RCPedia: Rtcs

Summary

Retrocopy Name	MRPS5P5	Plot displaying the genomic locations of a retrocopy (in chr4) and its respective parental gene (in chr2). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr4:163265426-163266573 UCSC
Coordinates (T2T)	chr4:166613277-166614424 UCSC
Coordinates (hg19)	chr4:164186578-164187725 UCSC
Strand	-
Parental Sequence	NM_031902.5
Parental seq. overlap	946 bp
Parental seq. overlap (%)	28.5%
Genomic Region	Intergenic
Retrocopy Summary	MRPS5P5, located on chr4:163265426-163266573, is a retrocopy of the parental gene MRPS5. 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	MRPS5
Full Name	mitochondrial ribosomal protein S5
Also known as	MRP-S5\|S5mt
Coordinate	chr2:95085369-95122003
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 S5P family. Pseudogenes corresponding to this gene are found on chromosomes 4q, 5q, and 18q. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	MRPS5P1
Bonobo	Pan paniscus	MRPS5P1
Gorilla	Gorilla gorilla	LOC101141821P1
Orangutan	Pongo abelii	MRPS5P1
Gibbon	Nomascus leucogenys	MRPS5P2
Green monkey	Chlorocebus sabaeus	MRPS5P1
Crab-eating macaque	Macaca fascicularis	MRPS5P1
Rhesus	Macaca mulatta	MRPS5P1
Baboon	Papio anubis	MRPS5P1
Golden snub-nosed monkey	Rhinopithecus roxellana	MRPS5P1
Marmoset	Callithrix jacchus	MRPS5P1
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

The Genotype-Tissue Expression project - (GTEx)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

Related Sequence

>MRPS5P5
AGGATTTGAACAGGGGTCAGATCATTGGTGAAGGGCATTATGGTTTCTGTGGCCTGGTCTGAATGTCTCTCTTATTAAAAATGGAGCAGTACAGATCATTGCCCAAAAAAGCAAGGAAGAACAGAAGGAGGAGGACAACATGACCCAGCAGAGAGAATAATGGGACCGGAAGAGGAGGATGAAGATAAATGAGAGCGAGGATGCAGTGGAAACTTGTGGGGAGGCATCAGTCTTAGCCCTCTGACCCTGGTCCCAACAGAGAAACATATGGTAATTTTGATACCAGGATACTTGAGGTAGGAAAGTTTTCAATAGGACAGCAAAAGAGGGAAGAAAGAGATTGGTAGGTGTCCTGCAGGCTGTGGGGAATGGACAACGAGCTTCAAGTTTTGCTGTTGTGAAAGCCACTAAATAAATAGATAGATGCTTTCAGAAAAGCAAAGAATAGAGCAATTCACTATTTGCATTATATAGAACGATATGAAGACCATACAATATTCCGTGATATTTCGTTAAGATTTAAAAGGAGGCATATCAAGATGAAGAAACAACCCAGAGGTTACAAGGTCTGCTGCCACAGGGGCATCAACACCATATGCCAGCTCGCTGGCATCAAAGACATGTATGCCAAGGTCTCTGGGTCCATCAGTATGCTCCCCCTCACCTGGGGCCTCTTCCATGGGCTCTCAGTCAGAAACCCGTCAACAGCTGGCAGGTAAGAAGGGCCTCCAAGTTGTGGAATTCTGGGAGGAATGTGACCCTCTGCCTATCGTGGTTTCCTCCCCAGGGGGACCTTGAAAAAGGAGCCAGGTGATGAGGTTCCACATATCAAACTGGACTTGGAAGAAGTGAATGCTCTACAGGGAATGTGGCGCTCTGTGCGGTCGGGTTTCTAGAGAGCCGCCACGTAACCTCTCTGGCCTTGTGCAGCCAGTGCCTGGTGCTGCCCAGCACCTAGGAAAGACTCAGCCCCTCACACCCTGGGATGTCACCTGGTTTTTTGTTTGTTTGAGGAGAGTTTAACCTTTAAATTGTTTATACATAAATAATTATAGCTTTAGCAGATGAGCTGTGGAAAGGTGTTTTAGCAGAGACTGGTGCTGGAGCa

>NM_031902.5
GCGGCTCGGACTCCAGCATGGCGACCGCGGTGCGCGCTGTGGGCTGCCTCCCCGTGCTGTGTAGCGGGACGGCAGGTCATTTATTGGGGAGGCAGTGTTCCCTAAACACCTTACCAGCAGCTTCCATTTTGGCATGGAAGAGTGTTCTCGGCAATGGCCATTTGTCATCACTGGGAACCAGAGACACCCATCCCTACGCCAGCTTGAGCCGTGCACTGCAGACACAATGCTGTATTTCTTCTCCCAGTCACCTGATGAGCCAGCAGTATAGACCATATAGTTTCTTCACTAAATTGACTGCAGATGAGCTGTGGAAAGGCGCTTTAGCAGAGACTGGTGCTGGAGCAAAAAAAGGAAGAGGCAAAAGAACTAAAAAGAAGAAAAGAAAGGATCTGAACAGGGGTCAGATCATTGGTGAAGGGCGTTATGGTTTTCTATGGCCCGGACTGAATGTCCCTCTTATGAAAAATGGAGCAGTGCAGACCATTGCCCAAAGAAGCAAGGAAGAGCAGGAGAAGGTGGAGGCAGACATGATCCAGCAGAGAGAAGAGTGGGACCGAAAGAAGAAGATGAAGGTTAAACGGGAGCGAGGATGGAGTGGAAACTCATGGGGAGGCATCAGTCTTGGCCCCCCTGACCCTGGTCCCTGTGGAGAAACATATGAGGATTTTGATACCAGGATACTTGAGGTAAGAAACGTTTTCACTATGACTGCGAAAGAGGGAAGAAAGAAATCGATCCGTGTCTTGGTGGCTGTGGGGAACGGAAAAGGAGCTGCAGGTTTTTCTATTGGGAAAGCTACTGATCGGATGGATGCTTTCAGGAAAGCAAAGAACAGAGCAGTTCACCATTTGCATTATATAGAACGATATGAAGACCATACAATATTCCATGATATTTCATTAAGATTTAAAAGGACGCATATCAAGATGAAGAAACAACCCAAAGGTTACGGCCTCCGCTGCCACAGGGCCATCATCACCATCTGCCGGCTCATTGGCATCAAAGACATGTATGCCAAGGTCTCTGGGTCCATTAATATGCTCAGCCTCACCCAGGGCCTCTTCCGTGGGCTCTCCAGACAGGAAACCCATCAACAGCTGGCTGATAAGAAGGGCCTCCATGTTGTGGAAATCCGGGAGGAATGTGGCCCTCTGCCCATTGTGGTTGCGTCCCCCCGGGGGCCCTTGAGGAAGGATCCAGAGCCAGAAGATGAGGTTCCAGACGTCAAACTGGACTGGGAAGATGTGAAGACTGCACAGGGAATGAAGCGCTCTGTGTGGTCTAATTTGAAGAGAGCCGCCACGTAACCTCTCTGGCCTTGTGCAGCCAGTTCCTGTGCTGCCCTGCACCTAGGAGAGACTCAGCCCCTCACAGCTTGGGATGTTACCTTGCCTTTTGTTTGTTTTGAGGGAAGTTTAATCTTTAAACTCTTTGGAAATAaataattatagctttcatttgttgagcacatgttatatgccaatgtgatagaacctttacatacatatctcagttCAAGACTACTTTAAATATTCATCCAAAGTAACAAAAGTAAATGAATTAGGGAGACGGGGTTAATAATTTGACCCAATCAGTAATAATGTACACAATGATAATTGCTGTAGTAATTATAGCTAATATATATGAACTCATTCATCCAAAGTGAATGTGATTAACTTCATTTTACAGAGCAGTTAAGTAACTTGACTACCGtgaggaacttccaaaccgttttccacagtggaaatggaagttgtaggctactattgggaatgttaaatggtatattaattgtataccattgcaattttgacttgtatttccctgatggctgatgatgttgaacatcttttcatgtgctgattggccatttgtatatgttttttggagaaatgtctattcagagcctttgcccatttaaaaagttattttttattattattgagttccttatagtttctagatataagcccccctatcatacatgctttacagaagtttttacccattctgtggaatatatatatttttatttctttgcatactctttctgccccacccacatcctctttctgggacactgatgaccaaaatgttgaatcttttactattgtcccgtgagtccctgaggcgctgtttattttttttccagtctgttttctctgtgttgctcagtttaggtaatttctattgttttatcttcagaataactggttatttactctttcctttccattctgctcttgaaccatccatgcagtactttaactttgactgtcattgtatatttcagttaaaatttccatttggtttattttttatgtcttctctttatttgctgaggctatttgctgagactttttttttctttaaatggcttcaagagtgtttataattgctcactgaagcatttttatggtggctgctttaaaatctttgtcatcaggtaggtgtggtggctcacgcctataaccccagcactttgtgaaggtgaggcaggaggattgcttcagcccaggagtttgagatcagcctaggcaacaaagtgagacctcatctctacaaaaagtaaaagtaaatttaaaagttagacacacatggtggtgtatgcctgtagtcccagctacataggaggctgaagtgggaggatcatttgattgcaggaggttgaggctgcagtgagccttgttcatgccactccagcctgggtggcagagtgagaccttgtctccaaaaaaaaaaaaaaaattgtcataaagtttcaacatctgtgtcatcttagtgttgacatcccttgaggttttttctcattcaagtttacaatgtcctagttcttgttatgatgagtgactttggctgtatcctggtcatcttcactgttatgaagctctgggagttatttaaatctctcagcatgcttcctctgacggtgctggtatgggatggggcactgcctcgttactgcctggtgaggatggagatccaggtttccTCCTGTCGCTGTCCTCGGGACCTCTGCTGAGGCCTTTCTGCTGGAAGTAGGAGGAGCACCCTAATGGCACCGTGGGATAGGGAGCAGGCCATGTTAGGCTGGATGGTGAAAGTTTTCAGCCTGTGACGTTGTCTGGTGTGGGTGGGTCCCCTTTTTTTGTGTGTGGTATTTTGCTAGAGTAAGGTAGTTATTTCCTAAAACTTATCTGTCCTGTTAGTTTTCCTTCTTAAGTACCTAACAAATATAaagacaatgaactttaagcaataaaagacaatgatcctttggagaggggaaacaaaa

>NM_031902.5 

GCGGCTCGGACTCCAGCATGGCGACCGCGGTGCGCGCTGTGGGCTGCCTCCCCGTGCTGTGTAGCGGGACGGCAGGTCATTTATTGGGGAGGCAGTGTTCCCTAAACACCTTACCAGCAGCTTCCATTTTGGCATGGAAGAGTGTTCTCGGCAATGGCCATTTGTCATCACTGGGAACCAGAGACACCCATCCCTACGCCAGCTTGAGCCGTGCACTGCAGACACAATGCTGTATTTCTTCTCCCAGTCACCTGATGAGCCAGCAGTATAGACCATATAGTTTCTTCACTAAATTGACTGCAGATGAGCTGTGGAAAGGCGCTTTAGCAGAGACTGGTGCTGGAGCAAAAAAAGGAAGAGGCAAAAGAACTAAAAAGAAGAAAAGAAAGGATCTGAACAGGGGTCAGATCATTGGTGAAGGGCGTTATGGTTTTCTATGGCCCGGACTGAATGTCCCTCTTATGAAAAATGGAGCAGTGCAGACCATTGCCCAAAGAAGCAAGGAAGAGCAGGAGAAGGTGGAGGCAGACATGATCCAGCAGAGAGAAGAGTGGGACCGAAAGAAGAAGATGAAGGTTAAACGGGAGCGAGGATGGAGTGGAAACTCATGGGGAGGCATCAGTCTTGGCCCCCCTGACCCTGGTCCCTGTGGAGAAACATATGAGGATTTTGATACCAGGATACTTGAGGTAAGAAACGTTTTCACTATGACTGCGAAAGAGGGAAGAAAGAAATCGATCCGTGTCTTGGTGGCTGTGGGGAACGGAAAAGGAGCTGCAGGTTTTTCTATTGGGAAAGCTACTGATCGGATGGATGCTTTCAGGAAAGCAAAGAACAGAGCAGTTCACCATTTGCATTATATAGAACGATATGAAGACCATACAATATTCCATGATATTTCATTAAGATTTAAAAGGACGCATATCAAGATGAAGAAACAACCCAAAGGTTACGGCCTCCGCTGCCACAGGGCCATCATCACCATCTGCCGGCTCATTGGCATCAAAGACATGTATGCCAAGGTCTCTGGGTCCATTAATATGCTCAGCCTCACCCAGGGCCTCTTCCGTGGGCTCTCCAGACAGGAAACCCATCAACAGCTGGCTGATAAGAAGGGCCTCCATGTTGTGGAAATCCGGGAGGAATGTGGCCCTCTGCCCATTGTGGTTGCGTCCCCCCGGGGGCCCTTGAGGAAGGATCCAGAGCCAGAAGATGAGGTTCCAGACGTCAAACTGGACTGGGAAGATGTGAAGACTGCACAGGGAATGAAGCGCTCTGTGTGGTCTAATTTGAAGAGAGCCGCCACGTAACCTCTCTGGCCTTGTGCAGCCAGTTCCTGTGCTGCCCTGCACCTAGGAGAGACTCAGCCCCTCACAGCTTGGGATGTTACCTTGCCTTTTGTTTGTTTTGAGGGAAGTTTAATCTTTAAACTCTTTGGAAATAaataattatagctttcatttgttgagcacatgttatatgccaatgtgatagaacctttacatacatatctcagttCAAGACTACTTTAAATATTCATCCAAAGTAACAAAAGTAAATGAATTAGGGAGACGGGGTTAATAATTTGACCCAATCAGTAATAATGTACACAATGATAATTGCTGTAGTAATTATAGCTAATATATATGAACTCATTCATCCAAAGTGAATGTGATTAACTTCATTTTACAGAGCAGTTAAGTAACTTGACTACCGtgaggaacttccaaaccgttttccacagtggaaatggaagttgtaggctactattgggaatgttaaatggtatattaattgtataccattgcaattttgacttgtatttccctgatggctgatgatgttgaacatcttttcatgtgctgattggccatttgtatatgttttttggagaaatgtctattcagagcctttgcccatttaaaaagttattttttattattattgagttccttatagtttctagatataagcccccctatcatacatgctttacagaagtttttacccattctgtggaatatatatatttttatttctttgcatactctttctgccccacccacatcctctttctgggacactgatgaccaaaatgttgaatcttttactattgtcccgtgagtccctgaggcgctgtttattttttttccagtctgttttctctgtgttgctcagtttaggtaatttctattgttttatcttcagaataactggttatttactctttcctttccattctgctcttgaaccatccatgcagtactttaactttgactgtcattgtatatttcagttaaaatttccatttggtttattttttatgtcttctctttatttgctgaggctatttgctgagactttttttttctttaaatggcttcaagagtgtttataattgctcactgaagcatttttatggtggctgctttaaaatctttgtcatcaggtaggtgtggtggctcacgcctataaccccagcactttgtgaaggtgaggcaggaggattgcttcagcccaggagtttgagatcagcctaggcaacaaagtgagacctcatctctacaaaaagtaaaagtaaatttaaaagttagacacacatggtggtgtatgcctgtagtcccagctacataggaggctgaagtgggaggatcatttgattgcaggaggttgaggctgcagtgagccttgttcatgccactccagcctgggtggcagagtgagaccttgtctccaaaaaaaaaaaaaaaattgtcataaagtttcaacatctgtgtcatcttagtgttgacatcccttgaggttttttctcattcaagtttacaatgtcctagttcttgttatgatgagtgactttggctgtatcctggtcatcttcactgttatgaagctctgggagttatttaaatctctcagcatgcttcctctgacggtgctggtatgggatggggcactgcctcgttactgcctggtgaggatggagatccaggtttccTCCTGTCGCTGTCCTCGGGACCTCTGCTGAGGCCTTTCTGCTGGAAGTAGGAGGAGCACCCTAATGGCACCGTGGGATAGGGAGCAGGCCATGTTAGGCTGGATGGTGAAAGTTTTCAGCCTGTGACGTTGTCTGGTGTGGGTGGGTCCCCTTTTTTTGTGTGTGGTATTTTGCTAGAGTAAGGTAGTTATTTCCTAAAACTTATCTGTCCTGTTAGTTTTCCTTCTTAAGTACCTAACAAATATAaagacaatgaactttaagcaataaaagacaatgatcctttggagaggggaaacaaaa

Publications

PMID - Link	Title

Summary

Parental Gene

Homology

Expression

The Genotype-Tissue Expression project - (GTEx)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

log10(TPM+1) <=> TPM

Related Sequence

Publications