RCPedia: Rtcs

Summary

Retrocopy Name	MRPS16P3	Plot displaying the genomic locations of a retrocopy (in chr22) and its respective parental gene (in chr10). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr22:35703835-35704519 UCSC
Coordinates (T2T)	chr22:36163581-36164265 UCSC
Coordinates (hg19)	chr22:36099882-36100566 UCSC
Strand	+
Parental Sequence	NM_016065.4
Parental seq. overlap	579 bp
Parental seq. overlap (%)	22.4%
Genomic Region	Intergenic
Retrocopy Summary	MRPS16P3, located on chr22:35703835-35704519, is a retrocopy of the parental gene MRPS16. Retrocopies of protein-coding genes, also known as processed pseudogenes, are intriguing genomic elements with implications in genome evolution and diseases. While some retrocopies are non-functional, there are examples of retrocopies (retrogenes) acquiring regulatory roles or exhibiting neofunctionalization unrelated to their parental genes.

Parental Gene

Gene Name	MRPS16
Full Name	mitochondrial ribosomal protein S16
Also known as	CGI-132\|COXPD2\|MRP-S16\|RPMS16\|S16mt
Coordinate	chr10:73248849-73252644
Strand	-
Gene summary	Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryotic ribosomes, where this ratio is reversed. Another difference between mammalian mitoribosomes and prokaryotic ribosomes is that the latter contain a 5S rRNA. Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical properties, which prevents easy recognition by sequence homology. This gene encodes a 28S subunit protein that belongs to the ribosomal protein S16P family. The encoded protein is one of the most highly conserved ribosomal proteins between mammalian and yeast mitochondria. Three pseudogenes (located at 8q21.3, 20q13.32, 22q12-q13.1) for this gene have been described. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	MRPS16P3
Bonobo	Pan paniscus	MRPS16P3
Gorilla	Gorilla gorilla	MRPS16P3
Orangutan	Pongo abelii	MRPS16P3
Gibbon	Nomascus leucogenys	Without Homology
Green monkey	Chlorocebus sabaeus	Without Homology
Crab-eating macaque	Macaca fascicularis	Without Homology
Rhesus	Macaca mulatta	Without Homology
Baboon	Papio anubis	Without Homology
Golden snub-nosed monkey	Rhinopithecus roxellana	Without Homology
Marmoset	Callithrix jacchus	Without Homology
Mouse lemur	Microcebus murinus	Without Homology
Mouse	Mus musculus	Without Homology
Rat	Rattus norvegicus	Without Homology
Chinese hamster	Cricetulus griseus	Without Homology
Rabbit	Oryctolagus cuniculus	Without Homology
Pig	Sus scrofa	Without Homology
Cow	Bos taurus	Without Homology
Sheep	Ovis aries	Without Homology
Dolphin	Tursiops truncatus	Without Homology
Horse	Equus caballus	Without Homology
Dog	Canis familiaris	Without Homology
Panda	Ailuropoda melanoleuca	Without Homology
Cat	Felis catus	Without Homology
Pale spear-nosed bat	Phyllostomus discolor	Without Homology
Velvety free-tailed bat	Molossus molossus	Without Homology
Greater mouse-eared bat	Myotis myotis	Without Homology
Kuhl's pipistrelle	Pipistrellus kuhlii	Without Homology
Greater horseshoe bat	Rhinolophus ferrumequinum	Without Homology
Egyptian rousette	Rousettus aegyptiacus	Without Homology
Sloth	Choloepus didactylus	Without Homology
Tasmanian Devil	Sarcophilus harrisii	Without Homology
Opossum	Monodelphis domestica	Without Homology
Platypus	Ornithorhynchus anatinus	Without Homology
Chicken	Gallus gallus	Without Homology
Turkey	Meleagris gallopavo	Without Homology
Zebra Finch	Taeniopygia guttata	Without Homology
Budgerigar	Melopsittacus undulatus	Without Homology
Painted Turtle	Chrysemys picta	Without Homology
Lizard	Anolis Carolinensis	Without Homology
Frog	Xenopus tropicalis	Without Homology
Zebrafish	Danio rerio	Without Homology
Drosophila	Drosophila melanogaster	Without Homology

Expression

Related Sequence

>MRPS16P3
AGCCCTGGGTGGCTGCACCAACTGGCCCTTCCACGGCACTGTGTCTGCTCACAGGTGTCCCAGGAACAGCCATTTCATAGAGCAGTTGGGCTCCTATGGTCCACTGCCCAACAGTCATTAAGAGCAACTCGTTCCCCTCAACCTGGAGAGGATCCGGCATTGGGTTGGCTGTGGGGCCCGCCTATGGAAAAGCTTCTCGGTCTTTCTGGCTTTTTTCCCCTGCATTCTATGCTGACCACAACTGCTGAGTGACTGCAAAGAAAACAGGCACATGAAGTTCTCTTAGCTTTTCAGAAAACAGATACAAAGGCTATAGGAACAGAAGTGAGTTCACTTCAGTGAGCAGAGCAGTGGGAACAAGACCAAGGGCTTCTCAAAATGCTTCTGCAGAGATCTTAATTTTGTTAGATTTAGAGGTCAATAAATGGAGTTTTCTGAGTCACTCGTGCTCTTCTGGCCTGGCCTGAGCAGGGCCCAGGGCAAGATTTACTTTTGTCTGACATAGAGCTGGGTCTTGGTACTAATGAGCTTTTTCAGACTTTGACTTGGGAAAGGCAGTGGCTATAAGCAGGATTGGACTTTTGGGTGGGGCCCTGGGTCTCTTGGACGAATTTACAATCTATTGCCTTCCAAGACTTTCTTCTTCAAAGCCCCAGTCAGACTGTTCATGGCCCATCCAAATCTT

>NM_016065.4
ATCCGCTTCCGGAGTCGAGGTTTTCGGGCTTGTACCGCTTGGCGGTGCGGCCTGGTGTCGGCTTGCAGGTTCTTTCTGTGTTTGTTCTCTGCCCTGCCAAGGCCGTAGAGCTGGTGCGTGCGGGTAGCGGGGCTCTCCGAGGAGCCGCACGCCGGCGGCACCATGGTCCACCTCACTACTCTCCTCTGCAAGGCCTACCGTGGGGGCCACTTAACCATCCGCCTTGCCCTGGGTGGCTGCACCAATCGGCCGTTCTACCGCATTGTGGCTGCTCACAACAAGTGTCCCAGGGATGGCCGTTTCGTAGAGCAGCTGGGCTCCTATGATCCATTGCCCAACAGTCATGGAGAAAAACTCGTTGCCCTCAACCTAGACAGGATCCGTCATTGGATTGGCTGCGGGGCCCACCTCTCTAAGCCTATGGAAAAGCTTCTGGGTCTTGCTGGCTTTTTCCCTCTGCATCCTATGATGATCACAAATGCTGAGAGACTGCGAAGGAAACGGGCACGTGAAGTCCTGTTAGCTTCTCAGAAAACAGATGCAGAAGCTACAGATACAGAGGCTACAGAAACATAAATGAGCTGACTTTAGTGAGCATAGCAGTGGGAACAAGGTCAAGGTCCTTTTGAAACACTGCAGCGATCTTAATTTTGTTAGATTTGGAGTTCAATAAATGGAGTATCCTGAGTTGCCCTTGCTCTTCTGGCCTGGCCTGCACAGGGCCCAGGGAGAGATTTGTTCTTGTGTGACTTAGAGCTGGGTGTGGGTACTAATTAGCTTTTTTCGACTTTGTCTTGGGATAGACAGTGGCTATGGGAGGATTGGACTTTTGAGTTGGGCTCTGGGTCTCTTGGACAACTTTACAATTTACTGGCTTCCAAGACTTCCTGCTTCAAAACCCCCAGCCAGACTATTCATGGCCCATTCAGATCTTCATGTTCATCCCACAAGTGCAAGAACAGTTAACCTTTCTTAATTGATTTTTGTAATTGGAGGTTTATATTGTCTTGCCTAATGCATAttctctttttttttttttttttgagacggagtcttgttctgttgccaggctggagtgcggtggtgcaatctcagctcactgcaatctccacctcctgggttcaagaggttctcctgcctcagcctcctgagtagccggggagctacaagcatgcaccaccacacccagctaattttttttttttttttgagaggagtctcgctctgtcgcccaggcttgagtgcagtggcgcgatctcggctcactgcaagctctgtctcctgggttcatgccattctcctgcttcagcctcccgagtagtcccaggagtagctgggactacaggtgcccaccaccacacccagctaatttttttgtatttttagtagagatggggtttcaccatgttatccaggatggttttgatctcctgacctcgtgatccgcccgccttggcctcccaaaagtgctgggattataggcgtgagccaccgcccgggcaaatttttgtatttttagtagagatggggtttcaccgtgttggccaggatggtctcaatctgaccttgtgatctgcccacctcggcctcccaaagtgctaggattactggcgtgagccaccactcctagccTTAATGCATATTCTTAAATATACAAAGGTAGATTTGTTATGAAAATTGCTTTGGGGCTCTAATAACCTACCTTTTAAGAATGAGAAACTGCTGGGCTTAAGGGAGTTCAGTATGAATCAAGATTGAACCATTCAAATGTGGCTGTGATTTCTGCATATATCATAGATGGGATCCTTCTGAGAATACTGGAATAGGGAATTAGGACACCAAGCCAATTCAGCTGTGAACCTTATTCTTGTACTTTTCTTTCTTGCTGGTAATTTTATGGAGCAGGTTAAGAAGGCTGCTCTGTGTTAGGATAAACTGTATACCAATAATGTTGACAACCTGTAATGAGTGTTGCATTTTACTTCTTGTATCTTTTCCTTCCTACCTTGATGCCAGTAATCTATAAGGGATCTTTATAGTTTGAATGTATTTGAATAACTTCAGTATACTTTAGTTCTACTTTTTTATTTGACTCACAACCATTCTTAGGTCTCAAGTATTCCCATGTGTTTTAAAAGCCTGAAGTCAGTGAGATGAAATTCAACATCAAGAATTTGAAGTAACTTGTAAGGAAAAATAATATAAAGATACCATTggggcagtggctcacacctgtaatctcagcactttgggaggctgaggtggaaggatcacttgaagccagagtttgagaccagcctgtgcaacacagcaagaccccgtctctacaaaaacttaaaaaattagctggctgtggtgttgctcacccatagttccagctactcgggaagctgaggcagtaagatcacttgagcccaggaggccgatgctgcagtgaactgtgattgttccactacagtccagcctgggtgacagagAAAAGAAAAAGAAAACATTACATAATTTGGCTAGAGCATAATAATTTGATTTTCTGGTTTTTGAAAATTTGAGTTGCAATAAAAGGATATTTCAGTGTGCGA

>NM_016065.4 

ATCCGCTTCCGGAGTCGAGGTTTTCGGGCTTGTACCGCTTGGCGGTGCGGCCTGGTGTCGGCTTGCAGGTTCTTTCTGTGTTTGTTCTCTGCCCTGCCAAGGCCGTAGAGCTGGTGCGTGCGGGTAGCGGGGCTCTCCGAGGAGCCGCACGCCGGCGGCACCATGGTCCACCTCACTACTCTCCTCTGCAAGGCCTACCGTGGGGGCCACTTAACCATCCGCCTTGCCCTGGGTGGCTGCACCAATCGGCCGTTCTACCGCATTGTGGCTGCTCACAACAAGTGTCCCAGGGATGGCCGTTTCGTAGAGCAGCTGGGCTCCTATGATCCATTGCCCAACAGTCATGGAGAAAAACTCGTTGCCCTCAACCTAGACAGGATCCGTCATTGGATTGGCTGCGGGGCCCACCTCTCTAAGCCTATGGAAAAGCTTCTGGGTCTTGCTGGCTTTTTCCCTCTGCATCCTATGATGATCACAAATGCTGAGAGACTGCGAAGGAAACGGGCACGTGAAGTCCTGTTAGCTTCTCAGAAAACAGATGCAGAAGCTACAGATACAGAGGCTACAGAAACATAAATGAGCTGACTTTAGTGAGCATAGCAGTGGGAACAAGGTCAAGGTCCTTTTGAAACACTGCAGCGATCTTAATTTTGTTAGATTTGGAGTTCAATAAATGGAGTATCCTGAGTTGCCCTTGCTCTTCTGGCCTGGCCTGCACAGGGCCCAGGGAGAGATTTGTTCTTGTGTGACTTAGAGCTGGGTGTGGGTACTAATTAGCTTTTTTCGACTTTGTCTTGGGATAGACAGTGGCTATGGGAGGATTGGACTTTTGAGTTGGGCTCTGGGTCTCTTGGACAACTTTACAATTTACTGGCTTCCAAGACTTCCTGCTTCAAAACCCCCAGCCAGACTATTCATGGCCCATTCAGATCTTCATGTTCATCCCACAAGTGCAAGAACAGTTAACCTTTCTTAATTGATTTTTGTAATTGGAGGTTTATATTGTCTTGCCTAATGCATAttctctttttttttttttttttgagacggagtcttgttctgttgccaggctggagtgcggtggtgcaatctcagctcactgcaatctccacctcctgggttcaagaggttctcctgcctcagcctcctgagtagccggggagctacaagcatgcaccaccacacccagctaattttttttttttttttgagaggagtctcgctctgtcgcccaggcttgagtgcagtggcgcgatctcggctcactgcaagctctgtctcctgggttcatgccattctcctgcttcagcctcccgagtagtcccaggagtagctgggactacaggtgcccaccaccacacccagctaatttttttgtatttttagtagagatggggtttcaccatgttatccaggatggttttgatctcctgacctcgtgatccgcccgccttggcctcccaaaagtgctgggattataggcgtgagccaccgcccgggcaaatttttgtatttttagtagagatggggtttcaccgtgttggccaggatggtctcaatctgaccttgtgatctgcccacctcggcctcccaaagtgctaggattactggcgtgagccaccactcctagccTTAATGCATATTCTTAAATATACAAAGGTAGATTTGTTATGAAAATTGCTTTGGGGCTCTAATAACCTACCTTTTAAGAATGAGAAACTGCTGGGCTTAAGGGAGTTCAGTATGAATCAAGATTGAACCATTCAAATGTGGCTGTGATTTCTGCATATATCATAGATGGGATCCTTCTGAGAATACTGGAATAGGGAATTAGGACACCAAGCCAATTCAGCTGTGAACCTTATTCTTGTACTTTTCTTTCTTGCTGGTAATTTTATGGAGCAGGTTAAGAAGGCTGCTCTGTGTTAGGATAAACTGTATACCAATAATGTTGACAACCTGTAATGAGTGTTGCATTTTACTTCTTGTATCTTTTCCTTCCTACCTTGATGCCAGTAATCTATAAGGGATCTTTATAGTTTGAATGTATTTGAATAACTTCAGTATACTTTAGTTCTACTTTTTTATTTGACTCACAACCATTCTTAGGTCTCAAGTATTCCCATGTGTTTTAAAAGCCTGAAGTCAGTGAGATGAAATTCAACATCAAGAATTTGAAGTAACTTGTAAGGAAAAATAATATAAAGATACCATTggggcagtggctcacacctgtaatctcagcactttgggaggctgaggtggaaggatcacttgaagccagagtttgagaccagcctgtgcaacacagcaagaccccgtctctacaaaaacttaaaaaattagctggctgtggtgttgctcacccatagttccagctactcgggaagctgaggcagtaagatcacttgagcccaggaggccgatgctgcagtgaactgtgattgttccactacagtccagcctgggtgacagagAAAAGAAAAAGAAAACATTACATAATTTGGCTAGAGCATAATAATTTGATTTTCTGGTTTTTGAAAATTTGAGTTGCAATAAAAGGATATTTCAGTGTGCGA

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