
NR_001280 | PCDHB17 | 1122 | 1140 | C | U | C | C | g | G | G | A | A | C | A | A | U | G | G | A | A | a | a | 40 | 3 | 12 | c | false | <90% | 2411 | ||
NM_018940 | PCDHB7 | 1296 | 1314 | u | U | C | C | g | G | G | A | A | C | A | A | U | G | G | A | A | a | g | 38 | 4 | 12 | c | false | <90% | 3715 | ||
NM_138393 | REEP6 | 135 | 153 | u | U | C | C | U | G | G | A | g | C | A | A | a | G | G | A | A | C | C | 27 | 3 | 7 | false | <90% | 1393 | |||
NM_000495 | COL4A5 | 3054 | 3072 | C | U | C | C | U | G | G | A | c | C | A | A | U | G | G | A | u | C | C | 16 | 2 | 8 | c | false | <90% | 6427 | ||
NM_033381 | COL4A5 | 3054 | 3072 | C | U | C | C | U | G | G | A | c | C | A | A | U | G | G | A | u | C | C | 16 | 2 | 8 | c | false | <90% | 6436 | ||
NM_033380 | COL4A5 | 3054 | 3072 | C | U | C | C | U | G | G | A | c | C | A | A | U | G | G | A | u | C | C | 16 | 2 | 8 | c | false | <90% | 6445 | ||
NM_001011539 | LOC441046 | 334 | 352 | u | U | C | C | U | G | G | A | g | C | A | A | U | G | G | A | c | C | C | 14 | 3 | 7 | c | false | <90% | 2004 | ||
NM_012206 | HAVCR1 | 234 | 252 | u | g | u | C | U | G | G | A | c | C | A | A | U | G | G | A | A | C | C | 6 | 4 | 10 | bc | false | <90% | 1440 | ||
NM_020424 | LYRM1 | 167 | 185 | a | U | C | C | U | G | G | A | A | u | A | A | U | G | G | g | A | C | C | -10 | 3 | 8 | c | false | <90% | 1673 | ||
NM_002472 | MYH8 | 2121 | 2139 | C | U | C | C | U | G | G | g | g | C | A | A | U | G | G | A | A | C | a | -27 | 3 | 9 | bc | false | <90% | 6016 |
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_170697 | ALDH1A2 | 2485 | 2503 | a | G | U | U | C | C | A | U | U | G | U | g | C | C | A | G | G | A | c | 59 | 3 | 10 | false | <90% | 3142 | |||
NM_170696 | ALDH1A2 | 2612 | 2630 | a | G | U | U | C | C | A | U | U | G | U | g | C | C | A | G | G | A | c | 59 | 3 | 10 | false | <90% | 3284 | |||
NM_003888 | ALDH1A2 | 2726 | 2744 | a | G | U | U | C | C | A | U | U | G | U | g | C | C | A | G | G | A | c | 59 | 3 | 10 | false | <90% | 3398 | |||
NM_031438 | NUDT12 | 2020 | 2038 | G | G | U | U | C | C | A | U | U | G | U | U | C | u | A | G | c | A | G | 56 | 2 | 13 | c | false | <90% | 3502 | ||
NM_003895 | SYNJ1 | 801 | 819 | u | G | U | U | C | C | A | U | U | G | U | U | C | u | g | G | G | A | G | 53 | 3 | 12 | c | false | <90% | 6997 | ||
NM_203446 | SYNJ1 | 867 | 885 | u | G | U | U | C | C | A | U | U | G | U | U | C | u | g | G | G | A | G | 53 | 3 | 12 | c | false | <90% | 7039 | ||
NM_006377 | UNC13B | 6318 | 6336 | u | G | U | g | C | C | A | U | U | G | U | U | a | C | A | G | G | A | G | 50 | 3 | 8 | false | <90% | 6398 | |||
NM_004634 | BRPF1 | 90 | 108 | G | c | c | U | C | C | A | U | U | G | U | U | C | C | A | G | c | A | G | 45 | 3 | 13 | c | false | <90% | 4710 | ||
NM_001003694 | BRPF1 | 90 | 108 | G | c | c | U | C | C | A | U | U | G | U | U | C | C | A | G | c | A | G | 45 | 3 | 13 | c | false | <90% | 4728 | ||
XM_001128519 | LOC728798 | 215 | 233 | a | a | a | U | C | C | A | U | U | G | U | U | C | C | u | G | G | A | G | 42 | 4 | 11 | c | false | <90% | 1425 | ||
NM_001017929 | FRMPD2 | 136 | 154 | a | a | a | U | C | C | A | U | U | G | U | U | C | C | u | G | G | A | G | 42 | 4 | 11 | c | false | <90% | 1884 | ||
NM_001042524 | LOC594834 | 136 | 154 | a | a | a | U | C | C | A | U | U | G | U | U | C | C | u | G | G | A | G | 42 | 4 | 11 | c | false | <90% | 1884 | ||
NM_152428 | FRMPD2 | 2983 | 3001 | a | a | a | U | C | C | A | U | U | G | U | U | C | C | u | G | G | A | G | 42 | 4 | 11 | c | false | <90% | 4731 | ||
NM_001018071 | FRMPD2 | 3049 | 3067 | a | a | a | U | C | C | A | U | U | G | U | U | C | C | u | G | G | A | G | 42 | 4 | 11 | c | false | <90% | 4797 | ||
NM_001877 | CR2 | 605 | 623 | G | G | c | U | C | C | A | U | U | G | c | U | C | C | A | G | G | A | u | 14 | 3 | 7 | c | false | <90% | 3982 | ||
NM_001006658 | CR2 | 605 | 623 | G | G | c | U | C | C | A | U | U | G | c | U | C | C | A | G | G | A | u | 14 | 3 | 7 | c | false | <90% | 4159 | ||
NM_030955 | ADAMTS12 | 1815 | 1833 | G | G | U | c | C | C | A | c | U | G | U | U | C | C | A | G | G | A | c | -3 | 3 | 10 | bc | false | <90% | 4955 | ||
NM_004523 | KIF11 | 3164 | 3182 | G | G | U | U | C | C | A | U | U | u | U | U | C | C | A | G | c | A | u | -11 | 3 | 9 | c | false | <90% | 4908 | ||
NM_001033522 | CSTF1 | 17 | 35 | G | c | c | U | C | C | A | U | U | u | U | U | C | C | A | G | G | A | G | -13 | 3 | 9 | bc | false | <90% | 2292 | ||
NM_001324 | CSTF1 | 150 | 168 | G | c | c | U | C | C | A | U | U | u | U | U | C | C | A | G | G | A | G | -13 | 3 | 9 | bc | false | <90% | 2323 | ||
NM_130768 | ASZ1 | 205 | 223 | u | G | U | U | u | C | A | U | U | G | g | U | C | C | A | G | G | A | G | -14 | 3 | 8 | c | false | <90% | 1831 | ||
NM_005808 | CTDSPL | 4187 | 4205 | u | G | U | U | C | C | A | U | U | c | U | c | C | C | A | G | G | A | G | -18 | 3 | 8 | false | <90% | 4422 | |||
NM_001008392 | CTDSPL | 4220 | 4238 | u | G | U | U | C | C | A | U | U | c | U | c | C | C | A | G | G | A | G | -18 | 3 | 8 | false | <90% | 4455 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 4558
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