Table 3

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

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

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.

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