Table 1.

Representative retrogenes in mammals and fruitflies.

Genes	Phylogenetic distribution	Features (Chromosomal origin / structure / type of selection / function)	References
Primates
GLUD2	Hominoids	Into X, positive selection, subcellular adaptation, adaptation to (neurotransmitter) glutamate metabolism	23,67
CDC14Bretro	Hominoids	Positive selection, subcellular adaptation, derived from cell cycle gene, brain/testis-specific expression	37,65
c1orf37-dup	Humans	Positive selection, transmembrane protein	66
PGAM3	Old World primates	Positive selection, phosphoglycerate mutase	64
TRIM5-CypA gene	Macaque lineage	Chimeric gene, retrovirus restriction, CypA portion derives from retroposition	72-74
TRIM5-CypA gene	New World monkeys	Chimeric gene, retrovirus restriction, CypA portion derives from retroposition	20
PIP5K1A- PSMD4 retrogene		Hominoids Chimeric gene, positive selection, subcellular change, fusion retrogene; stems from chimeric transcript of two adjacent parental genes	75
TAF1L, KIF4B	Old World primates	X-derived	37,101
RBMXL1	Old World primates	X-derived, chimeric gene, fusion to host gene UTR
Utp14c	Primates	X-derived, chimeric gene, evidence for it to be required for male fertility, fusion to host gene UTR	40
Rodents
Utp14b	Rodents	X-derived, chimeric gene, required for male fertility, fusion to host gene UTR exon	41,42
U2af1-rs1	Rodents	X-derived, paternally imprinted	57
PMSE2b	Mouse*	Inserted into a LINE1 which drives its transcription	51
Mammals
Cstf2t	All Mammals	X-derived, chimeric gene, required for male fertility, crucial for proper polyadenylation in meiosis/post-meiosis	43
HNRNPGT	Therians	X-derived, required for male fertility	44
Pgk2	Eutherians	X-derived, promoter inherited from parent, acquisition of a testisspecific enhancer, first described X-derived retrogene	14,60
Inpp5f, Nap1/5, Mcts2	Eutherians	X-derived, paternally imprinted, located in introns of host genes	57
KLF14	Eutherians	Maternally imprinted, accelerated evolution on the human lineage	58
USP26	Eutherians	Into X, among the 5 most positively selected gene in human-chimp comparison	102
Drosophila
jingwei (jgw)	D. yakuba, santomea and teisseri	Chimeric gene, positive selection, retrocopy encoded ADH domain evolved new substrate (alcohol) specificity	21,48
Sphinx( spx)	D. melanogaster	Chimeric gene, positive selection, retrocopy evolved into non- coding RNA gene that promotes male-female courtship	24,49
Adh-Twain	D. subobscura, guanche and madeirensis	Chimeric gene, positive selection, putative functional adaptation to new substrate specificity	103
mojoless (mjl)	Drosophila genus	X-derived, required for male fertility	104
Dntf-2r	D. melanogaster subgroup	Substitutions in an upstream proto-promoter element appear to have provided this gene with a new, testis-specific promoter

The cases listed here are representative of the different mechanisms that lead to the formation of retrogenes, their chromosomal distribution, and the type of function they may obtain. We refer to most of these genes in the main text.

^*Identified in mouse, phylogenetic distribution not established.