Automatic recommendation
OK - siRNA is specific for both sense and antisense (guide) strands
88 hits were found for GGAUGAAGAAGCAAUGGAA (51 guide strand hits and 37 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_021705 | NFYA | 1094 | 1112 | c | G | A | U | G | A | A | G | A | A | G | C | A | A | U | G | a | c | A | 71 | 3 | 15 | ac | false | <90% | 2747 | ||
NM_002505 | NFYA | 1181 | 1199 | c | G | A | U | G | A | A | G | A | A | G | C | A | A | U | G | a | c | A | 71 | 3 | 15 | ac | false | <90% | 2834 | ||
NM_001039479 | KIAA0317 | 1993 | 2011 | G | G | A | U | G | A | A | G | A | A | G | C | u | c | U | G | G | A | c | 65 | 3 | 12 | false | <90% | 5445 | |||
NM_004398 | DDX10 | 1826 | 1844 | c | G | A | U | G | A | A | G | A | A | G | a | A | A | U | G | G | A | A | 64 | 2 | 10 | false | <90% | 3204 | |||
NM_203394 | E2F7 | 5219 | 5237 | u | a | g | U | G | A | A | G | A | A | G | C | A | A | U | G | G | c | A | 64 | 4 | 14 | c | false | <90% | 5742 | ||
XR_015672 | LOC729830 | 4085 | 4103 | a | G | A | U | G | A | A | G | A | A | G | u | A | A | U | G | G | u | A | 61 | 3 | 10 | false | <90% | 4171 | |||
XM_001128362 | LOC731081 | 4124 | 4142 | a | G | A | U | G | A | A | G | A | A | G | u | A | A | U | G | G | u | A | 61 | 3 | 10 | false | <90% | 4210 | |||
XR_015504 | LOC731502 | 411 | 429 | a | G | A | U | G | A | A | G | A | A | G | a | A | A | U | G | G | c | u | 56 | 4 | 10 | false | <90% | 617 | |||
XR_015657 | LOC729796 | 411 | 429 | a | G | A | U | G | A | A | G | A | A | G | a | A | A | U | G | G | c | u | 56 | 4 | 10 | false | <90% | 617 | |||
NM_018183 | SBNO1 | 690 | 708 | a | G | A | U | G | A | A | G | A | A | G | a | A | A | U | G | G | g | u | 56 | 4 | 10 | false | <90% | 4179 | |||
NM_001469 | XRCC6 | 106 | 124 | c | G | A | U | G | A | A | G | A | A | G | C | A | g | a | G | G | A | A | 53 | 3 | 12 | c | false | <90% | 2156 | ||
XR_016904 | LOC401533 | 1822 | 1840 | u | a | A | U | G | A | A | G | A | A | G | a | A | A | U | G | G | A | A | 52 | 3 | 9 | false | <90% | 2672 | |||
XR_018409 | LOC401533 | 1822 | 1840 | u | a | A | U | G | A | A | G | A | A | G | a | A | A | U | G | G | A | A | 52 | 3 | 9 | false | <90% | 2672 | |||
NM_001316 | CSE1L | 1205 | 1223 | u | G | A | U | G | A | A | G | A | A | G | C | A | u | U | u | G | A | A | 52 | 3 | 12 | c | false | <90% | 3579 | ||
NM_005228 | EGFR | 3252 | 3270 | G | G | A | U | G | A | A | G | A | A | G | a | c | A | U | G | G | A | c | 50 | 3 | 11 | false | <90% | 5616 | |||
NM_024567 | HMBOX1 | 327 | 345 | c | a | g | U | G | A | A | G | A | A | G | C | A | u | U | G | G | A | A | 47 | 4 | 10 | c | false | <90% | 2427 | ||
NM_006390 | IPO8 | 2966 | 2984 | G | G | A | U | G | A | A | G | A | A | G | u | A | u | U | G | G | A | A | 46 | 2 | 11 | false | <90% | 5178 | |||
NM_198935 | SS18L1 | 3906 | 3924 | c | a | g | U | G | A | A | G | A | A | G | C | A | A | a | G | G | A | A | 42 | 4 | 11 | c | false | <90% | 4566 | ||
NM_182568 | FLJ36492 | 1663 | 1681 | G | G | u | U | G | A | A | G | A | A | G | a | A | A | U | G | G | A | g | 41 | 3 | 8 | false | <90% | 2306 | |||
NM_198830 | ACLY | 3018 | 3036 | a | G | A | U | G | A | A | G | A | A | G | g | A | A | g | G | G | A | A | 39 | 3 | 10 | false | <90% | 4420 | |||
NM_001096 | ACLY | 3048 | 3066 | a | G | A | U | G | A | A | G | A | A | G | g | A | A | g | G | G | A | A | 39 | 3 | 10 | false | <90% | 4450 | |||
NM_152730 | C6orf170 | 278 | 296 | G | a | u | U | G | A | A | G | A | A | G | a | A | A | U | G | G | A | A | 35 | 3 | 8 | false | <90% | 5132 | |||
NM_000492 | CFTR | 960 | 978 | c | u | g | g | G | A | A | G | A | A | G | C | A | A | U | G | G | A | A | 30 | 4 | 15 | bc | false | <90% | 6132 | ||
NM_033364 | C3orf15 | 1538 | 1556 | u | G | A | a | G | A | A | G | A | A | G | a | A | A | U | G | G | A | A | 27 | 3 | 7 | false | <90% | 4449 | |||
NM_020236 | MRPL1 | 1206 | 1224 | G | G | u | U | u | A | A | G | A | A | G | C | A | A | U | G | G | A | g | 23 | 3 | 13 | bc | false | <90% | 1377 | ||
NM_006093 | PRG3 | 332 | 350 | G | G | A | U | G | A | g | G | A | A | G | C | c | A | U | G | G | A | g | 18 | 3 | 6 | false | <90% | 868 | |||
NM_006197 | PCM1 | 4181 | 4199 | u | G | A | U | G | A | A | G | A | A | u | C | A | c | U | G | G | A | A | 17 | 3 | 9 | c | false | <90% | 8788 | ||
NM_004370 | COL12A1 | 1772 | 1790 | G | G | A | U | c | A | A | G | A | A | G | C | A | A | U | G | u | g | c | 17 | 4 | 11 | c | false | <90% | 11579 | ||
NM_024662 | NAT10 | 3017 | 3035 | a | G | A | U | G | A | A | G | c | A | G | C | A | A | a | G | G | A | A | 13 | 3 | 7 | c | false | <90% | 4002 | ||
NM_198202 | POP5 | 357 | 375 | G | G | c | U | G | c | A | G | A | A | G | C | A | A | U | G | G | A | g | 12 | 3 | 12 | bc | false | <90% | 660 | ||
NM_015918 | POP5 | 503 | 521 | G | G | c | U | G | c | A | G | A | A | G | C | A | A | U | G | G | A | g | 12 | 3 | 12 | bc | false | <90% | 801 | ||
NM_012308 | FBXL11 | 1225 | 1243 | G | G | A | U | G | A | g | G | A | A | G | C | A | g | U | G | G | A | u | 9 | 3 | 6 | c | false | <90% | 6210 | ||
NM_003917 | AP1G2 | 2122 | 2140 | u | G | A | U | G | A | g | G | A | A | G | C | A | A | a | G | G | A | A | 6 | 3 | 7 | c | false | <90% | 2876 | ||
NM_080545 | AP1G2 | 2545 | 2563 | u | G | A | U | G | A | g | G | A | A | G | C | A | A | a | G | G | A | A | 6 | 3 | 7 | c | false | <90% | 3305 | ||
NM_002482 | NASP | 507 | 525 | a | G | A | U | G | A | g | G | A | A | G | C | A | A | g | G | G | A | A | 6 | 3 | 7 | c | false | <90% | 3323 | ||
NM_172164 | NASP | 580 | 598 | a | G | A | U | G | A | g | G | A | A | G | C | A | A | g | G | G | A | A | 6 | 3 | 7 | c | false | <90% | 3396 | ||
NM_003666 | BLZF1 | 644 | 662 | c | a | c | U | G | A | A | a | A | A | G | C | A | A | U | G | G | A | A | 4 | 4 | 11 | bc | false | <90% | 2344 | ||
NM_014880 | CD302 | 277 | 295 | c | u | u | U | G | A | A | a | A | A | G | C | A | A | U | G | G | A | A | 4 | 4 | 11 | bc | false | <90% | 3740 | ||
NM_001018005 | TPM1 | 599 | 617 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1246 | |||
NM_000366 | TPM1 | 599 | 617 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1294 | |||
NM_001018008 | TPM1 | 439 | 457 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1566 | |||
NM_001018006 | TPM1 | 599 | 617 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1797 | |||
NM_001018004 | TPM1 | 599 | 617 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1797 | |||
NM_001018007 | TPM1 | 599 | 617 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1797 | |||
NM_001018020 | TPM1 | 599 | 617 | a | G | A | U | G | A | A | G | A | A | a | a | A | A | U | G | G | A | A | 2 | 3 | 9 | false | <90% | 1797 | |||
NM_005090 | PLA2G4B | 715 | 733 | G | G | A | U | G | A | A | G | A | g | G | C | c | A | U | G | G | A | g | 1 | 3 | 9 | false | <90% | 3369 | |||
NM_004094 | EIF2S1 | 1053 | 1071 | u | G | A | U | G | c | A | G | A | A | G | a | A | A | U | G | G | A | A | 0 | 3 | 7 | false | <90% | 4165 | |||
NM_013450 | BAZ2B | 5716 | 5734 | a | G | A | a | G | A | A | c | A | A | G | C | A | A | U | G | G | A | A | 0 | 3 | 11 | bc | false | <90% | 8145 | ||
NM_030906 | STK33 | 1710 | 1728 | a | G | A | U | G | A | u | G | A | A | G | g | A | A | U | G | G | A | A | -2 | 3 | 7 | false | <90% | 2707 | |||
NM_014168 | METTL5 | 492 | 510 | a | G | A | U | G | A | A | G | A | c | G | C | A | u | U | G | G | A | A | -4 | 3 | 8 | c | false | <90% | 956 | ||
NM_015202 | KIAA0556 | 3484 | 3502 | G | G | A | U | G | A | A | G | A | g | G | C | A | A | U | G | a | g | g | -13 | 4 | 9 | c | false | <90% | 6618 |
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_015216 | HISPPD1 | 3418 | 3436 | U | U | C | C | A | U | U | G | C | U | U | C | U | c | C | A | U | C | a | 75 | 2 | 13 | c | false | <90% | 5293 | ||
NM_020787 | ZNF624 | 1104 | 1122 | c | U | u | C | A | U | U | G | C | U | U | C | U | U | C | A | U | C | a | 73 | 3 | 15 | bc | false | <90% | 4225 | ||
NM_021992 | TMSL8 | 566 | 584 | U | U | C | C | A | U | U | G | C | U | U | C | a | U | a | A | U | C | u | 59 | 3 | 12 | false | <90% | 666 | |||
XM_001130218 | LOC728340 | 986 | 1004 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1842 | ||
XM_001126940 | LOC730394 | 986 | 1004 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1842 | ||
NM_001042490 | LOC730394 | 1061 | 1079 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1842 | ||
XM_001130670 | DKFZP686M0199 | 788 | 806 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1908 | ||
NM_001515 | GTF2H2 | 983 | 1001 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1951 | ||
XM_001130305 | LOC728340 | 844 | 862 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1964 | ||
XM_001127067 | LOC730394 | 844 | 862 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1964 | ||
XM_001130662 | DKFZP686M0199 | 844 | 862 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1964 | ||
XM_001130259 | LOC728340 | 850 | 868 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1970 | ||
XM_001126987 | LOC730394 | 850 | 868 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1970 | ||
XM_001130621 | DKFZP686M0199 | 850 | 868 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1970 | ||
XM_001130264 | LOC728340 | 870 | 888 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1990 | ||
XM_001127003 | LOC730394 | 870 | 888 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1990 | ||
XM_001130639 | DKFZP686M0199 | 870 | 888 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 1990 | ||
XM_001130269 | LOC728340 | 935 | 953 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2055 | ||
XM_001127012 | LOC730394 | 935 | 953 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2055 | ||
XM_001130283 | LOC728340 | 938 | 956 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2058 | ||
XM_001127036 | LOC730394 | 938 | 956 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2058 | ||
XM_001130682 | DKFZP686M0199 | 968 | 986 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2088 | ||
XM_001130316 | LOC728340 | 986 | 1004 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2106 | ||
XM_001127085 | LOC730394 | 986 | 1004 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2106 | ||
XM_001130651 | DKFZP686M0199 | 1061 | 1079 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2181 | ||
XM_001130293 | LOC728340 | 1073 | 1091 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2193 | ||
XM_001127054 | LOC730394 | 1073 | 1091 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2193 | ||
XM_001130279 | LOC728340 | 1247 | 1265 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2367 | ||
XM_001127024 | LOC730394 | 1247 | 1265 | c | a | C | C | A | U | U | G | C | U | U | C | U | U | u | A | U | C | u | 56 | 4 | 12 | c | false | <90% | 2367 | ||
NM_000924 | PDE1B | 871 | 889 | g | U | C | C | A | U | U | G | C | U | U | C | U | U | g | c | U | C | C | 47 | 3 | 13 | c | false | <90% | 3236 | ||
NM_018241 | TMEM34 | 1661 | 1679 | U | U | C | C | A | U | U | G | C | U | U | C | U | U | C | u | a | u | g | 42 | 4 | 15 | c | false | <90% | 2913 | ||
XR_015479 | LOC730791 | 1536 | 1554 | a | U | C | C | A | U | U | G | C | U | c | C | U | U | C | A | U | C | a | 31 | 3 | 9 | c | false | <90% | 2145 | ||
XR_015459 | LOC728277 | 1536 | 1554 | a | U | C | C | A | U | U | G | C | U | c | C | U | U | C | A | U | C | a | 31 | 3 | 9 | c | false | <90% | 2145 | ||
NM_020765 | ZUBR1 | 10032 | 10050 | c | U | C | C | A | g | U | G | C | U | U | C | U | U | C | c | U | C | C | 8 | 3 | 9 | c | false | <90% | 15882 | ||
NM_024926 | TTC26 | 822 | 840 | g | g | a | C | A | a | U | G | C | U | U | C | U | U | C | A | U | C | C | 3 | 4 | 13 | bc | false | <90% | 2113 | ||
XM_290811 | KIAA1713 | 5281 | 5299 | U | U | C | C | A | U | U | G | C | c | U | C | U | U | C | A | a | a | C | -8 | 3 | 9 | c | false | <90% | 7537 | ||
XM_937373 | KIAA1713 | 5429 | 5447 | U | U | C | C | A | U | U | G | C | c | U | C | U | U | C | A | a | a | C | -8 | 3 | 9 | c | false | <90% | 7685 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1954
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