RCPedia: Rtcs

Summary

Retrocopy Name	ATP5PBP3	Plot displaying the genomic locations of a retrocopy (in chr7) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr7:152748889-152750028 UCSC
Coordinates (T2T)	chr7:153922156-153923295 UCSC
Coordinates (hg19)	chr7:152445974-152447113 UCSC
Strand	+
Parental Sequence	NM_001688.5
Parental seq. overlap	919 bp
Parental seq. overlap (%)	34.9%
Genomic Region	Intergenic
Retrocopy Summary	ATP5PBP3, located on chr7:152748889-152750028, is a retrocopy of the parental gene ATP5PB. 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	ATP5PB
Full Name	ATP synthase peripheral stalk-membrane subunit b
Also known as	ATP5F1\|PIG47
Coordinate	chr1:111449464-111462773
Strand	+
Gene summary	This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the b subunit of the proton channel. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	ATP5PBP2
Bonobo	Pan paniscus	ATP5PBP2
Orangutan	Pongo abelii	ATP5PBP3
Gibbon	Nomascus leucogenys	ATP5PBP5
Green monkey	Chlorocebus sabaeus	ATP5F1P5
Crab-eating macaque	Macaca fascicularis	ATP5F1P2
Rhesus	Macaca mulatta	ATP5PBP2
Baboon	Papio anubis	ATP5PBP2
Golden snub-nosed monkey	Rhinopithecus roxellana	ATP5PBP3
Gorilla	Gorilla gorilla	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

>ATP5PBP3
CCATCTTGCTCCTGCCCCTGACAGAGTCTCCGGTCGGGGTCACAGGGATGCTAAGACTGCTGCCTGGACCTTCGATGACCACGCTGTCCCGGGTGGAACTTTCTGCCACTGCCACAGTGGCCCCCTCTCTGAAGAATGCAGCCTTCCTAGGTCCAGGGGTATTGTGGGCAACAAGGACCTTTCACCCAGGCAGCCACACCTTGCCCCTCTACCACCTTTTCCTGAAAATGGAGGAAAAGTTCGTCTTGGACTGATCCTTGAGGAATTCCTCAGGTTTCTTTATCTTAAAGCCGGTGTAACAGGACCCTGTGTGCTCGGAACTGGGCTTATCTTGTATGCTTTATCCAAAGAAATATATGTGATTATTGCAGAGACCTTCTCGACCATATCAGTAGTAGGGTTACCTGTCTATGCAATTAAAAAATATGGTGCCTCTGTTGCAGAATTTGCTGGTAAACTCAATGAGCAAAAACTTGCCCAACTAGAAGAGGCGAAGCAGGCTCCCATCAAACAAATCCGGGATGGAATTGATTTGGAGAAGTCACAGCAGGCACTAGTTCAGAAGCGCCATTACCTTTTTGATGTGCAGAGGAATAACATTGCTATGGCTTTGGAGGTTACTTACCAGGAACTACTGTATAAAGTATGTAAGGAAGTAAAGAATCGCCTGGACTATCATATATCTGTGCAGAACATGATGCATTGAAAGGAACAAGAGCACATGATCAATTGGGTGGAGAAGTACGTGGTGCAGAGCATCTCTGCACAGCAGGAAAAGGAGACAATTGCCAAGTGCATTGAAGACCTAAAGCTTCTGGCAAAGAAGGCTCAAGCACAGCCAGCTATGTAAATGTATCTATCCCAATTGAGACAGCTGGAAACAGTTGACTGTTTGTGTCTACTGAAGTTATAATTTACCTCTCCTAAAAGTGAAAAGTTTATTTCATAGAGTGAAAGCACAAAATCTATTGGCCAGTCAGATGTTTCTCATCCTTCTTACTCTGCATTTGAaATGAAA

>NM_001688.5
CATCTTGGTCCTGCCCTGACAGATTCTCCTATCGGGGTCACAGGGACGCTAAGATTGCTACCTGGACTTTCGTTGACCATGCTGTCCCGGGTGGTACTTTCCGCCGCCGCCACAGCGGCCCCCTCTCTGAAGAATGCAGCCTTCCTAGGTCCAGGGGTATTGCAGGCAACAAGGACCTTTCATACAGGGCAGCCACACCTTGTCCCTGTACCACCTCTTCCTGAATACGGAGGAAAAGTTCGTTATGGACTGATCCCTGAGGAATTCTTCCAGTTTCTTTATCCTAAAACTGGTGTAACAGGACCCTATGTACTCGGAACTGGGCTTATCTTGTACGCTTTATCCAAAGAAATATATGTGATTAGCGCAGAGACCTTCACTGCCCTATCAGTACTAGGTGTAATGGTCTATGGAATTAAAAAATATGGTCCCTTTGTTGCAGACTTTGCTGATAAACTCAATGAGCAAAAACTTGCCCAACTAGAAGAGGCGAAGCAGGCTTCCATCCAACACATCCAGAATGCAATTGATACGGAGAAGTCACAACAGGCACTGGTTCAGAAGCGCCATTACCTTTTTGATGTGCAAAGGAATAACATTGCTATGGCTTTGGAAGTTACTTACCGGGAACGACTGTATAGAGTATATAAGGAAGTAAAGAATCGCCTGGACTATCATATATCTGTGCAGAACATGATGCGTCGAAAGGAACAAGAACACATGATAAATTGGGTGGAGAAGCACGTGGTGCAAAGCATCTCCACACAGCAGGAAAAGGAGACAATTGCCAAGTGCATTGCGGACCTAAAGCTGCTGGCAAAGAAGGCTCAAGCACAGCCAGTTATGTAAATGTATCTATCCCAATTGAGACAGCTAGAAACAGTTGACTGACTAAATGGAAACTAGTCTATTTGACAAAGTCTTTCTGTGTTGGTGTCTACTGAAGTTATAGTTTACCCTTCCTAAAAATGAAAAGTTTGTTTCATATAGTGAGAGAACGAAATCTCTATCGGCCAGTCAGATGTTTCTCATCCTTCTTGCtctgcctttgagttgttccgtgatcacttctgaataagcagtttgcctttataaaaacttgctgcctgactaaagattaacaggttatagtttaaatttgtaattaattctaccatcttgcaataaagtgacaattgaatgaaacagggtttttcaagttgtataattctctgaaatactcagcttttgtcatatgggtaaaaattaaagatgtcattgaactACTGTCTTGTTTATGAGACCATTCAGTGGTGAACTGTTTCTGGCTGATAGGTTATGAGATATGTAAAGCTTTCTAGTACTCTTAAAATAACTAAATGGAGTATTATATATCAATTCATATCATTGACTTTATTATTTTAGTAGTATGCCTATAGAAAATATTATGGACTCAGAGTGTCATAAAATCACTCTTAAGAATCCATGCAGCAggccaggcacagtggctcacacctgtaatgcctgcactttggaaggccgagacaggcggatcacttgaggtcaggagtttgaaaccagccaggccaacacagtgaaaccctgtctctactaaaaatacaaaaggttagccgggcatggtggcaggcgcctgtaatcccagctactcaggaggctgaggcaggagaattgcttgaacgcaggaggcaaaggttgcagtgagctgagatcacgccactgcactccagcctgggcaacagacctcgactccatctagaaaaaaaaaaaaaaaaaTCCAGCAGACACCtatcaggaacatagaaaataacaagtgttggcaaggaagtggagaagttggaacacttgtgcactgttcgtagaaatatgaaatggtacagccattatggaaaagtgtggtgattcctcataaaattaaaatggaaataccatgatccagcaatcccagtcgacatatatactcaaaaaaattaaaagcagggtcttgaagagatacttgtgttccatggtgatagcagccattgttcacaatagctaaaacatagaagcagcccaatcggccatcagtagatgaatggataagcaaaatgtagtatatccatgcaatggaatattattccacttcaaggaagaaaattctgacactggctacagcatgaatgaaccttgaggacgttatgcagttttacaggatgagttatggagctggatagtggtgatggtggcacattaaggatgtatttaatactgttcttaaatggtacacttaaaaatggtaaattttatgtgtattttacAATCTTTTTTTAAATTGAAGAAAAATCCTGTAGATAAATTAGAAAATTCTTCCCTTCATAGGTTTATCTGCATTTGATTCTCCCATACTTGTACAAGGATTTATTTGTATTCAAATGGACAAATTACGCAATAGGAAATATTTGAAAATATTTATCATGGGTAATTGCTATTTTCATTGACTTCCTAAGATTTTATGTAATAATCATTTGAGTCAATATTGGTAGCTAATGTACTAATCTAATATTGAAATCAGATTGATATCTTTGTTACTTAAAGATAATTTGATTGGATCAGCAGTTATTTCAAattgattaaacaaaaaattataaaaca

>NM_001688.5 

CATCTTGGTCCTGCCCTGACAGATTCTCCTATCGGGGTCACAGGGACGCTAAGATTGCTACCTGGACTTTCGTTGACCATGCTGTCCCGGGTGGTACTTTCCGCCGCCGCCACAGCGGCCCCCTCTCTGAAGAATGCAGCCTTCCTAGGTCCAGGGGTATTGCAGGCAACAAGGACCTTTCATACAGGGCAGCCACACCTTGTCCCTGTACCACCTCTTCCTGAATACGGAGGAAAAGTTCGTTATGGACTGATCCCTGAGGAATTCTTCCAGTTTCTTTATCCTAAAACTGGTGTAACAGGACCCTATGTACTCGGAACTGGGCTTATCTTGTACGCTTTATCCAAAGAAATATATGTGATTAGCGCAGAGACCTTCACTGCCCTATCAGTACTAGGTGTAATGGTCTATGGAATTAAAAAATATGGTCCCTTTGTTGCAGACTTTGCTGATAAACTCAATGAGCAAAAACTTGCCCAACTAGAAGAGGCGAAGCAGGCTTCCATCCAACACATCCAGAATGCAATTGATACGGAGAAGTCACAACAGGCACTGGTTCAGAAGCGCCATTACCTTTTTGATGTGCAAAGGAATAACATTGCTATGGCTTTGGAAGTTACTTACCGGGAACGACTGTATAGAGTATATAAGGAAGTAAAGAATCGCCTGGACTATCATATATCTGTGCAGAACATGATGCGTCGAAAGGAACAAGAACACATGATAAATTGGGTGGAGAAGCACGTGGTGCAAAGCATCTCCACACAGCAGGAAAAGGAGACAATTGCCAAGTGCATTGCGGACCTAAAGCTGCTGGCAAAGAAGGCTCAAGCACAGCCAGTTATGTAAATGTATCTATCCCAATTGAGACAGCTAGAAACAGTTGACTGACTAAATGGAAACTAGTCTATTTGACAAAGTCTTTCTGTGTTGGTGTCTACTGAAGTTATAGTTTACCCTTCCTAAAAATGAAAAGTTTGTTTCATATAGTGAGAGAACGAAATCTCTATCGGCCAGTCAGATGTTTCTCATCCTTCTTGCtctgcctttgagttgttccgtgatcacttctgaataagcagtttgcctttataaaaacttgctgcctgactaaagattaacaggttatagtttaaatttgtaattaattctaccatcttgcaataaagtgacaattgaatgaaacagggtttttcaagttgtataattctctgaaatactcagcttttgtcatatgggtaaaaattaaagatgtcattgaactACTGTCTTGTTTATGAGACCATTCAGTGGTGAACTGTTTCTGGCTGATAGGTTATGAGATATGTAAAGCTTTCTAGTACTCTTAAAATAACTAAATGGAGTATTATATATCAATTCATATCATTGACTTTATTATTTTAGTAGTATGCCTATAGAAAATATTATGGACTCAGAGTGTCATAAAATCACTCTTAAGAATCCATGCAGCAggccaggcacagtggctcacacctgtaatgcctgcactttggaaggccgagacaggcggatcacttgaggtcaggagtttgaaaccagccaggccaacacagtgaaaccctgtctctactaaaaatacaaaaggttagccgggcatggtggcaggcgcctgtaatcccagctactcaggaggctgaggcaggagaattgcttgaacgcaggaggcaaaggttgcagtgagctgagatcacgccactgcactccagcctgggcaacagacctcgactccatctagaaaaaaaaaaaaaaaaaTCCAGCAGACACCtatcaggaacatagaaaataacaagtgttggcaaggaagtggagaagttggaacacttgtgcactgttcgtagaaatatgaaatggtacagccattatggaaaagtgtggtgattcctcataaaattaaaatggaaataccatgatccagcaatcccagtcgacatatatactcaaaaaaattaaaagcagggtcttgaagagatacttgtgttccatggtgatagcagccattgttcacaatagctaaaacatagaagcagcccaatcggccatcagtagatgaatggataagcaaaatgtagtatatccatgcaatggaatattattccacttcaaggaagaaaattctgacactggctacagcatgaatgaaccttgaggacgttatgcagttttacaggatgagttatggagctggatagtggtgatggtggcacattaaggatgtatttaatactgttcttaaatggtacacttaaaaatggtaaattttatgtgtattttacAATCTTTTTTTAAATTGAAGAAAAATCCTGTAGATAAATTAGAAAATTCTTCCCTTCATAGGTTTATCTGCATTTGATTCTCCCATACTTGTACAAGGATTTATTTGTATTCAAATGGACAAATTACGCAATAGGAAATATTTGAAAATATTTATCATGGGTAATTGCTATTTTCATTGACTTCCTAAGATTTTATGTAATAATCATTTGAGTCAATATTGGTAGCTAATGTACTAATCTAATATTGAAATCAGATTGATATCTTTGTTACTTAAAGATAATTTGATTGGATCAGCAGTTATTTCAAattgattaaacaaaaaattataaaaca

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