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.

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

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