Table 2.
Type I retrocopy-exon acquisition events
| Parent Gene/RetroGene | Fig | Evolutionary Event and possible consequences | Evidence | Hs | Pan | Pon | Rhesus | Marm |
| PPP1R14BLIMK2 | 1A-1 | Retro adds PKC-activated phosphatase-1 inhibitor domain to LIM, Zinc binding, PDZ kinase gene at alternatively spliced C-terminal exon. | 2 spliced mRNAs, 4 spliced ESTs Reviewed RefSeq | 686 aa | y but stop codon after 13 aa | y but stop codon after 19 aa | n | n |
| CENTG2/CTGLF1 | 1A-2 | Retro adds centaurin domain to C-terminal of cyclin gene,. | 2 spliced mRNAs, 2 spliced ESTs | 663 aa | y but seq. gap | Y | y 3 and 63 bp insertion, but 3 in-frame stops, occurring after 450 aa | n |
| C10ORF26/BCAP29 | 1A-3 | 14 aa alternative 3' exon sense orientation out of frame wrt coding region of parent | 6 spliced ESTs | 244 aa | y 244 aa | y 233 aa | y 241 aa | Not assembled |
| RPL32/RPS29 | 1A-4 | Retro insertion triggered new alt spliced C-terminal exon for RPS29. Most of the retro became 3' UTR. | 1 spliced mRNA, > 20 spliced ESTs | 67 aa | y 67aa | y 67 aa | y 64aa | y 81 aa |
| MLTT6/AF1/BRPF3 | 1A-5 | Retro contributed PHD/zinc finger with bromodomain. | 3 spliced mRNAs, > 10 spliced ESTs | 1205 aa | y 1205 aa | y 1205 aa | y 1006 aa | y 885 aa |
| ATP5/GPR142 | 1A-6 | Retro swapped in C-terminal portion of GPCR. New ligand in primates? | 2 spliced mRNAs, 2 spliced ESTs | 462 aa | y but frameshift early in ORF | y but frameshift early in ORF | y 462 aa | y but frameshift early in ORF |
| RPL21/BRCA1 | 1B-1 | Antisense internal cassette (alt spliced) exon inserted by retro. | 1 spliced mRNA | 1354 aa | y 100% open | y 100% open | y 100% open | n |
| CYCS/RORA | 1B-2 | Antisense alt. spliced internal cassette exon contributed by retro. Protein evidence in Swiss-Prot and PDB | 1 spliced mRNA PDB 1N83,1SOX | 556 aa | y in frame stop in first 20 aa | y 556 aa | y late translational start (31aa shorter) | y difficult to check ORF. |
| RRAS2/SCP2 | 1B-3 | Antisense retro triggered shorter alternative transcript in apes. | 2 spliced mRNAs, 3 spliced ESTs | 332 aa | y 332aa | N | n | n |
| FLJ10324/KIAA0415 | 1B-3 | Antisense, ancient | 8 spliced mRNAs | 807 aa | y | Seq gap | y | |
| /HLA-F | 1B-3 | Antisense, alt. spliced C-terminus | 2 spliced mRNAs | 377 aa | y | y | ||
| EIF3S6/C6orf148 | 1B-4 | Retro contributed internal 15 aa antisense exon. | 2 spliced mRNAs, 5 spliced ESTs | 238 aa | y 100% open | y 100% open | y no ORF splice site has indel | |
| RPS15A/HK1 | 1B-5 | Antisense retro triggered slightly later start via novel exon. Alternative translation initiation. Reviewed RefSeq. | 1 spliced mRNA 2 spliced ESTs | 905 aa | y 905 aa | y 100% open | y 905 aa | n/a |
| RPL24/DENN1B | 1B-5 | Primate specific antisense internal cassette exon generated short alt spliced transcript encoding 396 aa. Possible alternative translation initiation. | 6 spliced mRNAs | 396 aa | y 396 aa | y ORF ok but missing splice site | y no start codon | |
| RPL18/CSMD3 | 1B-6 | Antisense retro triggered different start via novel exon. | 1 spliced mRNA | 3667 aa | seq gap | f/s wrt human. | y f/s wrt to human. Same as PPY | |
Examples of specific categories of retrocopy insertion events shown in Figure 2 with designation of parent gene. Genomic locations of the examples are cross-referenced in [see Additional File 1]. y; indicates presence of the retrogene in this species, n; indicates its absence, aa; amino acids in potential encoded entire protein, f/s; frame shift, wrt; with respect.