Table 1

Description and distribution of expressed retrocopy events

Type of event

Parent gene contribution

Count

Percentage


Type I – Exon acquisition (host gene modified by retrocopy)

New 5' exon (UTR and/or N-terminal protein coding)

10

1%


New 3' exon (UTR and/or C-terminal protein coding)

18

2%


New internal exon

6

1%


Type II – duplication (no host gene involved)

Single exon

624

86%


Exons/introns generated, post insertion

55

8%


Type III – novel genes (no host gene involved)

Antisense, majority of ORF out-of-frame wrt to parent, and other cases (e.g., from non-genic regions)

13

2%


Total

726


Type I: retrocopy inserted into or near an existing gene. A portion of the retrocopy contributes, mostly by alternative splicing, a new sequence to a pre-existing mRNA. Type I events can be divided into cases that add new N- or C-terminal encoding exons or internal exons. Type II: duplicated gene inserted at a locus where no prior gene existed. Type II events often acquired 5' or 3' UTR portions from the locus of integration after the insertion. Type III: novel gene sequence, whose encoded protein has little or no amino acid sequence similarity to that of the retrocopy's parent. Frequently, Type III events include SINEs, LINEs, LTRs etc., as well as unannotated sequences as additional contributors to gene candidates.

Baertsch et al. BMC Genomics 2008 9:466   doi:10.1186/1471-2164-9-466

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