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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name GCSHP7
Plot displaying the genomic locations of a retrocopy (in chr3) and its respective parental gene (in chr16). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr3:49252129-49252275  UCSC
Coordinates (T2T) chr3:49280210-49280356  UCSC
Coordinates (hg19) chr3:49289562-49289708  UCSC
Strand -
Parental Sequence NM_004483.5
Parental seq. overlap 133 bp
Parental seq. overlap (%) 8.5%
Genomic Region Intragenic (IHO1)
Retrocopy Summary GCSHP7, located on chr3:49252129-49252275, is a retrocopy of the parental gene GCSH. 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 GCSH
Full Name glycine cleavage system protein H
Also known as GCE|NKH
Coordinate chr16:81081945-81096395
Strand -
Gene summary Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase). The protein encoded by this gene is the H protein, which transfers the methylamine group of glycine from the P protein to the T protein. Defects in this gene are a cause of nonketotic hyperglycinemia (NKH). Two transcript variants, one protein-coding and the other probably not protein-coding,have been found for this gene. Also, several transcribed and non-transcribed pseudogenes of this gene exist throughout the genome.[provided by RefSeq, Jan 2010]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes GCSHP3
Bonobo Pan paniscus GCSHP4
Gorilla Gorilla gorilla GCSHP3
Orangutan Pongo abelii GCSHP3
Green monkey Chlorocebus sabaeus GCSHP9
Crab-eating macaque Macaca fascicularis GCSHP2
Rhesus Macaca mulatta GCSHP2
Baboon Papio anubis GCSHP4
Marmoset Callithrix jacchus GCSHP10
Gibbon Nomascus leucogenys Without Homology
Golden snub-nosed monkey Rhinopithecus roxellana 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

>GCSHP7
GTAAATTCACAAACACTAATGGATAACAACAGAAAATGGCATGAAAACAGTAGGAATCAGCAATTTTGCACAGGAAGTTTTGGGAAATGTTTACTGTAGTCTCCCTGCAGTTGGGAAAAAATTGAACAAACAAGATGAATTTGGTg
>NM_004483.5
ACCGCCTCCGCGCCTCCATCCAGCCGGCTCCCTCCGGCCGCGAACTGCCCCTCCCCGCCCCGCCTCCCGGCGCGGGTGGCCGAGGCGTAGCGCTGCGACCCCCGCACCCCTGCGAACATGGCGCTGCGAGTGGTGCGGAGCGTGCGGGCCCTGCTCTGCACCCTGCGCGCGGTCCCGTCACCCGCCGCGCCCTGCCCGCCGAGGCCCTGGCAGCTGGGGGTGGGCGCCGTCCGTACGCTGCGCACTGGACCCGCTCTGCTCTCGGTGCGTAAATTCACAGAGAAACACGAATGGGTAACAACAGAAAATGGCATTGGAACAGTGGGAATCAGCAATTTTGCACAGGAAGCGTTGGGAGATGTTGTTTATTGTAGTCTCCCTGAAGTTGGGACAAAATTGAACAAACAAGATGAGTTTGGTGCTTTGGAAAGTGTGAAAGCTGCTAGTGAACTCTATTCTCCTTTATCAGGAGAAGTAACTGAAATTAATGAAGCTCTTGCAGAAAATCCAGGACTTGTAAACAAATCTTGTTATGAAGATGGTTGGCTGATCAAGATGACACTGAGTAACCCTTCAGAACTAGATGAACTTATGAGTGAAGAAGCATATGAGAAATACATAAAATCTATTGAGGAGTGAAAATGGAACTCCTAAATAAACTAGTATGAAATAACGCAAGCCAGCAGAGTTGTCTTAAATTAGTGGTGGATAGAAGACTTAGAATAGAAACTTTTAGTATTACCGATGGGGAAAAAAAAACTACTGTTAACACTGCTAATGAAAGAAAATGCCCTTTAACTTTCTAATGATTATAGATAAATATAATATGCGTCTTTTTCACAATATCCTATGATTTTTAGACTAGGCTCTAGTGTTCAGAATTCATGAAATTATCCATGGTAAAAACTAGTTATAAAAATTACATAATTCAAAGATAACATTGTTATTCTTAAGCCTTATATAATATTGTAACTTGCATGTATCCATACCTGGATTTGGGATGAAATACTTAATGATCTTTCCATTGGAAATAACTGGAAGTGAAGAGGTTTTGTTGCTTGTACAGTGTCAGATGAGGAACACCACTATCTTAATTTTGCGATACACTGCATTTGCTGGTGCTATTTTTATACAGTGAAGCAACAGCTTTGCAGCAAAATAATAAAATACTTCTTCGTTAATCATGTTTGTTTTGATGTTAATATTTCATTTAGTAACTCTGCTAGTATTTGTGAAAGTGCTAACTTTAACTTACGGAAAGTTACTTTTTAAAAGGAAATTTAAGCCAGAACAATGCAAAGCTCCAAGAAAATGTTTTCTTTAGTCACAAATCTGGTTTTTCTTAAGCCAAGATCTGTCACCTTTAACATAATAAAAAATAAATCACCAACTTTGATTTTCTATCATGCGAGGTCTGAAGAAAGAAGAGGAAAGACAGAGGAAGGTGGAAGTTTTGATCAGTATAGCACATGGTGTTTTTAAGTTGTTAAACCACGTTCAGGTTTCCACTTAAGTCATGGGAATAAAAGTGGACAAGGACTGAAGCTTTATGAGCTCAGA

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