Automatic recommendation
Warning - siRNA is specific for only the antisense (guide) strand
94 hits were found for GCCUCAUCUUCUUGUUGGU (32 guide strand hits and 62 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_000038 | APC | 9901 | 9919 | c | C | u | U | C | A | U | C | U | U | C | U | U | G | U | U | G | c | a | 70 | 4 | 14 | c | false | <90% | 10719 | ||
NM_001079878 | CNGA3 | 641 | 659 | G | C | C | U | C | A | U | C | U | U | C | U | U | G | c | U | G | c | g | 67 | 3 | 14 | c | false | <90% | 3794 | ||
NM_001298 | CNGA3 | 641 | 659 | G | C | C | U | C | A | U | C | U | U | C | U | U | G | c | U | G | c | g | 67 | 3 | 14 | c | false | <90% | 3848 | ||
NM_025139 | ARMC9 | 1440 | 1458 | G | C | C | U | C | A | U | C | U | U | C | U | g | G | c | U | G | G | U | 64 | 2 | 12 | false | <90% | 2178 | |||
NM_144973 | MGC24039 | 5324 | 5342 | u | C | C | U | C | A | U | C | U | U | C | U | g | G | U | a | G | G | U | 61 | 3 | 11 | false | <90% | 9409 | |||
XM_290597 | GLT8D3 | 3632 | 3650 | a | a | a | U | C | A | U | C | U | U | C | U | a | G | U | U | G | G | U | 56 | 4 | 9 | false | <90% | 7493 | |||
XM_936720 | GLT8D3 | 3632 | 3650 | a | a | a | U | C | A | U | C | U | U | C | U | a | G | U | U | G | G | U | 56 | 4 | 9 | false | <90% | 7493 | |||
NM_003830 | SIGLEC5 | 1506 | 1524 | G | C | C | U | C | A | U | C | U | U | C | U | U | u | U | U | a | a | U | 54 | 3 | 13 | c | false | <90% | 2130 | ||
NM_002060 | GJA4 | 714 | 732 | u | C | a | U | C | A | U | C | U | U | C | a | U | G | U | U | G | G | U | 44 | 3 | 8 | false | <90% | 1710 | |||
NM_014698 | TMEM63A | 684 | 702 | a | C | a | U | C | A | U | C | U | U | C | c | U | G | U | U | G | G | U | 44 | 3 | 8 | false | <90% | 4074 | |||
NR_003143 | MYADML | 755 | 773 | G | C | C | U | C | A | U | C | U | U | C | g | U | G | U | U | c | a | U | 40 | 3 | 11 | false | <90% | 2173 | |||
XM_208333 | MGC48637 | 1968 | 1986 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 2729 | ||
XM_001128986 | LOC728980 | 2231 | 2249 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 3211 | ||
NM_032264 | NBPF3 | 3199 | 3217 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 3783 | ||
NM_173638 | NBPF15 | 3450 | 3468 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4046 | ||
XM_001133185 | LOC728936 | 3194 | 3212 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4211 | ||
XM_001133188 | LOC728936 | 3475 | 3493 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4492 | ||
XM_001133155 | LOC728936 | 3767 | 3785 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4784 | ||
XM_001133176 | LOC728936 | 3881 | 3899 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4898 | ||
NM_183372 | NBPF11 | 4211 | 4229 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4902 | ||
XM_001133169 | LOC728936 | 3905 | 3923 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 4922 | ||
XM_001133179 | LOC728936 | 4076 | 4094 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 5093 | ||
XM_001133191 | LOC728936 | 4094 | 4112 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 5111 | ||
XM_001133181 | LOC728936 | 4605 | 4623 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | U | 34 | 3 | 9 | c | false | <90% | 5622 | ||
NM_024746 | KIAA1822L | 141 | 159 | G | C | C | U | C | A | U | a | U | U | C | U | U | G | U | U | G | G | g | 32 | 2 | 10 | bc | false | <90% | 2582 | ||
NM_173170 | IL1F5 | 1128 | 1146 | c | C | C | U | C | A | U | C | a | U | C | U | U | G | U | U | G | u | g | 30 | 4 | 8 | c | false | <90% | 2689 | ||
NM_012275 | IL1F5 | 1156 | 1174 | c | C | C | U | C | A | U | C | a | U | C | U | U | G | U | U | G | u | g | 30 | 4 | 8 | c | false | <90% | 2717 | ||
XR_015220 | LOC730476 | 4154 | 4172 | u | C | C | U | C | A | U | C | U | U | u | U | U | G | U | U | G | u | c | 29 | 4 | 9 | c | false | <90% | 5174 | ||
NM_021628 | ALOXE3 | 2415 | 2433 | u | C | C | U | C | c | U | C | U | U | C | U | g | G | U | U | G | G | U | 24 | 3 | 6 | false | <90% | 3362 | |||
XM_379636 | C9orf122 | 664 | 682 | u | g | C | U | C | c | U | C | U | U | C | U | U | G | U | U | G | G | U | 23 | 3 | 13 | bc | false | <90% | 3436 | ||
XM_940165 | C9orf122 | 664 | 682 | u | g | C | U | C | c | U | C | U | U | C | U | U | G | U | U | G | G | U | 23 | 3 | 13 | bc | false | <90% | 3436 | ||
NM_006590 | USP39 | 839 | 857 | a | u | a | U | C | A | U | g | U | U | C | U | U | G | U | U | G | G | U | 4 | 4 | 11 | bc | false | <90% | 2234 |
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_004316 | ASCL1 | 1007 | 1025 | g | C | C | A | A | C | A | A | G | A | A | G | A | U | G | A | G | u | a | 90 | 3 | 16 | ac | false | <90% | 2482 | ||
NM_000458 | TCF2 | 874 | 892 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | G | c | G | c | C | 71 | 2 | 15 | c | false | <90% | 2816 | ||
NM_006481 | TCF2 | 874 | 892 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | G | c | G | c | C | 71 | 2 | 15 | c | false | <90% | 4192 | ||
NM_018387 | STRBP | 1534 | 1552 | c | C | C | A | A | C | A | A | G | A | A | G | A | U | G | A | a | a | C | 71 | 3 | 15 | ac | false | <90% | 3019 | ||
NM_003747 | TNKS | 3467 | 3485 | g | u | C | A | A | C | A | A | G | A | A | G | u | U | G | A | G | G | g | 71 | 4 | 10 | false | <90% | 9599 | |||
NM_014461 | CNTN6 | 1128 | 1146 | u | C | C | A | A | C | A | A | G | A | A | G | A | U | G | A | a | G | g | 69 | 3 | 15 | ac | false | <90% | 3530 | ||
NM_003898 | SYNJ2 | 1879 | 1897 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | G | u | G | G | g | 68 | 2 | 15 | c | false | <90% | 6738 | ||
NM_003410 | ZFX | 1650 | 1668 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | a | A | G | u | u | 67 | 3 | 14 | c | false | <90% | 5811 | ||
NM_006207 | PDGFRL | 183 | 201 | A | C | C | A | A | C | A | A | G | A | A | G | g | U | G | A | a | G | C | 66 | 2 | 12 | false | <90% | 1502 | |||
NM_002467 | MYC | 1333 | 1351 | A | g | g | A | A | C | A | A | G | A | A | G | A | U | G | A | G | G | a | 64 | 3 | 15 | bc | false | <90% | 2377 | ||
NM_018590 | GALNACT-2 | 931 | 949 | A | u | g | A | A | C | A | A | G | A | A | G | A | U | G | A | G | G | a | 64 | 3 | 15 | bc | false | <90% | 3745 | ||
NM_015542 | UPF2 | 1728 | 1746 | A | a | g | A | A | C | A | A | G | A | A | G | A | U | G | A | G | G | a | 64 | 3 | 15 | bc | false | <90% | 5185 | ||
NM_080599 | UPF2 | 1784 | 1802 | A | a | g | A | A | C | A | A | G | A | A | G | A | U | G | A | G | G | a | 64 | 3 | 15 | bc | false | <90% | 5223 | ||
NM_014970 | KIFAP3 | 2072 | 2090 | c | u | C | A | A | C | A | A | G | A | A | G | A | U | G | A | u | G | a | 58 | 4 | 14 | ac | false | <90% | 2997 | ||
NM_003411 | ZFY | 1200 | 1218 | c | u | C | A | A | C | A | A | G | A | A | G | A | U | G | A | a | G | a | 58 | 4 | 14 | ac | false | <90% | 4556 | ||
NM_001037329 | CNGA4 | 1035 | 1053 | A | u | C | A | A | C | A | A | G | A | A | G | A | U | G | A | c | c | a | 57 | 4 | 14 | ac | false | <90% | 1851 | ||
NM_019063 | EML4 | 329 | 347 | A | g | C | A | A | C | A | A | G | A | A | G | A | U | G | A | a | a | u | 57 | 4 | 14 | ac | false | <90% | 5539 | ||
NM_001082575 | HRNBP3 | 737 | 755 | A | C | C | A | A | C | A | A | G | A | A | G | A | c | G | g | G | G | a | 49 | 3 | 13 | c | false | <90% | 2696 | ||
NM_000260 | MYO7A | 633 | 651 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | u | g | G | G | g | 44 | 3 | 14 | c | false | <90% | 7367 | ||
XR_018621 | LOC392227 | 451 | 469 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | c | A | c | c | a | 44 | 4 | 14 | c | false | <90% | 494 | ||
XR_016970 | LOC392227 | 451 | 469 | A | C | C | A | A | C | A | A | G | A | A | G | A | U | c | A | c | c | a | 44 | 4 | 14 | c | false | <90% | 494 | ||
XR_015528 | DKFZP434B061 | 262 | 280 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 997 | ||
XM_001130267 | LOC729444 | 215 | 233 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 1055 | ||
XR_015212 | LOC727962 | 253 | 271 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 1695 | ||
XM_001130329 | LOC729461 | 253 | 271 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 1720 | ||
XM_001126757 | FLJ26056 | 299 | 317 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 1870 | ||
NM_181485 | ZGPAT | 1627 | 1645 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | g | 32 | 4 | 12 | c | false | <90% | 1898 | ||
NM_001083113 | ZGPAT | 1654 | 1672 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | g | 32 | 4 | 12 | c | false | <90% | 1925 | ||
NM_032527 | ZGPAT | 1746 | 1764 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | g | 32 | 4 | 12 | c | false | <90% | 2017 | ||
XM_931343 | LOC653135 | 370 | 388 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 3219 | ||
XM_932721 | LOC653264 | 370 | 388 | A | C | C | c | A | C | A | A | G | A | A | G | A | U | G | A | c | u | u | 32 | 4 | 12 | c | false | <90% | 3220 | ||
NM_000335 | SCN5A | 3367 | 3385 | A | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | a | 31 | 2 | 12 | bc | false | <90% | 8501 | ||
NM_198056 | SCN5A | 3367 | 3385 | A | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | a | 31 | 2 | 12 | bc | false | <90% | 8504 | ||
NM_001106 | ACVR2B | 1323 | 1341 | g | u | g | c | A | C | A | A | G | A | A | G | A | U | G | A | G | G | C | 30 | 4 | 15 | bc | false | <90% | 11373 | ||
NM_024781 | CCDC102B | 823 | 841 | A | C | C | A | A | a | A | A | G | A | A | G | A | U | G | A | G | c | u | 29 | 3 | 11 | c | false | <90% | 2015 | ||
NM_005252 | FOS | 663 | 681 | A | C | C | A | A | C | u | A | G | A | A | G | A | U | G | A | G | a | a | 26 | 3 | 10 | c | false | <90% | 2084 | ||
NM_013449 | BAZ2A | 2332 | 2350 | A | g | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | C | 25 | 2 | 13 | bc | false | <90% | 8934 | ||
NM_152349 | KRT222P | 444 | 462 | c | u | C | A | A | C | A | c | G | A | A | G | A | U | G | A | G | G | C | 24 | 3 | 11 | bc | false | <90% | 1735 | ||
NM_001004304 | ZNF740 | 460 | 478 | g | C | C | A | g | C | A | A | G | A | A | G | A | U | G | A | u | G | C | 23 | 3 | 11 | c | false | <90% | 4256 | ||
NM_145802 | SEPT6 | 1006 | 1024 | g | g | C | A | A | C | A | A | G | A | u | G | A | U | G | A | G | G | g | 20 | 4 | 8 | c | false | <90% | 2575 | ||
NM_145800 | SEPT6 | 1006 | 1024 | g | g | C | A | A | C | A | A | G | A | u | G | A | U | G | A | G | G | g | 20 | 4 | 8 | c | false | <90% | 2620 | ||
NM_015129 | SEPT6 | 1006 | 1024 | g | g | C | A | A | C | A | A | G | A | u | G | A | U | G | A | G | G | g | 20 | 4 | 8 | c | false | <90% | 3407 | ||
NM_145799 | SEPT6 | 1006 | 1024 | g | g | C | A | A | C | A | A | G | A | u | G | A | U | G | A | G | G | g | 20 | 4 | 8 | c | false | <90% | 4716 | ||
NM_015693 | INTU | 137 | 155 | c | a | C | A | A | g | A | A | G | A | A | G | A | U | G | A | G | G | a | 18 | 4 | 12 | bc | false | <90% | 3238 | ||
NM_080629 | COL11A1 | 1116 | 1134 | u | u | C | A | A | a | A | A | G | A | A | G | A | U | G | A | G | G | a | 18 | 4 | 12 | bc | false | <90% | 7327 | ||
NM_147233 | NCOA1 | 4931 | 4949 | u | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | a | G | C | 11 | 3 | 10 | c | false | <90% | 6892 | ||
NM_003743 | NCOA1 | 4934 | 4952 | u | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | a | G | C | 11 | 3 | 10 | c | false | <90% | 6895 | ||
NM_147223 | NCOA1 | 4991 | 5009 | u | C | C | A | A | g | A | A | G | A | A | G | A | U | G | A | a | G | C | 11 | 3 | 10 | c | false | <90% | 6952 | ||
XR_015454 | LOC729119 | 539 | 557 | A | C | a | A | A | C | c | A | G | A | A | G | A | U | G | A | G | G | a | 9 | 3 | 11 | bc | false | <90% | 615 | ||
XR_015529 | LOC731578 | 539 | 557 | A | C | a | A | A | C | c | A | G | A | A | G | A | U | G | A | G | G | a | 9 | 3 | 11 | bc | false | <90% | 615 | ||
NM_002129 | HMGB2 | 744 | 762 | A | C | g | A | A | C | c | A | G | A | A | G | A | U | G | A | G | G | a | 9 | 3 | 11 | bc | false | <90% | 1277 | ||
NM_194301 | GARNL1 | 7425 | 7443 | A | C | C | A | A | a | A | A | G | A | A | G | A | U | G | g | G | G | a | 5 | 3 | 9 | c | false | <90% | 7851 | ||
NM_014990 | GARNL1 | 7456 | 7474 | A | C | C | A | A | a | A | A | G | A | A | G | A | U | G | g | G | G | a | 5 | 3 | 9 | c | false | <90% | 7882 | ||
NM_147152 | ITSN2 | 2299 | 2317 | A | g | a | A | A | C | u | A | G | A | A | G | A | U | G | A | G | G | C | 2 | 3 | 12 | bc | false | <90% | 4558 | ||
NM_019595 | ITSN2 | 2218 | 2236 | A | g | a | A | A | C | u | A | G | A | A | G | A | U | G | A | G | G | C | 2 | 3 | 12 | bc | false | <90% | 6027 | ||
NM_006277 | ITSN2 | 2299 | 2317 | A | g | a | A | A | C | u | A | G | A | A | G | A | U | G | A | G | G | C | 2 | 3 | 12 | bc | false | <90% | 6092 | ||
NM_014959 | CARD8 | 2317 | 2335 | A | C | C | A | A | a | A | A | G | A | A | a | A | U | G | A | G | G | g | -2 | 3 | 6 | false | <90% | 5059 | |||
NM_007117 | TRH | 464 | 482 | g | C | C | g | A | C | g | A | G | A | A | G | A | U | G | A | G | G | C | -5 | 3 | 12 | bc | false | <90% | 1561 | ||
NM_182483 | NSFL1C | 1092 | 1110 | A | C | C | A | A | g | A | u | G | A | A | G | A | U | G | A | G | G | a | -30 | 3 | 10 | bc | false | <90% | 3451 | ||
NM_018839 | NSFL1C | 1190 | 1208 | A | C | C | A | A | g | A | u | G | A | A | G | A | U | G | A | G | G | a | -30 | 3 | 10 | bc | false | <90% | 3551 | ||
NM_016143 | NSFL1C | 1190 | 1208 | A | C | C | A | A | g | A | u | G | A | A | G | A | U | G | A | G | G | a | -30 | 3 | 10 | bc | false | <90% | 3644 | ||
NM_015169 | RRS1 | 966 | 984 | A | C | C | A | A | u | A | A | G | c | A | G | A | U | G | A | G | G | g | -51 | 3 | 8 | bc | false | <90% | 1724 |
3 prime UTR Seed matches
Hits to same gene : 0
Hits to other genes : 1887
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