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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name ATP5F1CP1
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Plot displaying the genomic locations of a retrocopy (in chr14) and its respective parental gene (in chr10). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr14:53990930-53992023  UCSC
Coordinates (T2T) chr14:48199134-48200227  UCSC
Coordinates (hg19) chr14:54457648-54458741  UCSC
Strand -
Parental Sequence NM_001001973.3
Parental seq. overlap 1018 bp
Parental seq. overlap (%) 92.5%
Genomic Region Intergenic
Retrocopy Summary ATP5F1CP1, located on chr14:53990930-53992023, is a retrocopy of the parental gene ATP5F1C. 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 ATP5F1C
Full Name ATP synthase F1 subunit gamma
Also known as ATP5C|ATP5C1|ATP5CL1
Coordinate chr10:7788159-7807801
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 consists of three main subunits (a, b, c). This gene encodes the gamma subunit of the catalytic core. Alternatively spliced transcript variants encoding different isoforms have been identified. This gene also has a pseudogene on chromosome 14. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes ATP5F1CP1
Bonobo Pan paniscus ATP5F1CP1
Gorilla Gorilla gorilla ATP5F1CP1
Orangutan Pongo abelii ATP5F1CP1
Gibbon Nomascus leucogenys ATP5F1CP1
Green monkey Chlorocebus sabaeus ATP5C1P1
Crab-eating macaque Macaca fascicularis ATP5C1P1
Rhesus Macaca mulatta ATP5F1CP1
Baboon Papio anubis ATP5F1CP1
Golden snub-nosed monkey Rhinopithecus roxellana ATP5F1CP1
Marmoset Callithrix jacchus ATP5F1CP5
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)

Adipose SubcutaneousMuscle SkeletalArtery TibialArtery CoronaryHeart Atrial AppendageAdipose VisceralUterusVaginaBreast Mammary TissueSkin Not Sun ExposedMinor Salivary GlandBrain CortexAdrenal GlandThyroidLungSpleenPancreasEsophagus MuscularisEsophagus MucosaEsophagus Gastroesophageal JunctionStomachColon SigmoidSmall Intestine Terminal IleumColon TransverseProstateTestisNerve TibialSkin Sun ExposedHeart Left VentricleBrain CerebellumWhole BloodArtery AortaPituitaryBrain Frontal CortexBrain CaudateBrain Nucleus AccumbensBrain PutamenBrain HypothalamusBrain Spinal CordBrain HippocampusBrain Anterior Cingulate CortexOvaryBrain Cerebellar HemisphereLiverBrain Substantia NigraKidney CortexBrain AmygdalaCervix EctocervixFallopian TubeCervix EndocervixBladderKidney Medulla00.10.20.30.4
log10(TPM+1)

Related Sequence

>ATP5F1CP1
ACCGACTTTCAGCAGGGCTGCGGCTACCATGTTCTCTCATGCGGGCATCACTGGGCTGTTGGCCTGGACCTTGCAGCCACAATGGATTCAAGTTCGAAATACAGCAACTTCGAAAGATGTTACCAAGCGACTAAAGTCCATCAAAAACATCCAGAAAATTACCAAGTCTATGCAAATGGTAGCAGCAGCAAAATACGCCCAAGCTGAGAGAGAGCTGAAACCAGCTTGAATATATGGATTGGGATCTTTGGCTCTGGAGAAAAAGCTGGTATCAAGGTGCCTGAAGACAACAAGAAACACCTCCTTATTGGTGTGTCCTCAGATCGAGGACTGTGTGGCGCTATTCATTCCTCCATTGCTAAACAGATGAAAAGCGAGGTTGCTACACTAACAGCAGCTGGGAAAGAAGTTATGCTTGTTGGAATTGGTGACAAAATCAGGGGCGTACTTTACAGGATGCATTCTGACCAGTTTCTGGTGGCATTAAAAGAAGTGAGAAGAAATCCCCCTGCTTTTGGAAATGTGTCAGTCATTGCCCTTGAATTACTAAATTCTGGATATGAATTTGATGAAGGCTCCATCATCTTTAATCAGTTCAAGTCTGTCATCTCGTATAAGACTGAAGAAAAGCCCATCTTTTTCCTTAATACCATTGCAAGTGCCGAGAGCATGAGTATCTACTATAATATTGATGCTGAGGTGCTGCAAAATTACCAGGAATACAGTCTGGCCAACAGCATCTACTACTCTCTGAAGGAGTCCACCACTAGTGAGCAGAGTGCCAGGATGACAGCCATGGACAACACCAGCAAGAATGCCTCTGAGATGATTGACAAATTGACATTGACATTCAACTGTACCCGCCAAGCTGTCATCACAAAAGAGTTGACTGAAATTATCTTTGGTGCTGTAGCTCTGGATTAATGAAAATCAAGTTCCATCCTCAGACAAGGGGTAAAGAAGGAAAATTCAGCCAGCTGATTTTGTTTTTAGCTTACTGTTGTCTTTGTCAGAAGAAAGTGTTCCTCCATTGTTTTAATTACTGAAGACAGCAAGATAAGTGTAAATTATTTTACAATAAACAACTTAAAATC
>NM_001001973.3
CTGACCGACCTTCAGCAGGGCTGTGGCTACCATGTTCTCTCGCGCGGGTGTCGCTGGGCTGTCGGCCTGGACCTTGCAGCCGCAATGGATTCAAGTTCGAAATATGGCAACTTTGAAAGATATCACCAGGAGACTAAAGTCCATCAAAAACATCCAGAAAATTACCAAGTCTATGAAAATGGTAGCGGCAGCAAAATATGCCCGAGCTGAGAGAGAGCTGAAACCAGCTCGAATATATGGATTGGGATCTTTAGCTCTGTATGAAAAAGCTGATATCAAGGGGCCTGAAGACAAGAAGAAACACCTCCTTATTGGTGTGTCCTCAGATCGAGGACTGTGTGGTGCTATTCATTCCTCCATTGCTAAACAGATGAAAAGCGAGGTTGCTACACTAACAGCAGCTGGGAAAGAAGTTATGCTTGTTGGAATTGGTGACAAAATCAGAGGCATACTTTATAGGACTCATTCTGACCAGTTTCTGGTGGCATTCAAAGAAGTGGGAAGAAAGCCCCCCACTTTTGGAGATGCGTCAGTCATTGCCCTTGAATTACTAAATTCTGGATATGAATTTGATGAAGGCTCCATCATCTTTAATAAATTCAGGTCTGTCATCTCCTATAAGACAGAAGAAAAGCCCATCTTTTCCCTTAATACCGTTGCAAGTGCTGACAGCATGAGTATCTATGACGATATTGATGCTGACGTGCTGCAAAATTACCAAGAATACAATCTGGCCAACATCATCTACTACTCTCTGAAGGAGTCCACCACTAGTGAGCAGAGTGCCAGGATGACAGCCATGGACAATGCCAGCAAGAATGCTTCTGAGATGATTGACAAATTGACATTGACATTCAACCGTACCCGCCAAGCTGTCATCACAAAAGAGTTGATTGAAATTATCTCTGGTGCTGCAGCTCTGGATTAATGAAAATCAAGTTCCATCCTCAGACAAGAGGTAAAGAAGGAAAATTCAGCCAGTTGATTTTGTTTTTAGCTTACTGCTGCCTTTGTCCGAAGAAACTGTTCCTCCATTATTTGAATTACTGAAGACAGCAAGATATTTGTAAATTATCTTAAAATAAACAACTTAAAATAAAA

Publications

PMID - Link Title
23259602Genome-wide association scan of dental caries in the permanent dentition.
8168843Chromosomal localization of genes required for the terminal steps of oxidative metabolism: alpha and gamma subunits of ATP synthase and the phosphate carrier.