| Subfamily | Gene name | Gene holoname | Name in SilkDB | Conserved domain (addition to SET) | ORF length (bp) | Chromosome number | Scaffold | ESTs | Probe | -value | Methylase activity in other species |
| SUV39 | BmG9a-like/Ehmt2 | Euchromatic histone-lysine N-methyltransferase 2 | BGIBMGA007949 | Ankyrin repeats, Pre-SET, and ALAD | 4161 | 15 | nscaf2888 | 7 | sw00703, sw17591, sw15556, and sw17724 | | H3K9, H3K27 | BmSetdb1 | SET-domain, bifurcated 1 | BGIBMGA011407 | Tudor, MBD, Pre-SET, and Post-SET | 2895 | 23 |
Nscaf3026 | No | sw21024, sw18443 | 0.0 | H3K9 | BmSu(var)3-9 | Suppressor of variegation 3-9 | BGIBMGA011500, BGIBMGA011499 | CHROMO, Pre-SET, and Post-SET | 1782 | 23 |
Nscaf3027 | 12 | sw11427, sw04471 | 0.0 | H3K9 |
| SET1 | BmMll | Myeloid/lymphoid or mixed-lineage leukemia | BGIBMGA010221 | PHD, FYRN, FYRC, and Post-SET | 12657 | 7 | nscaf2986 | 2 | sw12266, sw14974 | 0.0 | H3K4 | BmSet1 | SET-domain-containing 1 | BGIBMGA012978 | Post-SET | 4080 | 16 |
Nscaf3058 | No | sw14237, sw14238, sw16463, and sw04801 | 0.0 | H3K4 | BmTrr | Trithorax-related | BGIBMGA002503, BGIBMGA002502 | PHD, FYRN, and Post-SET | — | 9 | nscaf2511 | 4 | sw05846, sw04238, sw06661, and sw10095 | 0.0
| H3K4 | BmMll5 | Myeloid/lymphoid or mixed-lineage leukemia 5 | BGIBMGA004310 | PHD | | 20 | nscaf2789 | No | sw00989, sw16148 | | H3K4 | BmSET2 | SET-domain-containing 2 | BGIBMGA003106 | AWS, Post-SET | 3633 | 4 | nscaf2589 | No | sw11671, sw11672 | | H3K36 |
| SET2 | BmNsd1 | Nuclear receptor binding SET-domain protein 1 | BGIBMGA002246 | PWWP, PHD, AWS, and Post-SET | 6600 | 26 | nscaf2330 | 3 | sw11742 | | H3K36, H4K20 | BmAsh1 | Absent, small, or homeotic discs 1 | BGIBMGA001497 | AWS, Post-SET, BROMO, PHD, and BAH | 8754 | 21 | nscaf2136 | 2 | sw11562 | 0.0 | H3K4, H3K9, and H4K20 |
| SUV4-20 | BmSu(var)4-20 | Suppressor of variegation 4-20 | BGIBMGA000919 | — | 2094 | 13 |
Nscaf1898 | 4 | sw13536 | | H4K20 |
| EZ | BmE(z) | Enhancer of zeste | BGIBMGA014476 | SANT, CxC | | — | Scaffold707 | 6 | sw15702, sw16217 | 0.0 | H3K27 |
| SMYD | | | BGIBMGA014048 | zf-MYND | 1782 | — |
Nscaf3115 | 1 | sw10812 | | — | | | BGIBMGA007907 | — | 1881 | 15 | nscaf2888 | No | sw11109 | | — | | | BGIBMGA002076 | — | 2232 | 1 | nscaf2210 | 1 | sw19609 | | — | | | BGIBMGA011073 | — | 1155 | 23 |
Nscaf3015 | No | sw20741 | | — | | | BGIBMGA002109 | — | 1071 | 1 | nscaf2210 | No | sw18112, sw02496 | | — | | | BGIBMGA008839 | zf-MYND | | 3 | nscaf2927 | No | sw17374, sw17507 | | — | | | BGIBMGA008939 | zf-MYND | | 3 | nscaf2930 | No | sw08614 | | — | | | BGIBMGA008838 | — | | 3 | nscaf2927 | No | sw21409 | | — | | | BGIBMGA008923 | — | | 3 | nscaf2930 | No | sw21256 | | — | | | BGIBMGA003139 | — | | 4 | nscaf2589 | No | sw05603 | | — |
| Others | BmSet8/PR-set7 | SET-domain-containing (lysine methyltransferase) 8 | BGIBMGA012853 | — | 912 | 16 |
Nscaf3058 | 1 | — | | H4K20 | BmSetmar | SET-domain and mariner transposase fusion gene | BGIBMGA007557 | — | 810 | 15 | nscaf2887 | 2 | — | | — |
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