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Table 3 Type III novel retrogenes that are out of frame or reverse sense with respect to the parent gene

From: Retrocopy contributions to the evolution of the human genome

Parent Gene/Retro Fig Evolutionary Event Evidence of Expression Human Chimp Orangutan Rhesus Marmoset
MARK2/FLJ25758 2A Out of frame 4 mRNAs and 4 ESTs 81 aa 81 aa 81 aa 96 aa n
KRT18/FLJ40504 2B Human specific, 2 exons: first out of the blue and second from antisense retro 3 spliced mRNAs, 10 spliced ESTs 259 aa stop after 114 aa truncated to 152 aa by f/s, frame shift in ATG disrupts ORF first exon in sequencing gap f/s 2 stops n
RPL13A/NM_203308 2C 3 coding exons: first from MIR, second unknown source, third from antisense retrocopy 1 spliced mRNAs, 5 spliced ESTs 170 aa 170 aa y 134 aa early stop, exon1,2 open partially deleted in rhesus stop in first 10% of ORF
HMG2/c15ORF21 2D C-terminal exon from retro (partially out of frame), first coding exon from LTR 2 spliced mRNAs, 2 spliced ESTs 172 aa Disrupted Disrupted 4 stop codons, 1st at 10 aa. y 72 aa due to f/s.
HMG2/c15ORF21 2D C-terminal coding exonfrom retro (partially out-of-frame), first coding exon from L2 LINE 4 spliced mRNAs, 17 spliced ESTs 163 aa Disrupted Disrupted 4 stop codons, 1st at 10 aa. y 63 aa due to f/s.
HMG2/c15ORF21 2D Out-of-frame sense retrocopy 4 spliced mRNAs, 17 spliced ESTs 150 aa Disrupted Disrupted 4 stop codons, 1st at 10 aa. y 56 aa due to f/s.
RPL7A/Q9BR82 2E Novel primate specific gene candidate, peri centromeric 1 spliced mRNA, 20 spliced ESTs 89 aa y 86 aa Check transMap y but part of gene inverted Not assembled
NAP1L1/CT47 2F Primate specific cancer testis gene candidate. Swiss-Prot Q5JQC4 1 spliced mRNA, 10 spliced ESTs 288 aa seq gap in chimp 291 aa about 80% common with human (ensembl) y good ORF 15 bp multiple of 3 indel. 287 aa
RCN1/AF318337 2G Antisense retrocopy combined with Alu 1 spliced mRNA, 3 spliced ESTs 123 aa y 127 aa n AluY and retro are missing n n
RCN1/AK127569 2G Antisense retrocopy combined with Alu 2 spliced mRNAs, > 20 spliced ESTs 61 aa y 60 aa n AluY and retro are missing n n
LOC116236 c20ORF91 2H Novel gene candidate with 4 coding exons: first from LTR, second and forth unknown sources and third from antisense retrocopy 2 spliced mRNAs, 3 spliced ESTs 154 aa chimp not assembled in this region y retro exon is open (assembly not complete) n n
SNAG1/FLJ25328 2I Human specific 5 spliced mRNAs, 13 spliced ESTs 205 aa y 5 stops y good ORF but gap (or deletion) in first 50aa y 107 aa, starts later in first exon y multi exon gene unknown ORF
c18ORF24/FLJ13355 2J Novel 2 exon gene mostly from LINE and antisense retrocopy 4 spliced mRNAs, 6 spliced ESTs 154 aa y but stop codon after 30 aa y 137 aa includes LINE y but short 78 aa LINE not present
c18ORF24/FLJ13355 2J Novel 2 exon gene mostly from LINE and antisense retrocopy 1 spliced mRNA, 4 spliced ESTs 147 aa y but stop codon after 30 aa y 127 aa includes LINE y but short 78 aa LINE not present
IQCK/FLJ32894 2K Antisense novel gene, possible NMD 1 spliced mRNA, 2 unspliced mRNA, 4 ESTs 166 aa y 169 aa y 169 aa early in frame stop n
  1. Details of candidate genes showing parent gene, expression evidence and phylogeny shown in Figure 2. y; indicates presence of the retrogene in this species, n; indicates its absence, aa; amino acids in potential encoded protein, f/s; frame shift, wrt; with respect to.