Table II. The most abundant domains and motifs in proteins from different nuclear compartments.
| Compartment | Most common motif amongst known proteins | Abundance in human proteome |
|---|---|---|
| Splicing speckles | RRM 25/65 (38%) | 7th |
| RS 21/65 (32%) | not known | |
| Nucleolus | DExD/H box helicase 6/109 (6%) | 38th |
| WD40 6/109 (6%) | 8th | |
| PML bodies | bromodomain 3/24 (13%) | 168th |
| Sand 3/24 (13%) | 405th | |
| Nuclear periphery | transmembrane 18/70 (26%) | not known |
| FG repeats 11/70 (16%) | not known | |
| Chromatin | chromodomain 10/62 (16%) | 184th |
| bromodomain 7/62 (11%) | 168th | |
| AT hook 7/62 (11%) | not known | |
| PHD finger 6/62 (10%) | 75th | |
| C2H2 zinc finger 6/62 (10%) | 2nd | |
| Diffuse | C2H2 zinc finger 6/50 (12%) | 2nd |
| HLH 6/50 (12%) | 37th |
The most frequent motifs or domains present in the sequences of proteins, which have been reported in the literature in nuclear subcompartments, were identified using the SMART tool (http://smart.embl-heidelberg.de/). The proportions (%) of the localized proteins containing these sequences were compared with the frequency with which the same motifs have been detected in the human genome sequence (http://www.ensembl.org/IPtop500.html).