RCPedia: Rtcs

Summary

Retrocopy Name	PDHA1P1	Plot displaying the genomic locations of a retrocopy (in chr3) and its respective parental gene (in chrX). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr3:57800479-57801042 UCSC
Coordinates (T2T)	chr3:57840847-57841410 UCSC
Coordinates (hg19)	chr3:57786206-57786769 UCSC
Strand	-
Parental Sequence	NM_000284.4
Parental seq. overlap	472 bp
Parental seq. overlap (%)	14.1%
Genomic Region	Intragenic (SLMAP)
Retrocopy Summary	PDHA1P1, located on chr3:57800479-57801042, is a retrocopy of the parental gene PDHA1. 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	PDHA1
Full Name	pyruvate dehydrogenase E1 subunit alpha 1
Also known as	E1alpha\|PDHA\|PDHAD\|PDHCE1A\|PHE1A
Coordinate	chrX:19343906-19361718
Strand	+
Gene summary	The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle. The PDH complex is composed of multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). The E1 enzyme is a heterotetramer of two alpha and two beta subunits. This gene encodes the E1 alpha 1 subunit containing the E1 active site, and plays a key role in the function of the PDH complex. Mutations in this gene are associated with pyruvate dehydrogenase E1-alpha deficiency and X-linked Leigh syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Mar 2010]

Homology

Species	Scientific Name	Retrocopy
Bonobo	Pan paniscus	PDHA1P1
Gibbon	Nomascus leucogenys	PDHA1P1
Baboon	Papio anubis	PDHA1P1
Golden snub-nosed monkey	Rhinopithecus roxellana	PDHA1P1
Mouse lemur	Microcebus murinus	PDHA1P2
Dolphin	Tursiops truncatus	PDHA1P1
Horse	Equus caballus	PDHA1P2
Dog	Canis familiaris	PDHA1P1
Panda	Ailuropoda melanoleuca	PDHA1P1
Egyptian rousette	Rousettus aegyptiacus	PDHA1P1
Sloth	Choloepus didactylus	LOC119524040P1
Chimpanzee	Pan troglodytes	Without Homology
Gorilla	Gorilla gorilla	Without Homology
Orangutan	Pongo abelii	Without Homology
Green monkey	Chlorocebus sabaeus	Without Homology
Crab-eating macaque	Macaca fascicularis	Without Homology
Rhesus	Macaca mulatta	Without Homology
Marmoset	Callithrix jacchus	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
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
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

>PDHA1P1
CTTTCTGTCCCAGAAATTCTTGTAGAGCTTACAGGACAAAGAGGAGGTTGTGCTAAAGGAAAAGTAGGATCAATGCATATGTATGCCAAGAACTTCTACAGGAGCCATGGCATTGTCAGAGCTCAGGTCTCCTGGGAGCTGGTATTGGCTTGGCCTGTGAGTATAACGGAAAAGATGAGGTCTGAATGACTTTATATTTGAGGCCTACAATATAGCCGCTTTGTGGAAATTACCTCCTATTTTCATCTGTGAGAATAAAACTGCTATGGAATAAGAGCATCTGTTGAGACAGCAGCACCTAGCACTGATTACTATAAGACAGGCAATTTTGTACCTGGACTAAGGATAGACAGAATGAATATTCTATGTGTCCATGAGGCAACAAAGTTTGCCTGTTGTATATTTGGAAAGGGGACCATACTGATGAAGCTGCAGACTTACCATTATCAAGGCACAGTGTAAGTGATCCTGGAGTCAGCTGTACACAAGAAGAAATTCAAGAAGCAAGAGGACTGACTCTATTATGCTTCTCAAAGATAAAATGGTAAATAGCAATCTTGCCAA

>NM_000284.4
GGTGCGACTGAGGCGTGGCGTCTGCTGGGGCACCTGAAGGAGACTTGGGGGCACCCGCGTCGTGCCTCCTGGGTTGTGAGGAGTCGCCGCTGCCGCCACTGCCTGTGCTTCATGAGGAAGATGCTCGCCGCCGTCTCCCGCGTGCTGTCTGGCGCTTCTCAGAAGCCGGCAAGCAGAGTGCTGGTAGCATCCCGTAATTTTGCAAATGATGCTACATTTGAAATTAAGaaatgtgaccttcaccggctggaagaaggccctcctgtcacaacagtgctcaccagggaggatgggctcaaatactacaggatgatgCAGACTGTACGCCGAATGGAGTTGAAAGCAGATCAGCTGTATAAACAGAAAATTATTCGTGGTTTCTGTCACTTGTGTGATGGTCAGGAAGCTTGCTGTGTGGGCCTGGAGGCCGGCATCAACCCCACAGACCATCTCATCACAGCCTACCGGGCTCACGGCTTTACTTTCACCCGGGGCCTTTCCGTCCGAGAAATTCTCGCAGAGCTTACAGGACGAAAAGGAGGTTGTGCTAAAGGGAAAGGAGGATCGATGCACATGTATGCCAAGAACTTCTACGGGGGCAATGGCATCGTGGGAGCGCAGGTGCCCCTGGGCGCTGGGATTGCTCTAGCCTGTAAGTATAATGGAAAAGATGAGGTCTGCCTGACTTTATATGGCGATGGTGCTGCTAACCAGGGCCAGATATTCGAAGCTTACAACATGGCAGCTTTGTGGAAATTACCTTGTATTTTCATCTGTGAGAATAATCGCTATGGAATGGGAACGTCTGTTGAGAGAGCGGCAGCCAGCACTGATTACTACAAGAGAGGCGATTTCATTCCTGGGCTGAGAGTGGATGGAATGGATATCCTGTGCGTCCGAGAGGCAACAAGGTTTGCTGCTGCCTATTGTAGATCTGGGAAGGGGCCCATCCTGATGGAGCTGCAGACTTACCGTTACCACGGACACAGTATGAGTGACCCTGGAGTCAGTTACCGTACACGAGAAGAAATTCAGGAAGTAAGAAGTAAGAGTGACCCTATTATGCTTCTCAAGGACAGGATGGTGAACAGCAATCTTGCCAGTGTGGAAGAACTAAAGGAAATTGATGTGGAAGTGAGGAAGGAGATTGAGGATGCTGCCCAGTTTGCCACGGCCGATCCTGAGCCACCTTTGGAAGAGCTGGGCTACCACATCTACTCCAGCGACCCACCTTTTGAAGTTCGTGGTGCCAATCAGTGGATCAAGTTTAAGTCAGTCAGTTAAGGGGAGGAGAAGGAGAGGTTATACCTTCAGGGGGCTACCAGACAGTGTTCTCAACTTGGTTAAGGAGGAAGAAAACCCAGTCAATGAAATTCAATGAAATTCTTGGAAACTTCCATTAAGTGTGTAGATTGAGCAGGTAGTAATTGCATGCAGTTTGTACATTAGTGCATTAAAAGATGAATTATTGAGTGCTTAAAGATTATTTTTGACTTAAAATAGTATACTTTGAACAAATACTCTAATTATGAAAAGGAAGAACAATTCCTTGTATGCCTGTTTCCCCTGCCCCCAGCCACCTTTTTGGGAGGAGACCATTATGGCGGGGCCCCTCACAGCATTCTACCAACCATAGCACCCACCCCGAGCAGCGCTGGTGCTGCAGCCTGTTCGCGCTGACCATTTCTCTACAAGATACAATATTTATTATCAGGCAAGAGGACAGTTCCATTTTAAAATAAGACTTTTGTAATCATTCCAATTTTGTAATCATTTCAAAGGCCACATAACTTAGTTTTCTCTACTTACACATTCAGTATAAATATGAAGCTATTTTCTGTTCATATCAAACATTAACTACAAGGCACATTCGTATCAGTTTTGTGTTTCTCAAATTGAAGTACCATACCAGTTCTGAGGCAGTGTCCCAGCTTCCATGTTTGTTAAATACCCCTTGTTTGTTTCACCATTCCAGCAAGTGCTGAAGGGTGTACtttttttgagacagggtcgggctctgttgcccaggctggagtgcagtggtgtgatcatggctcactgcagcctccacacctcctgggctcaagcaatcctcccacctcagcctcctgcatagctgggactacaagtgAATTTCCTAATATTCCGGGAGGTCAAAACCAAGGCTCACTGTTTTCACAATACACACAGTTCTATGTTTATAAATAACAGGTTTCAAAAGAAACTCAGGACAGTATTTAAAACAAGTTCTTAAACTATTAATTGAACAATGGCATTTTTAAATATGTAAACACAGCGGAATTCGTGTATACACTAACAGAAGCTTTAACAAAACATGTAGCGTGGTGGGACACTCTGCCACAGCTTAGCTGATTGGTATCAAGCCTTGTCTTTGGTTTCTGAGGCCTCCTGAGCCCTTCTGTACTGGGAGACCGCACTCCAGAGTCTGCAGAGGAGACCACCCCTGGGAAACAAACACAGCTGTCTTCAGAGTCAGTGCTTCAAGCCAACAGAGCTTAAAACTGCAGTCCCTAATTTAAAAACCTAATGAAAATAAAAACATTCTcctcacatatggaggtgacgctcgtgtcccagcagtagtaggacatggccttagagGTACGTACCTGCAGAGAGCTGGCTATTTCAAATGACTCGGGAACAAGAAGGCAGGCTGCAGTTTAAAGAAGGGGGTGGGTCCAGCGTGCAGGCACGCTTGCCATGTGCCTCCACCCACTCCCAGCCAGGCATTAATGGCAGGAGATTGGCCAGCTCTTCTCTGTCACATTCCTATTTCTGACTTCTGCCTGGCTTTCAGTTTCTGCCCCACCTTGGCTTTTTCCCAGCTTGAACCTAATAGAACTCCAGAGTTTGGGGGGAGGCCCAGCCCTTTGTTTTCTGCTCTTGAAGCATATTCACACATAAAAAGTTGTATTCTCTTATACAAACTGTTTTGAGGCTCTTACCGTAGTCGAAGGTATCTTAGATCTTCCTTAGTGATCTCATTAAGAATATCCGAAAGTGTATAACCCTCTTCAACAATCTGAAACAAAGATCAGATCCTTAAGAGCTGAGCAGCTGTGTAACAACAGCATAAGAATTTCTTTGTTGTAAATTTACCTTTTCAATTGTCTTTGCATCAGCTCCTTGCAGCCGCAACCAGTCTATAAGCTCTTTATCTGTTCTCTGCCCGTAGGGGCCTGCTGGGTTCTCTGTAATACCTGTAACGATTGGCAATTTGTTATATATTAGTCTAACCATAAAACTCTTCAAAAGTAACCAGTTGGATTAATAAATGATTCCAGAATGTAAATGTGATGTGAAAAAGAGATGAATTAACCCTGTA

>NM_000284.4 

GGTGCGACTGAGGCGTGGCGTCTGCTGGGGCACCTGAAGGAGACTTGGGGGCACCCGCGTCGTGCCTCCTGGGTTGTGAGGAGTCGCCGCTGCCGCCACTGCCTGTGCTTCATGAGGAAGATGCTCGCCGCCGTCTCCCGCGTGCTGTCTGGCGCTTCTCAGAAGCCGGCAAGCAGAGTGCTGGTAGCATCCCGTAATTTTGCAAATGATGCTACATTTGAAATTAAGaaatgtgaccttcaccggctggaagaaggccctcctgtcacaacagtgctcaccagggaggatgggctcaaatactacaggatgatgCAGACTGTACGCCGAATGGAGTTGAAAGCAGATCAGCTGTATAAACAGAAAATTATTCGTGGTTTCTGTCACTTGTGTGATGGTCAGGAAGCTTGCTGTGTGGGCCTGGAGGCCGGCATCAACCCCACAGACCATCTCATCACAGCCTACCGGGCTCACGGCTTTACTTTCACCCGGGGCCTTTCCGTCCGAGAAATTCTCGCAGAGCTTACAGGACGAAAAGGAGGTTGTGCTAAAGGGAAAGGAGGATCGATGCACATGTATGCCAAGAACTTCTACGGGGGCAATGGCATCGTGGGAGCGCAGGTGCCCCTGGGCGCTGGGATTGCTCTAGCCTGTAAGTATAATGGAAAAGATGAGGTCTGCCTGACTTTATATGGCGATGGTGCTGCTAACCAGGGCCAGATATTCGAAGCTTACAACATGGCAGCTTTGTGGAAATTACCTTGTATTTTCATCTGTGAGAATAATCGCTATGGAATGGGAACGTCTGTTGAGAGAGCGGCAGCCAGCACTGATTACTACAAGAGAGGCGATTTCATTCCTGGGCTGAGAGTGGATGGAATGGATATCCTGTGCGTCCGAGAGGCAACAAGGTTTGCTGCTGCCTATTGTAGATCTGGGAAGGGGCCCATCCTGATGGAGCTGCAGACTTACCGTTACCACGGACACAGTATGAGTGACCCTGGAGTCAGTTACCGTACACGAGAAGAAATTCAGGAAGTAAGAAGTAAGAGTGACCCTATTATGCTTCTCAAGGACAGGATGGTGAACAGCAATCTTGCCAGTGTGGAAGAACTAAAGGAAATTGATGTGGAAGTGAGGAAGGAGATTGAGGATGCTGCCCAGTTTGCCACGGCCGATCCTGAGCCACCTTTGGAAGAGCTGGGCTACCACATCTACTCCAGCGACCCACCTTTTGAAGTTCGTGGTGCCAATCAGTGGATCAAGTTTAAGTCAGTCAGTTAAGGGGAGGAGAAGGAGAGGTTATACCTTCAGGGGGCTACCAGACAGTGTTCTCAACTTGGTTAAGGAGGAAGAAAACCCAGTCAATGAAATTCAATGAAATTCTTGGAAACTTCCATTAAGTGTGTAGATTGAGCAGGTAGTAATTGCATGCAGTTTGTACATTAGTGCATTAAAAGATGAATTATTGAGTGCTTAAAGATTATTTTTGACTTAAAATAGTATACTTTGAACAAATACTCTAATTATGAAAAGGAAGAACAATTCCTTGTATGCCTGTTTCCCCTGCCCCCAGCCACCTTTTTGGGAGGAGACCATTATGGCGGGGCCCCTCACAGCATTCTACCAACCATAGCACCCACCCCGAGCAGCGCTGGTGCTGCAGCCTGTTCGCGCTGACCATTTCTCTACAAGATACAATATTTATTATCAGGCAAGAGGACAGTTCCATTTTAAAATAAGACTTTTGTAATCATTCCAATTTTGTAATCATTTCAAAGGCCACATAACTTAGTTTTCTCTACTTACACATTCAGTATAAATATGAAGCTATTTTCTGTTCATATCAAACATTAACTACAAGGCACATTCGTATCAGTTTTGTGTTTCTCAAATTGAAGTACCATACCAGTTCTGAGGCAGTGTCCCAGCTTCCATGTTTGTTAAATACCCCTTGTTTGTTTCACCATTCCAGCAAGTGCTGAAGGGTGTACtttttttgagacagggtcgggctctgttgcccaggctggagtgcagtggtgtgatcatggctcactgcagcctccacacctcctgggctcaagcaatcctcccacctcagcctcctgcatagctgggactacaagtgAATTTCCTAATATTCCGGGAGGTCAAAACCAAGGCTCACTGTTTTCACAATACACACAGTTCTATGTTTATAAATAACAGGTTTCAAAAGAAACTCAGGACAGTATTTAAAACAAGTTCTTAAACTATTAATTGAACAATGGCATTTTTAAATATGTAAACACAGCGGAATTCGTGTATACACTAACAGAAGCTTTAACAAAACATGTAGCGTGGTGGGACACTCTGCCACAGCTTAGCTGATTGGTATCAAGCCTTGTCTTTGGTTTCTGAGGCCTCCTGAGCCCTTCTGTACTGGGAGACCGCACTCCAGAGTCTGCAGAGGAGACCACCCCTGGGAAACAAACACAGCTGTCTTCAGAGTCAGTGCTTCAAGCCAACAGAGCTTAAAACTGCAGTCCCTAATTTAAAAACCTAATGAAAATAAAAACATTCTcctcacatatggaggtgacgctcgtgtcccagcagtagtaggacatggccttagagGTACGTACCTGCAGAGAGCTGGCTATTTCAAATGACTCGGGAACAAGAAGGCAGGCTGCAGTTTAAAGAAGGGGGTGGGTCCAGCGTGCAGGCACGCTTGCCATGTGCCTCCACCCACTCCCAGCCAGGCATTAATGGCAGGAGATTGGCCAGCTCTTCTCTGTCACATTCCTATTTCTGACTTCTGCCTGGCTTTCAGTTTCTGCCCCACCTTGGCTTTTTCCCAGCTTGAACCTAATAGAACTCCAGAGTTTGGGGGGAGGCCCAGCCCTTTGTTTTCTGCTCTTGAAGCATATTCACACATAAAAAGTTGTATTCTCTTATACAAACTGTTTTGAGGCTCTTACCGTAGTCGAAGGTATCTTAGATCTTCCTTAGTGATCTCATTAAGAATATCCGAAAGTGTATAACCCTCTTCAACAATCTGAAACAAAGATCAGATCCTTAAGAGCTGAGCAGCTGTGTAACAACAGCATAAGAATTTCTTTGTTGTAAATTTACCTTTTCAATTGTCTTTGCATCAGCTCCTTGCAGCCGCAACCAGTCTATAAGCTCTTTATCTGTTCTCTGCCCGTAGGGGCCTGCTGGGTTCTCTGTAATACCTGTAACGATTGGCAATTTGTTATATATTAGTCTAACCATAAAACTCTTCAAAAGTAACCAGTTGGATTAATAAATGATTCCAGAATGTAAATGTGATGTGAAAAAGAGATGAATTAACCCTGTA

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