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Table 3 Fields for pseudogene features in the psiDR annotation file

From: The GENCODE pseudogene resource

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
  1. *Pol2, RNA polymerase II.