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Table 1 Genome segments identified by PseudoGeneQuest

From: PseudoGeneQuest – Service for identification of different pseudogene types in the human genome

# Tag in the result file Explanation
1 ALREADY KNOWN GENE Hits overlapping genes annotated in the genome files.
2 KNOWN PSEUDOGENE Results overlapping with records in pseudogene.org.
3 REAL GENE OR EXON The hit matches almost exactly to the query. Frequently parts of yet un-annotated or predicted genes.
4 PSEUDOGENE FRAGMENT Covers <70% of the length of the query. Small parts of pseudogenes.
5 PSEUDOGENE Covers >70% of the length of the query and the reading frame is broken. Processed pseudogenes with high homology to the query sequence.
6 MISCELLANEOUS Covers >70% of the length of the query and the reading frame is intact.
7 PUTATIVE NEW GENE The hit has uninterrupted reading frame. Un-annotated gene.
8 DUPLICATED PSEUDOGENE Multiexon hit with <50% repeat content. A recent duplication of a gene.
9 INTERRUPTED PROCESSED PSEUDOGENE Multiexon hit with >50% repeat content. Old processed pseudogenes which accumulated repeats.