Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
45 hits were found for GCAAAAUGAGGAAUUGAAU (21 guide strand hits and 24 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_001001654 | MED8 | 1094 | 1112 | u | u | A | A | A | A | U | G | A | G | G | A | A | a | U | G | A | A | U | 67 | 3 | 11 | c | false | <90% | 1193 | ||
NM_001001653 | MED8 | 1137 | 1155 | u | u | A | A | A | A | U | G | A | G | G | A | A | a | U | G | A | A | U | 67 | 3 | 11 | c | false | <90% | 1236 | ||
NM_201542 | MED8 | 1137 | 1155 | u | u | A | A | A | A | U | G | A | G | G | A | A | a | U | G | A | A | U | 67 | 3 | 11 | c | false | <90% | 2038 | ||
NM_198572 | SPATC1 | 134 | 152 | G | g | A | A | A | A | U | G | A | G | G | A | A | c | U | G | A | A | g | 64 | 3 | 11 | c | false | <90% | 2040 | ||
NM_001077445 | PHF16 | 4165 | 4183 | u | C | A | A | A | A | U | G | A | G | G | A | A | g | a | G | A | A | U | 53 | 3 | 12 | c | false | <90% | 4685 | ||
NM_014735 | PHF16 | 4412 | 4430 | u | C | A | A | A | A | U | G | A | G | G | A | A | g | a | G | A | A | U | 53 | 3 | 12 | c | false | <90% | 4932 | ||
NM_002119 | HLA-DOA | 2667 | 2685 | G | C | A | A | A | A | U | G | A | G | G | g | u | U | U | G | A | A | c | 50 | 3 | 11 | false | <90% | 3485 | |||
NM_032817 | ITIH5 | 4575 | 4593 | c | C | A | A | A | A | U | G | A | G | u | A | A | U | U | G | A | A | U | 36 | 2 | 9 | c | false | <90% | 5671 | ||
NM_030569 | ITIH5 | 5235 | 5253 | c | C | A | A | A | A | U | G | A | G | u | A | A | U | U | G | A | A | U | 36 | 2 | 9 | c | false | <90% | 6331 | ||
NM_002908 | REL | 2033 | 2051 | G | C | A | A | A | A | U | G | A | G | c | A | A | U | U | G | A | g | U | 36 | 2 | 10 | c | false | <90% | 2592 | ||
NM_014112 | TRPS1 | 8636 | 8654 | G | a | A | A | A | u | U | G | A | G | G | A | A | U | U | G | A | A | a | 20 | 3 | 12 | bc | false | <90% | 9990 | ||
NM_024678 | NARS2 | 501 | 519 | G | C | A | A | A | A | U | G | u | G | G | A | A | c | U | G | A | A | g | 15 | 3 | 8 | c | false | <90% | 2110 | ||
NR_003263 | SDHAP3 | 14026 | 14044 | u | C | A | A | A | A | U | G | A | G | u | A | A | U | U | u | A | A | U | 10 | 3 | 9 | c | false | <90% | 21323 | ||
NM_003566 | EEA1 | 2740 | 2758 | u | C | A | g | c | A | U | G | A | G | G | A | A | U | U | G | A | A | U | 9 | 3 | 14 | bc | false | <90% | 8019 | ||
NM_004586 | RPS6KA3 | 5176 | 5194 | a | C | A | A | A | A | U | G | A | G | a | g | A | U | U | G | A | A | U | 2 | 3 | 9 | false | <90% | 7723 | |||
XM_001124597 | LOC730411 | 3182 | 3200 | a | u | g | A | A | A | g | G | A | G | G | A | A | U | U | G | A | A | U | 0 | 4 | 12 | bc | false | <90% | 7333 | ||
NM_001040441 | ZBTB8 | 3182 | 3200 | a | u | g | A | A | A | g | G | A | G | G | A | A | U | U | G | A | A | U | 0 | 4 | 12 | bc | false | <90% | 7333 | ||
NM_006197 | PCM1 | 1433 | 1451 | a | C | u | A | A | A | U | G | A | a | G | A | A | U | U | G | A | A | U | -4 | 3 | 9 | bc | false | <90% | 8788 | ||
NM_199160 | LHX6 | 1386 | 1404 | a | C | A | A | A | A | g | G | c | G | G | A | A | U | U | G | A | A | U | -28 | 3 | 10 | bc | false | <90% | 3273 | ||
NM_014368 | LHX6 | 1490 | 1508 | a | C | A | A | A | A | g | G | c | G | G | A | A | U | U | G | A | A | U | -28 | 3 | 10 | bc | false | <90% | 3377 | ||
NM_005359 | SMAD4 | 339 | 357 | G | C | A | A | A | A | a | G | A | G | c | A | A | U | U | G | A | A | a | -32 | 3 | 7 | c | false | <90% | 3220 |
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_017769 | KIAA1333 | 4264 | 4282 | u | U | U | C | A | A | U | U | C | C | U | C | A | U | U | U | g | a | C | 71 | 3 | 15 | ac | false | <90% | 5534 | ||
NM_139054 | ADAMTS18 | 3138 | 3156 | A | g | U | C | A | A | U | U | C | C | U | C | A | U | U | c | U | G | C | 62 | 2 | 13 | c | false | <90% | 3739 | ||
NM_199355 | ADAMTS18 | 3141 | 3159 | A | g | U | C | A | A | U | U | C | C | U | C | A | U | U | c | U | G | C | 62 | 2 | 13 | c | false | <90% | 5510 | ||
NM_001010927 | TIAM2 | 2090 | 2108 | g | U | U | a | A | A | U | U | C | C | U | C | A | U | U | U | U | a | C | 58 | 3 | 13 | c | false | <90% | 2668 | ||
NM_012454 | TIAM2 | 5338 | 5356 | g | U | U | a | A | A | U | U | C | C | U | C | A | U | U | U | U | a | C | 58 | 3 | 13 | c | false | <90% | 5916 | ||
XM_001125825 | FUBP3 | 180 | 198 | A | U | U | C | A | A | U | U | C | C | U | C | A | c | U | U | g | a | a | 49 | 4 | 13 | c | false | <90% | 3130 | ||
NM_003934 | FUBP3 | 207 | 225 | A | U | U | C | A | A | U | U | C | C | U | C | A | c | U | U | g | a | a | 49 | 4 | 13 | c | false | <90% | 3175 | ||
XM_001128545 | FUBP3 | 489 | 507 | A | U | U | C | A | A | U | U | C | C | U | C | A | c | U | U | g | a | a | 49 | 4 | 13 | c | false | <90% | 3439 | ||
NM_152618 | BBS12 | 2616 | 2634 | A | U | U | C | A | g | U | U | C | C | U | C | A | U | U | U | U | u | C | 34 | 2 | 11 | c | false | <90% | 3260 | ||
NM_000072 | CD36 | 1311 | 1329 | u | U | U | C | A | c | U | U | C | C | U | C | A | U | U | U | U | c | u | 27 | 4 | 11 | c | false | <90% | 1983 | ||
NM_001001547 | CD36 | 1378 | 1396 | u | U | U | C | A | c | U | U | C | C | U | C | A | U | U | U | U | c | u | 27 | 4 | 11 | c | false | <90% | 2050 | ||
NM_001001548 | CD36 | 1311 | 1329 | u | U | U | C | A | c | U | U | C | C | U | C | A | U | U | U | U | c | u | 27 | 4 | 11 | c | false | <90% | 2338 | ||
XM_001131201 | LOC729751 | 1733 | 1751 | A | U | U | C | A | A | g | U | C | C | U | C | A | U | U | U | U | a | g | 26 | 3 | 10 | c | false | <90% | 1904 | ||
XM_001131019 | LOC731846 | 1733 | 1751 | A | U | U | C | A | A | g | U | C | C | U | C | A | U | U | U | U | a | g | 26 | 3 | 10 | c | false | <90% | 1904 | ||
NM_014839 | LPPR4 | 465 | 483 | A | U | U | C | c | A | U | U | C | C | U | C | A | U | g | U | U | G | C | 23 | 2 | 9 | c | false | <90% | 4988 | ||
NM_144567 | ANGEL2 | 3481 | 3499 | A | U | U | u | A | A | U | U | u | C | U | C | A | U | U | U | U | G | g | -1 | 3 | 9 | bc | false | <90% | 4668 | ||
NM_001079534 | CPEB1 | 1952 | 1970 | u | U | U | u | A | g | U | U | C | C | U | C | A | U | U | U | U | G | C | -2 | 3 | 13 | bc | false | <90% | 3095 | ||
NM_001079533 | CPEB1 | 1967 | 1985 | u | U | U | u | A | g | U | U | C | C | U | C | A | U | U | U | U | G | C | -2 | 3 | 13 | bc | false | <90% | 3110 | ||
NM_001079535 | CPEB1 | 2053 | 2071 | u | U | U | u | A | g | U | U | C | C | U | C | A | U | U | U | U | G | C | -2 | 3 | 13 | bc | false | <90% | 3196 | ||
NM_030594 | CPEB1 | 2059 | 2077 | u | U | U | u | A | g | U | U | C | C | U | C | A | U | U | U | U | G | C | -2 | 3 | 13 | bc | false | <90% | 3202 | ||
NM_025015 | HSPA12A | 3108 | 3126 | A | U | U | u | A | A | U | U | C | C | a | C | A | U | U | U | U | G | a | -3 | 3 | 7 | c | false | <90% | 5739 | ||
NM_024910 | ZNF767 | 997 | 1015 | A | U | U | u | A | c | U | U | C | C | U | C | A | U | U | U | U | G | g | -5 | 3 | 12 | bc | false | <90% | 3520 | ||
NM_001012756 | ZNF260 | 5071 | 5089 | c | U | U | C | u | g | U | U | C | C | U | C | A | U | U | U | U | G | C | -16 | 3 | 13 | bc | false | <90% | 5407 | ||
NM_007136 | ZNF80 | 1827 | 1845 | A | U | U | C | A | g | U | U | C | u | U | C | A | U | U | U | U | G | C | -46 | 2 | 9 | bc | false | <90% | 2560 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 2776
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