Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
29 hits were found for GGAGUGUCUGGAGCAACAU (18 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_198255 | TERT | 1791 | 1809 | a | G | A | G | U | G | U | C | U | G | G | A | G | C | A | A | g | u | U | 71 | 3 | 15 | ac | false | <90% | 3982 | ||
NM_198253 | TERT | 1791 | 1809 | a | G | A | G | U | G | U | C | U | G | G | A | G | C | A | A | g | u | U | 71 | 3 | 15 | ac | false | <90% | 4018 | ||
NM_001077401 | ACVRL1 | 2987 | 3005 | G | G | A | G | U | G | U | C | U | G | G | A | G | C | A | c | C | u | c | 66 | 3 | 15 | c | false | <90% | 4126 | ||
NM_000020 | ACVRL1 | 3124 | 3142 | G | G | A | G | U | G | U | C | U | G | G | A | G | C | A | c | C | u | c | 66 | 3 | 15 | c | false | <90% | 4263 | ||
NM_015215 | CAMTA1 | 3687 | 3705 | a | G | A | G | U | G | U | C | U | G | G | A | G | C | A | c | C | u | g | 64 | 4 | 14 | c | false | <90% | 8457 | ||
NM_000090 | COL3A1 | 2869 | 2887 | G | G | A | G | U | G | U | C | U | G | G | A | c | C | A | A | a | A | g | 61 | 3 | 12 | false | <90% | 5490 | |||
NM_003043 | SLC6A6 | 834 | 852 | a | G | A | G | U | G | U | C | U | G | G | A | u | C | A | c | C | A | U | 61 | 3 | 11 | false | <90% | 6516 | |||
NM_178491 | R3HDML | 741 | 759 | u | c | A | G | U | G | U | C | U | G | G | g | G | C | A | A | C | A | c | 47 | 4 | 9 | false | <90% | 1377 | |||
NM_006612 | KIF1C | 312 | 330 | G | G | A | G | U | G | U | C | U | G | G | A | G | C | u | A | u | g | g | 44 | 4 | 14 | c | false | <90% | 4202 | ||
NM_153759 | DNMT3A | 1995 | 2013 | G | G | A | G | U | G | U | C | U | G | G | A | G | C | A | u | g | g | c | 42 | 4 | 15 | c | false | <90% | 3604 | ||
NM_022552 | DNMT3A | 2705 | 2723 | G | G | A | G | U | G | U | C | U | G | G | A | G | C | A | u | g | g | c | 42 | 4 | 15 | c | false | <90% | 4314 | ||
NM_175629 | DNMT3A | 2786 | 2804 | G | G | A | G | U | G | U | C | U | G | G | A | G | C | A | u | g | g | c | 42 | 4 | 15 | c | false | <90% | 4395 | ||
XR_015632 | LOC731857 | 621 | 639 | G | G | A | G | U | G | U | C | U | G | G | u | G | C | c | A | C | A | g | 36 | 3 | 11 | false | <90% | 1805 | |||
XR_015463 | LOC729141 | 621 | 639 | G | G | A | G | U | G | U | C | U | G | G | u | G | C | c | A | C | A | g | 36 | 3 | 11 | false | <90% | 1805 | |||
NM_001008239 | C18orf25 | 767 | 785 | G | G | A | G | U | G | U | C | U | G | G | u | G | C | c | A | C | A | g | 36 | 3 | 11 | false | <90% | 5290 | |||
NM_145055 | C18orf25 | 767 | 785 | G | G | A | G | U | G | U | C | U | G | G | u | G | C | c | A | C | A | g | 36 | 3 | 11 | false | <90% | 5473 | |||
NM_002942 | ROBO2 | 2159 | 2177 | a | c | A | G | a | G | U | C | U | G | G | A | G | C | A | A | C | A | a | 30 | 4 | 13 | bc | false | <90% | 6235 | ||
XM_001133217 | LOC732392 | 1030 | 1048 | G | G | A | G | a | G | U | C | U | G | G | A | G | C | A | g | C | A | c | 17 | 3 | 10 | c | false | <90% | 1902 |
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 | |||||||||||||
XR_019011 | LOC651042 | 1740 | 1758 | A | a | G | U | U | G | C | U | C | C | A | G | A | C | A | C | U | a | a | 80 | 3 | 15 | ac | false | <90% | 1853 | ||
NM_020808 | SIPA1L2 | 3813 | 3831 | A | a | G | U | U | G | C | U | C | C | A | G | u | C | A | C | U | C | C | 78 | 2 | 10 | false | <90% | 6501 | |||
NM_007126 | VCP | 735 | 753 | u | U | G | U | U | G | C | U | C | C | A | G | A | C | A | C | a | g | u | 66 | 4 | 15 | ac | false | <90% | 3198 | ||
NM_213596 | FOXN4 | 822 | 840 | A | U | c | U | U | G | C | U | C | C | A | G | A | C | u | C | U | C | C | 55 | 2 | 11 | c | false | <90% | 2958 | ||
NM_000017 | ACADS | 151 | 169 | A | U | G | U | U | G | C | U | C | C | A | G | A | C | A | u | g | C | C | 50 | 2 | 15 | c | false | <90% | 1829 | ||
NM_003488 | AKAP1 | 515 | 533 | g | c | a | U | U | G | C | U | C | C | A | G | A | C | A | C | a | C | C | 43 | 4 | 13 | c | false | <90% | 3968 | ||
XR_018496 | LOC648895 | 986 | 1004 | c | U | G | U | g | G | C | U | C | C | A | G | A | C | A | C | U | a | a | 38 | 4 | 12 | c | false | <90% | 2264 | ||
XR_016461 | LOC442156 | 986 | 1004 | c | U | G | U | g | G | C | U | C | C | A | G | A | C | A | C | U | a | a | 38 | 4 | 12 | c | false | <90% | 2264 | ||
NM_015172 | BAT2D1 | 7182 | 7200 | c | U | G | U | U | G | C | U | u | C | A | G | u | C | A | C | U | C | C | 27 | 3 | 7 | false | <90% | 10394 | |||
NM_012096 | APPL1 | 1486 | 1504 | u | U | G | U | U | G | C | c | C | C | A | G | A | C | A | C | c | C | C | 12 | 3 | 8 | c | false | <90% | 6061 | ||
NM_018164 | C12orf11 | 76 | 94 | c | U | G | U | g | G | C | a | C | C | A | G | A | C | A | C | U | C | C | -15 | 3 | 11 | bc | false | <90% | 2635 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1703
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