Yale Pseudo60 Track Settings
 
Yale Pseudogenes based on Ensembl Release 60   (All Genes and Gene Predictions tracks)

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Data version: December 2010
Data last updated: 2010-12-23

Description

This track shows pseudogenes identified by the Yale Pseudogene Pipeline. Pseudogenes are defined in this analysis as genomic sequences that are similar to known genes with various inactivating disablements (e.g., premature stop codons or frameshifts) in their "putative" protein coding regions. Pseudogenes are flagged as either recently processed, recently duplicated, or of uncertain origin (either ancient fragments or resulting from a single-exon parent). NOTE: There are 4 pseudogenes missing - these had overlapping coordinates in the blocks representing exons and their identifiers are:

  • PGOMOU00000130313
  • PGOMOU00000139101
  • PGOMOU00000136201
  • PGOMOU00000128816

Methods

Briefly, the protein sequences of known human genes (as annotated by Ensembl Release 60) were used to search for similarities, not overlapping with known genes. It was determined whether the matching sequences were disabled copies of genes based on the occurrences of premature stop codons or frameshifts. The intron-exon structure of the functional gene was further used to infer whether a pseudogene was recently duplicated or processed. A duplicated pseudogene retains the intron-exon structure of its parent functional gene, whereas a processed pseudogene shows evidence that this structure has been spliced out. Small pseudogene sequences that cannot be confidently assigned to either the processed or duplicated category may be ancient fragments. Further details are in the references below.

Credits

These data were generated by the pseudogene annotation group in the Gerstein Lab at Yale University.

References

More information is available from Pseudogene.org.

Zhang Z, Harrison PM, Liu Y, Gerstein M. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome. Genome Res. 2003 Dec;13(12):2541-58. PMID: 14656962; PMC: PMC403796

Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M. Integrated pseudogene annotation for human chromosome 22: evidence for transcription. J Mol Biol. 2005 May 27;349(1):27-45. PMID: 15876366