Table 3.
Fields for pseudogene features in the psiDR annotation file
| Field | Explanation | psiDR value |
|---|---|---|
| Transcript ID | Pseudogene ID from GENCODE annotation. Used for cross-referencing | |
| Parent | Protein ID, Gene ID, chromosome, start, end and strand. Detailed in section 'Parents of pseudogenes' | |
| Sequence similarity | The percentage of pseudogene sequence preserved from parent | |
| Transcription | Evidence for pseudogene transcription and validation results. May be tagged as EST, BodyMap, RT-PCR or None, which represent pseudogene expression evidence from corresponding data sources. Multiple tags are separated by commas. Detailed in section 'Transcription of pseudogenes' | 1, transcription; 0, otherwise |
| DNaseI hypersensitivity | A categorical result indicating whether the pseudogene has easily accessible chromatin, predicted by a model integrating DNaseI hypersensitivity values within 4 kb genomic regions upstream and downstream of the 5' end of pseudogenes. Detailed in section 'Chromatin signatures of pseudogenes' | 1, has Dnase hypersensitivity in upstream; 0, otherwise |
| Chromatin state | Whether a pseudogene maintains an active chromatin state, as predicted by a model using Segway segmentation. Detailed in section 'Chromatin signatures of pseudogenes' | 1, active chromatin; 0, otherwise |
| Active Pol2* binding | Whether Pol2 binds to the upstream region of a pseudegene. Detailed in section 'Upstream regulatory elements' | 1, active binding site; 0, otherwise |
| Active promoter region | Whether there are active promoter regions in the upstream of pseudogenes. Detailed in section 'Upstream regulatory elements' | 1, active binding site; 0, otherwise |
| Conservation | Conservation of pseudogenes is derived from the divergence between human, chimp and mouse DNA sequences. Detailed in section 'Evolutionary constraint on pseudogenes' | 1, conserved; 0, otherwise |
*Pol2, RNA polymerase II.