Table 3. Candidate CM domains.
| Domain | Molucular Function | Biological Process | Co-occurring CM domain |
| Pescadillo_N | Unkown | cell proliferation | BRCT |
| IMS | damaged DNA binding domain (interpro) | DNA repair | BRCT |
| DDT | predicted to be a DNA binding domain | Unkown | Bromodomain, PHD, MBD |
| PCAF_N | a domain in the histone acetylase PCAF | regulation of transcription, DNA-dependent | Bromodomain, Acetyltransf_1 |
| Pre-SET | structural, stablize SET domain, DNA binding | chromatin modification | SET, Chromo, MBD |
| zf-C5HC2 | predicted to bind DNA | Unkown | JmjC, JmjN, PHD |
| Chromo_shadow | Required for Heterochromatin Spreading. | Unkown | Chromo |
| PLU-1 | putative DNA/chromatin binding domain | Unkown | JmjC, JmjN, PHD |
| HAND | putative DNA/nucleosome binding domain | ATP-dependent chromatin remodeling | SNF2_N, Helicase_C, Myb_DNA_binding |
| SNase | nucleic acid binding | Unkown | TUDOR |
| QLQ | putative protein interaction domain | regulation of transcription | SNF2_N, Helicase_C, Bromodomain |
| SLIDE | DNA binding | chromatin remodeling | SNF2_N, Helicase_C, Myb_DNA_binding |
| NIF | putative phosphatase | Unkown | BRCT |
| Rubis-subs-bind | histone binding | Unkown | SET |
| RFC1 | ATP binding | DNA replication | BRCT |
| TBP-binding | TBP binding to suppress transcription | Unkown | Bromodomain |
| Bromo_TP | predicted to bind DNA | Unkown | PHD |
| BRK | Unkown | Unkown | SNF2_N, Helicase_C, Bromodomain, Chromo |
| HARP | Single-strand DNA-depedent ATPase | chromatin modification | SNF2_N, Helicase_C |
| zf-C2HC | DNA binding zinc finger domain | regulation of transcription, DNA-dependent | MOZ_SAS, MBT |
| CBFD_NFYB_HMF | sequence-specifid DNA binding | Unkown | Histone |
| HIRAN | predicted to bind DNA, damaged DNA | Unkown | SNF2_N, Helicase_C |
| HSA | predicted to bind DNA | Unkown | SNF2_N, Helicase_C, Bromodomain |
| ELM2 | putative protein interaction domain | Unkown | BAH, Myb_DNA_binding |
| XRCC1_N | specifically binds single-strand break DNA | single strand break repair | BRCT |
| TRF | Telomeric DNA binding, protein binding | telomere maintenance via telomerase | Myb_DNA_binding |
| HNH | Nucleic acid binding, endonuclease | Unkown | SNF2_N, Helicase_C |
| Nbs1_C | protein-protein interaction domain | Unkown | BRCT |
| SANTA | putative protein-protein interaction domain | Unkown | Myb_DNA_binding |
| Amino_oxidase | catalytic domain of LSD1 | Unkown | SWIRM |
| SMN | RNA binding | mRNA processing, spliceosome assembly | TUDOR |
| FYRC | DNA binding | Unkown | PHD, SET |
| DUF1086 | Unkown | Unkown | SNF2_N, Helicase_C, PHD, Chromo |
| SAND | DNA binding | Unkown | Bromodomain, PHD |
| DUF1087 | Unkown | Unkown | SNF2_N, Helicase_C, PHD, Chromo |
| FYRN | DNA binding | Unkown | PHD, SET |
| ARID | DNA binding | Unkown | JmjC, JmjN, PHD |
| zf-C2H2 | DNA binding | Unkown | BAH, Myb_DNA_binding, Bromodomain |
| 53-BP1_Tudor | mediates interaction with H3K79me | Unkown | BRCT |
| Sp100 | Unkown | Unkown | Bromodomain, PHD |
| CHDNT | DNA binding | regulation of transcription | SNF2_N, Helicase_C, PHD, Chromo |
| RecQ5 | DNA helicase | Unkown | Helicase_C |
| zf-CXXC | DNA binding | Unkown | JmjC, BAH, MBD, SET, PHD, DNA_methylase |
| ZZ | protein-protein interaction domain | Unkown | Myb_DNA_binding, Bromodomain |
| CHDCT2 | DNA binding | regulation of transcription | SNF2_N, Helicase_C, PHD, Chromo |
| GATA | DNA binding | regulation of transcription, DNA-dependent | Myb_DNA_binding, BAH |
| DSHCT | ATP binding | Unkown | Helicase_C |
The prediction of candidate CM domains was performed as described in the text. Function annotations are largely based on the literature and Pfam database. Co-occurring CM domain: known CM domains that combine with a candidate CM domain in a single protein.