RCPedia: Rtcs

Summary

Retrocopy Name	MRPS33P2	Plot displaying the genomic locations of a retrocopy (in chr4) and its respective parental gene (in chr7). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr4:38006222-38007156 UCSC
Coordinates (T2T)	chr4:37975297-37976232 UCSC
Coordinates (hg19)	chr4:38007843-38008777 UCSC
Strand	-
Parental Sequence	NM_053035.3
Parental seq. overlap	341 bp
Parental seq. overlap (%)	7.7%
Genomic Region	Intragenic (TBC1D1)
Retrocopy Summary	MRPS33P2, located on chr4:38006222-38007156, is a retrocopy of the parental gene MRPS33. 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	MRPS33
Full Name	mitochondrial ribosomal protein S33
Also known as	CGI-139\|MRP-S33\|PTD003\|S33mt
Coordinate	chr7:141002610-141014952
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. The 28S subunit of the mammalian mitoribosome may play a crucial and characteristic role in translation initiation. This gene encodes a 28S subunit protein that is one of the more highly conserved mitochondrial ribosomal proteins among mammals, Drosophila and C. elegans. Splice variants that differ in the 5' UTR have been found for this gene; all variants encode the same protein. Pseudogenes corresponding to this gene are found on chromosomes 1q, 4p, 4q, and 20q [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	MRPS33P3
Bonobo	Pan paniscus	MRPS33P3
Gorilla	Gorilla gorilla	MRPS33P2
Orangutan	Pongo abelii	MRPS33P2
Gibbon	Nomascus leucogenys	MRPS33P3
Green monkey	Chlorocebus sabaeus	MRPS33P2
Crab-eating macaque	Macaca fascicularis	MRPS33P2
Rhesus	Macaca mulatta	MRPS33P2
Baboon	Papio anubis	MRPS33P1
Golden snub-nosed monkey	Rhinopithecus roxellana	MRPS33P1
Marmoset	Callithrix jacchus	MRPS33P2
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

>MRPS33P2
TAGTGTTGGTCCCTCAAGAGGGAAAATTTCTTCCTCTGTGGCAGAGAGAAGAAAATGCATCTACTGTCTTTCCACATATTGGAGGAATGTCATCTTCCTAAAGGAAGGTTATTTGGAGGTTATCATCTCCTTGTTGAAGTCTAATCCAGTTAAATGGTGACTGGTTTCTTGAACACACTTTAACTGTGCAAAACTATTTTGGCCTTGGCTGTGTAATATAAGGTTTACCTAATTCTCTAATGAAATGAATACAGTGGGTGAGGAAAGTCAAGTCCAGGGACTCCAGTTCCTTGCCACTCAAGAAATGTCTTCTCTTTCAGAATATGCCCTGCGCATGTCTCGTCTCAGTGCTCAGCTATTTGGTGAAGTCGCCAGGCCGACTGATTCCAAGTCTATGAAAATGGTGACACTGTTTAGTGAACCACCCTTGGCCAAGAAGAAGGAGACTTATGACTGGGTATCCAGATGACAACACTTACTCCACACTCATGGGAACACTCTGGTTTCTTGGATTCTGCAGAGATGAGCATCAGGATTTTAAGGATGAGCAAAGATGACAAAAGAAGCTTCGTGGAAAGGGGAAACCAAAGAAAGGAGAGGGGAAAAGAGCAGCATAAAAGAAATAGTGTTGg

>NM_053035.3
CTTCCGGGACGAGGGCGCGTGGGTGAGGAAGGTCAGGTCTAGGAACTCTAACTCCTTGCCACTCAAGAAATGTCCTCCCTTTCAGAATATGCCTTCCGCATGTCTCGTCTCAGTGCCCGGCTATTTGGTGAAGTCACCAGGCCTACTAATTCCAAGTCTATGAAAGTGGTGAAACTGTTTAGTGAACTGCCCTTGGCCAAGAAGAAGGAGACTTATGATTGGTATCCAAATCACCACACTTACGCTGAACTCATGCAGACGCTCCGATTTCTTGGACTCTACAGAGATGAGCATCAGGATTTTATGGATGAGCAAAAACGACTAAAGAAGCTTCGTGGAAAGGAGAAACCAAAGAAAGGAGAAGGGAAAAGAGCAGCAAAAAGGAAATAGTGTTGGTCCCTCAAGAGGGAGACTTTCTTCCTCAGTGGCGGAGAGAAGAAAGTGCATTTATTGTCTTTCCACCTATTGGAGGAATGTCATCTTCCTAAATGAAGTTTATTTGGAGGAACACAGTCATCTCCTTGGTGAAATCTAATCCGGTTACATTGTGGCTGGTTTCTTGAACACATTCTAACTGTGCAAAATTATCTTGGCCTTGGCCGTGTAATGTGAGGTTTACCTGATTCTCTAATGAAATAAATACCTAAGTTATTGTTTGATGATTTGTTTGGGGTGGGATGGGATGCTGGGGGAATGGAGGGGAAACCTCATTAAGTGAGCATCCTATAGTGTCCTCATTTCTCCCTTCTTGCTTACTGACTCACCCAGCCCTAAACTTCTTTCATCTTGGGCCTTTCAGCCACTGTCTCCACCACCAAGCTCACAAACTTTGTGTGTGTCTTCACCTACTCCTTTGAGAAATCTATTAAGATGAATTTGTAGAGTAAGTATCTTTTAAAAGGAAGtattgaatacctgctctgtacaagatattggggccctggtaatacacgtggttagcaagagaaatactccctacctcatgtaagtttcagtcttgtgggagggactaatattacataattacatacaattgtattacatgctacaaaggaaaaagccagacttctataagagcatggatggatggatgaatgcagagagagatagccagaagcccaaatcacattagggagtttaaagaaagcttccctaaagaaatgatatttaagccaggcgctgttgctcacacctgtaatcccaccactttgggaggccgaggtgggtggatcacaaggtcaagagatcgagaccattttggccaacatggtgaaaccccacctactaaaaatgcaaaaattagctgggcgtcgtggcatgcacctgtagtctcagctactcgggatgctgaggcaggagaatcgcttgaacccgggaggcaaaggttgcagtgagttgagatcacgccactgcactccagcctggcaacagagcaagactacatctcaaaaaaaaaatgatatttaagctgaaccttgaagaataaataagaggttgccaaaaggaaaatggtgagaaaggggtttgaggcagagagtactatttgcaaagccctaaggtatgaagaaattgtctgttcaagaaacaCTGAGTTTGTTCATGGTTGGCTGTAAGAAAACAGAGGCCAGATCATGAAGGGCTTTGGAAATTCTGTGGAAAAGCTTGAACATAACTAGAAGTTCTATGAGGGATGACTGTTGTATAGATTTGAGTAGCTCGCTGCTGGTTTTATTGTATTCCAGCAATGAGTTTCCAAAGAAATTGTGAAGGCTTggccgggcacagtggctcacgcctgtaatcccagcactttgggaggtcgaggcgggtggatcacgaggtcaggggatcgagaccatcctggctaacatggtgaaaccccgtctctactaaaaaatgcaaaaaagttagccgggcgtggtggtgggtgcctgtagtcccagctacttgggaggctgaggcaggagaatggcagggaggcggagcttgcagtaagctgagatggtgccactgcactccagcctgggcaacaaagcgagactctgtctcaaaaaaaaaaTTGTGAAGGCTTCTCTGATTTTTTTTTCCAACAGTTGTTCTGAATCTTTAGCATGTCCAGTAATTTTTTAATAACtttttattattgtagtaaaaacataaaattaatgatcttaaccatatttaagtgtacaatagtgtcaatattcaAACATATTATTCAAAAAATAATCAAAATATAAAAGCATTTTAGTGCGATAGTATTTATTGGAGTATGTATAGCAGCTACTCCAGCCACAGTTTTCTTTCTCTGTAACACTCAATGATTCCTGAAGTAGAAAGATTCCCAGTACATATGTTTAAATGAATGCTATTTTTAAAGATACCTAATCCAGATGGTATGGCTAGGGCCTATTTTATAGCCTGTTTAAAAAAATAAAATAAAATAAAATTGGGTGGTTTGTATGTGGTAGAAGTGAATTCCAGCAAAAGGAGAattcattcatttagacctttttttttgtttgagacggagtctcactctcaccagctggagtgcagtggcgcaatctcagctcactgcaagctccacctcccgggttcacgccattctcctgcctcagcctcccaagtagctgggactacaggcgcccaccaccacgcccggctaatattttgtatttttagtagagaaggtgtctcactgtgttagccaggatggtctcaacctcttgacctcctgatccacccacctcagactcccaaagtgctggaattacaggcatgagccaccacacccagcccatttagaactttttactgagcacctgccatgtgctcgacacgtgatagttgtagaggatacagagacaaatagacttagtccctAAGACTGTGTGAATGAGCATGTGTGTATTACAAAGTATTGGCAAGATCTCAGAAACGTGCTTAGAAAAGTGCAGATGCACTGTTATTCTTGGCCAATGCAGCTGAGCCAGGTGTAGGTGGATGACTACCCCAGGATGTTGAGCTGAGAAACAGGATCTCAGCCTGAACCCAATGTAGCTCAGCAGATGTTTGAATTATGTGATCTCCAGCTTTTGGGAAAGATCTGAATGTAAGAGGAACTTAAGAGAATTAGCATGATATTTTAAAGAGAATAACTGCATTACATTCTAACAGCAGACCTGAGTCGGAAAACAAGTAAAGAATCGATGTATTGGTTTGCCGATGGAAGAGCTTCAGTGAGATCTCAGACCCTGACCCTGCAGTGAGCCTTGGCAATGATTGACAGGGAAGTTTGTAGATAACGCAGAAGTAGATTAGTGTGCCACTGCTCCAGGCTGAAAATCAGAAATGAAAGCTAAAATACATTTGTACATAAGCTATACCTTCAATTGATAGAGCAAGCTGTGTGACTCAAAACAGCCTGTACAGAAGTACGATGGACCAGCTGGAAGGTATCAATAGAAGATAAGGAAAAGTTAACTCTTGACACCAGGGAAGTCAACAAATTTCAGGACAACAGTGACCAATGGTTAAGATGGTGACTAAGTGTAATCAGAAAAAAATCTTTAACTCCAAGTTTAGACTAGCCAGTTTGTTTAATTGGATTTCTCTGGTCAAAACCTAAACTATTGGTGCTTTCTAACCTGTGGGGATCAGTGTGCATAGACCATTTTGCCCTCGATTTcagcataacatagtaaaaagactgggttttagattcaaaagtcatgggtttgtgatacagtgtacttactgattatgtgacgtcagttacttctctgaacctctttccttctctataaaatcataatgcttcactggattaatgaaataagatatttgtgaaaagaactctgtaaattataaaaagttaAAAACTTTTACATATAGCACATTATGTGACTAGTAAGTACTGCTGTGTCTTACTAGCGCAATTTTCTGTGGCAGCATTGACACGTATCTCCTAAAAATATAAAGTTCCCCACGTTTACAAGCAGCATGATAGGTTCAGGAAGAGGAGGTAGATGAGAGGTAACATCTTATTATTTATGTAATTATGGGCTCCATAAGTTTATTTTTTAAGCACCATATATGTGTGTGTTTCAAAATAAACATAAGGCATCATATATTTAAACATATATAACCATAATGCTTGTATTTATAAATCATTTTCCAAGAAAGAATAAATCAAAATTTGAAATTC

>NM_053035.3 

CTTCCGGGACGAGGGCGCGTGGGTGAGGAAGGTCAGGTCTAGGAACTCTAACTCCTTGCCACTCAAGAAATGTCCTCCCTTTCAGAATATGCCTTCCGCATGTCTCGTCTCAGTGCCCGGCTATTTGGTGAAGTCACCAGGCCTACTAATTCCAAGTCTATGAAAGTGGTGAAACTGTTTAGTGAACTGCCCTTGGCCAAGAAGAAGGAGACTTATGATTGGTATCCAAATCACCACACTTACGCTGAACTCATGCAGACGCTCCGATTTCTTGGACTCTACAGAGATGAGCATCAGGATTTTATGGATGAGCAAAAACGACTAAAGAAGCTTCGTGGAAAGGAGAAACCAAAGAAAGGAGAAGGGAAAAGAGCAGCAAAAAGGAAATAGTGTTGGTCCCTCAAGAGGGAGACTTTCTTCCTCAGTGGCGGAGAGAAGAAAGTGCATTTATTGTCTTTCCACCTATTGGAGGAATGTCATCTTCCTAAATGAAGTTTATTTGGAGGAACACAGTCATCTCCTTGGTGAAATCTAATCCGGTTACATTGTGGCTGGTTTCTTGAACACATTCTAACTGTGCAAAATTATCTTGGCCTTGGCCGTGTAATGTGAGGTTTACCTGATTCTCTAATGAAATAAATACCTAAGTTATTGTTTGATGATTTGTTTGGGGTGGGATGGGATGCTGGGGGAATGGAGGGGAAACCTCATTAAGTGAGCATCCTATAGTGTCCTCATTTCTCCCTTCTTGCTTACTGACTCACCCAGCCCTAAACTTCTTTCATCTTGGGCCTTTCAGCCACTGTCTCCACCACCAAGCTCACAAACTTTGTGTGTGTCTTCACCTACTCCTTTGAGAAATCTATTAAGATGAATTTGTAGAGTAAGTATCTTTTAAAAGGAAGtattgaatacctgctctgtacaagatattggggccctggtaatacacgtggttagcaagagaaatactccctacctcatgtaagtttcagtcttgtgggagggactaatattacataattacatacaattgtattacatgctacaaaggaaaaagccagacttctataagagcatggatggatggatgaatgcagagagagatagccagaagcccaaatcacattagggagtttaaagaaagcttccctaaagaaatgatatttaagccaggcgctgttgctcacacctgtaatcccaccactttgggaggccgaggtgggtggatcacaaggtcaagagatcgagaccattttggccaacatggtgaaaccccacctactaaaaatgcaaaaattagctgggcgtcgtggcatgcacctgtagtctcagctactcgggatgctgaggcaggagaatcgcttgaacccgggaggcaaaggttgcagtgagttgagatcacgccactgcactccagcctggcaacagagcaagactacatctcaaaaaaaaaatgatatttaagctgaaccttgaagaataaataagaggttgccaaaaggaaaatggtgagaaaggggtttgaggcagagagtactatttgcaaagccctaaggtatgaagaaattgtctgttcaagaaacaCTGAGTTTGTTCATGGTTGGCTGTAAGAAAACAGAGGCCAGATCATGAAGGGCTTTGGAAATTCTGTGGAAAAGCTTGAACATAACTAGAAGTTCTATGAGGGATGACTGTTGTATAGATTTGAGTAGCTCGCTGCTGGTTTTATTGTATTCCAGCAATGAGTTTCCAAAGAAATTGTGAAGGCTTggccgggcacagtggctcacgcctgtaatcccagcactttgggaggtcgaggcgggtggatcacgaggtcaggggatcgagaccatcctggctaacatggtgaaaccccgtctctactaaaaaatgcaaaaaagttagccgggcgtggtggtgggtgcctgtagtcccagctacttgggaggctgaggcaggagaatggcagggaggcggagcttgcagtaagctgagatggtgccactgcactccagcctgggcaacaaagcgagactctgtctcaaaaaaaaaaTTGTGAAGGCTTCTCTGATTTTTTTTTCCAACAGTTGTTCTGAATCTTTAGCATGTCCAGTAATTTTTTAATAACtttttattattgtagtaaaaacataaaattaatgatcttaaccatatttaagtgtacaatagtgtcaatattcaAACATATTATTCAAAAAATAATCAAAATATAAAAGCATTTTAGTGCGATAGTATTTATTGGAGTATGTATAGCAGCTACTCCAGCCACAGTTTTCTTTCTCTGTAACACTCAATGATTCCTGAAGTAGAAAGATTCCCAGTACATATGTTTAAATGAATGCTATTTTTAAAGATACCTAATCCAGATGGTATGGCTAGGGCCTATTTTATAGCCTGTTTAAAAAAATAAAATAAAATAAAATTGGGTGGTTTGTATGTGGTAGAAGTGAATTCCAGCAAAAGGAGAattcattcatttagacctttttttttgtttgagacggagtctcactctcaccagctggagtgcagtggcgcaatctcagctcactgcaagctccacctcccgggttcacgccattctcctgcctcagcctcccaagtagctgggactacaggcgcccaccaccacgcccggctaatattttgtatttttagtagagaaggtgtctcactgtgttagccaggatggtctcaacctcttgacctcctgatccacccacctcagactcccaaagtgctggaattacaggcatgagccaccacacccagcccatttagaactttttactgagcacctgccatgtgctcgacacgtgatagttgtagaggatacagagacaaatagacttagtccctAAGACTGTGTGAATGAGCATGTGTGTATTACAAAGTATTGGCAAGATCTCAGAAACGTGCTTAGAAAAGTGCAGATGCACTGTTATTCTTGGCCAATGCAGCTGAGCCAGGTGTAGGTGGATGACTACCCCAGGATGTTGAGCTGAGAAACAGGATCTCAGCCTGAACCCAATGTAGCTCAGCAGATGTTTGAATTATGTGATCTCCAGCTTTTGGGAAAGATCTGAATGTAAGAGGAACTTAAGAGAATTAGCATGATATTTTAAAGAGAATAACTGCATTACATTCTAACAGCAGACCTGAGTCGGAAAACAAGTAAAGAATCGATGTATTGGTTTGCCGATGGAAGAGCTTCAGTGAGATCTCAGACCCTGACCCTGCAGTGAGCCTTGGCAATGATTGACAGGGAAGTTTGTAGATAACGCAGAAGTAGATTAGTGTGCCACTGCTCCAGGCTGAAAATCAGAAATGAAAGCTAAAATACATTTGTACATAAGCTATACCTTCAATTGATAGAGCAAGCTGTGTGACTCAAAACAGCCTGTACAGAAGTACGATGGACCAGCTGGAAGGTATCAATAGAAGATAAGGAAAAGTTAACTCTTGACACCAGGGAAGTCAACAAATTTCAGGACAACAGTGACCAATGGTTAAGATGGTGACTAAGTGTAATCAGAAAAAAATCTTTAACTCCAAGTTTAGACTAGCCAGTTTGTTTAATTGGATTTCTCTGGTCAAAACCTAAACTATTGGTGCTTTCTAACCTGTGGGGATCAGTGTGCATAGACCATTTTGCCCTCGATTTcagcataacatagtaaaaagactgggttttagattcaaaagtcatgggtttgtgatacagtgtacttactgattatgtgacgtcagttacttctctgaacctctttccttctctataaaatcataatgcttcactggattaatgaaataagatatttgtgaaaagaactctgtaaattataaaaagttaAAAACTTTTACATATAGCACATTATGTGACTAGTAAGTACTGCTGTGTCTTACTAGCGCAATTTTCTGTGGCAGCATTGACACGTATCTCCTAAAAATATAAAGTTCCCCACGTTTACAAGCAGCATGATAGGTTCAGGAAGAGGAGGTAGATGAGAGGTAACATCTTATTATTTATGTAATTATGGGCTCCATAAGTTTATTTTTTAAGCACCATATATGTGTGTGTTTCAAAATAAACATAAGGCATCATATATTTAAACATATATAACCATAATGCTTGTATTTATAAATCATTTTCCAAGAAAGAATAAATCAAAATTTGAAATTC

Publications

PMID - Link	Title
No publications available for this retrocopy

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