ENCODE Pseudogenes

6-Jan-2006 Freeze Pseudogenes (or version 2)

File of 201 concensus pseudogenes in ENCODE coordinates is available in two formats: one-line per pseudogene or one-line per pseudoexon, pseudointron etc.

This version of the pseudogenes has been extensively curated by Adam Frankish. (It is also available in hg17 chromosome coordinates (one-line per pseudogene or one-line per pseudoexon, pseudointron etc) or as a set in a DB.)

The difference between lists of Oct-15-2005 and Jan-6-2006 is available.

15-Oct-2005 Freeze Pseudogenes (or version 1)

Text file of 198 concensus pseudogenes in ENCODE coordinates in two formats: one-line per pseudogene or one-line per pseudoexon
(Also available in hg17 chromosome coordinates (one-line per pseudogene or one-line per pseudoexon) or as a set in a DB, and with alignments to parent proteins.)

Roadmap to the 15-Oct Concensus

There are 4 components of the concensus -- GIS, HAVANA, UCSC-retro, and Yale. Here is a description of how the concensus was generated and a table showing how the concensus intersects with its 4 components (plus UCSC-duplicated and 19 GENCODE exons).

Further Information

Supplement of manuscript describing ENCODE pseudogenes
Summary of Calls
Yale Encode Page
Section of Encode Wiki devoted to pseudogenes (username is "encode")
Pseudogene.org

Comments to Deyou Zheng (deyou.zheng at yale.edu).