IV. ChromDB Nomenclature
All sequences entered into the database are given a ChromDB ID (identifier). The same ID is use to denote both a transcript and a protein. Formal names, as well as alias, are presented on individual gene record pages and can be entered into the "Quick Search"text box to access genes. ChromDB IDs are composed with of a three- to five-letter symbol followed by a number, e.g., BRD4 or BRD106.
If you do not know the ChromDB ID, you can use the "Quick Search" text box at the top right of each webpage as an "ID converter".
Letter symbols: Protein groups unified by homologous features are represented by different letter.
Numerals: Because it is often not possible to determine orthologous relationships unambiguously, especially as IDs are assigned to chromatin genes in newly sequenced genomes, ChromDB IDs do NOT imply orthology. Each organism has a unique number series, Arabidopsis genes are indicated by the numerals 1-99, maize by 101-199, and japonica rice by 701-799, etc.
Prefixes: Prefixes, such At for Arabidopsis thaliana and Zm for Zea mays, would be redundant in this ID system, because species are indicated by the numeric series. However, we may institute an additional name in the future that implies orthology.
Synonyms: Previously published gene designations and formal names are presented in ChromDB as synonyms or alias. Note that the designation with priority in literature should be used in publications. ChromDB IDs may be used for genes not previously named in the literature.
Protein Group Classification Key:
| 1 | Non Chromatin Related Proteins |
| 2 | Histones and Histone Linker Proteins |
| 3 | Nucleosome Organization: Assembly and Displacement |
| 4 | Histone Modifications |
| 5 | Histone Modification-Associated Proteins and Complexes |
| 6 | Modified-Histone Binding Proteins |
| 7 | DNA Modifying Proteins |
| 8 | Non-histone DNA Binding Proteins |
| 9 | RNAi Components |
| 10 | Chromosome Dynamics |
Protein Group Classifications (*key shown above)
| 1 | ABHF | Alpha_Beta Hydrolase Fold Super Family |
| 2 | HON | Histone H1 linker protein |
| 2 | SMH | Single myb histone protein group |
| 2 | HMGA | High Mobility Group Family A |
| 2 | HTA | Histone H2A Family |
| 2 | HTB | Histone H2B |
| 2 | HTR | Histone H3 Family |
| 2 | HFO | Histone H4 |
| 3 | SSRP | Histone chaperone (Pob3 and SSRP homologs; FACT complex proteins) |
| 3 | NFA | Nucleosome/chromatin assembly complex proteins (Nap1 homologs) |
| 3 | NFE | Nucleosome positioning into regularly spaced arrays (Acf1 homologs) |
| 3 | NFF | Nucleosome/chromatin assembly complex proteins (Cac1 homologs) |
| 3 | NFB | Nucleosome/chromatin assembly complex proteins (Cac2 homologs) |
| 3 | HIRA | HIRA protein group |
| 3 | SGA | Nucleosome assembly factor (ASF1 homologs) |
| 3 | HSC | Histone chaperone for Htz1p/H2A-H2B dimer |
| 3 | RTTHC | Rtt106 histone chaperones |
| 4 | PADF | Peptidyl arginine deiminase, type IV |
| 4 | SAEO | SUMO1 activating enzyme subunit 1 |
| 4 | SAET | SUMO1 activating enzyme subunit 2 |
| 4 | PARP | poly (ADP-ribose) polymerase family, member 1 |
| 4 | HUPA | Histone ubiquitination proteins group A (Bre1 homologs) |
| 4 | HUPB | Histone ubiquitination proteins group B (Rad6 homologs) |
| 5 | HMTA | Set1 complex component (Ash2/Bre2 homologs) |
| 5 | SSC | SAS4 protein group (yeast-specific) |
| 5 | SWDA | COMPASS (Set1C) complex protein (SWD1 homologs) |
| 5 | SWDB | COMPASS (Set1C) complex protein (SWD2 homologs) |
| 5 | SWDC | COMPASS (Set1C) complex protein (SWD3 homologs) |
| 5 | HXA | Histone acetyltransferase complex component (Ada2 homologs) |
| 5 | SNT | Histone deacetylase complex protein (Sin3 homologs) |
| 5 | HCP | Sin3 complex components (SAP18 homologs) |
| 5 | YDG | Yeats Domain Proteins |
| 6 | INGF | Inhibitor of Growth protein group (ING1-5 homologs) |
| 6 | MRG | MRG domain-containing proteins |
| 6 | GTE | Global transcription factor group E (Bdf1, BRD4 and BRD2 (RING3) homologs) |
| 6 | BRD | Diverse bromodomain-containing proteins (polybromo1, yeast RSC, and human BRD homologs) |
| 6 | BRAT | Bromodomain-containing proteins containing AAA ATPase domains |
| 6 | BRWD | Bromodomain-containing proteins containing WD40 domain repeats |
| 6 | CRD | Diverse group of chromodomain-containing proteins |
| 7 | VIM | Variant in Methylation |
| 7 | DMT | DNA methyltransferases |
| 7 | DNG | Superfamily of DNA glycosylases |
| 8 | DEK | DEK_C domain proteins |
| 8 | HMGB | High Mobility Group Family B |
| 8 | EBP | BAH-PHD domain-containing protein group |
| 8 | MBD | Methyl binding domain proteins |
| 8 | GAGA | GAGA factor proteins (insect-specific) |
| 8 | ARID | ARID/BRIGHT DNA binding domain group |
| 9 | DCL | Dicer-Like group |
| 9 | DRB | Double stranded RNA-Binding protein group |
| 9 | SGS | Suppressor of gene silencing |
| 9 | NRPDB | RNA Polymerase IV Small Subunit |
| 9 | NRPDA | RNA Polymerase IV Large Subunit |
| 9 | RDR | RNA-dependent RNA polymerases |
| 9 | RHEL | RNA helicases |
| 9 | HEN | HUA Enhancer |
| 9 | DRSH | Animal-specific class II Ribonuclease III proteins (Drosho homologs) |
| 9 | AGO | Argonaute gene family |
| 10 | CPC | Condensin complex component; SMC protein group |
| 10 | CPD | Condensin complex component, non-SMC subunit (Cnd1 homologs) |
| 10 | CPG | Condensin complex component, non-SMC subunit |
| 10 | CPH | Condensin complex component; Barren domain-containing, non-SMC subunit |
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