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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name PSMC5P1
Plot displaying the genomic locations of a retrocopy (in chr7) and its respective parental gene (in chr17). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr7:30372368-30372671  UCSC
Coordinates (T2T) chr7:30510065-30510368  UCSC
Coordinates (hg19) chr7:30411984-30412287  UCSC
Strand +
Parental Sequence NM_002805.6
Parental seq. overlap 279 bp
Parental seq. overlap (%) 20.9%
Genomic Region Intergenic
Retrocopy Summary PSMC5P1, located on chr7:30372368-30372671, is a retrocopy of the parental gene PSMC5. 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 PSMC5
Full Name proteasome 26S subunit, ATPase 5
Also known as RPT6|S8|SUG-1|SUG1|TBP10|TRIP1|p45|p45/SUG
Coordinate chr17:63827431-63832019
Strand +
Gene summary The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes one of the ATPase subunits, a member of the triple-A family of ATPases which have a chaperone-like activity. In addition to participation in proteasome functions, this subunit may participate in transcriptional regulation since it has been shown to interact with the thyroid hormone receptor and retinoid X receptor-alpha. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes PSMC5P1
Bonobo Pan paniscus PSMC5P1
Gorilla Gorilla gorilla PSMC5P1
Orangutan Pongo abelii PSMC5P1
Gibbon Nomascus leucogenys PSMC5P2
Green monkey Chlorocebus sabaeus PSMC5P2
Crab-eating macaque Macaca fascicularis PSMC5P1
Rhesus Macaca mulatta PSMC5P1
Baboon Papio anubis PSMC5P1
Golden snub-nosed monkey Rhinopithecus roxellana PSMC5P1
Marmoset Callithrix jacchus PSMC5P1
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

>PSMC5P1
TGGCTTTGAGGCCACCAAGAGTATCACGGTTTATCACGGCTGCTAATACGATTGATATCCTGGACTCGGCACTGCTTTGCCCAGGGCACATTGACAGAAAAATTGAATTCCCAACCTGCAATGAGTAGGCCTGGCTGGTCACTTTGAAGATTCATTCTCAGAAATGAACCTGACCCAGGGGATCAACCTGAGAAAAATTGCTGAGCTTATGCCAGGAGCATCAGGCTGAAGTGAAGGGCATGTGCACAGAAACCGGCATGTATGCCCTGAGTAGCGAGTCCATGTCACTCAGAAGGACTTTGAG
>NM_002805.6
GCTTCCGCGCTTGCGCGCCAAGACGGCTCGGATGCCGGCGGTCTCTGCTGAAGAGAGAAGATGGCGCTTGACGGACCAGAGCAGATGGAGCTGGAGGAGGGGAAGGCAGGCAGCGGACTCCGCCAATATTATCTGTCCAAGATTGAAGAACTCCAGCTGATTGTGAATGATAAGAGCCAAAACCTCCGGAGGCTGCAGGCACAGAGGAACGAACTAAATGCTAAAGTTCGCCTATTGCGGGAGGAGCTACAGCTGCTGCAGGAGCAGGGCTCCTATGTGGGGGAAGTAGTCCGGGCCATGGATAAGAAGAAAGTGTTGGTCAAGGTACATCCTGAAGGTAAATTTGTTGTAGACGTGGACAAAAACATTGACATCAATGATGTGACACCCAATTGCCGGGTGGCTCTAAGGAATGACAGCTACACTCTGCACAAGATCCTGCCCAACAAGGTAGACCCATTAGTGTCACTGATGATGGTGGAGAAAGTACCAGATTCAACTTATGAGATGATTGGTGGACTGGACAAACAGATCAAGGAGATCAAAGAAGTGATCGAGCTGCCTGTTAAGCATCCTGAGCTCTTCGAAGCACTGGGCATTGCTCAGCCCAAGGGAGTGCTGCTGTATGGACCTCCAGGCACTGGGAAGACACTGTTGGCCCGGGCTGTGGCTCATCATACGGACTGTACCTTTATTCGTGTCTCTGGCTCTGAACTGGTACAGAAATTCATAGGGGAAGGGGCAAGAATGGTGAGGGAGCTGTTTGTCATGGCACGGGAACATGCTCCATCTATCATCTTCATGGACGAAATCGACTCCATCGGCTCCTCGCGGCTGGAGGGGGGTTCTGGAGGGGACAGTGAAGTGCAGCGCACGATGCTGGAGTTGCTCAACCAGCTCGACGGCTTTGAGGCCACCAAGAACATCAAGGTTATCATGGCTACTAATAGGATTGATATCCTGGACTCGGCACTGCTTCGCCCAGGGCGCATTGACAGAAAAATTGAATTCCCACCCCCCAATGAGGAGGCCCGGCTGGACATTTTGAAGATTCATTCTCGGAAGATGAACCTGACCCGGGGGATCAACCTGAGAAAAATTGCTGAGCTCATGCCAGGAGCATCAGGGGCTGAAGTGAAGGGCGTGTGCACAGAAGCTGGCATGTATGCCCTGCGAGAACGGCGAGTCCATGTCACTCAGGAGGACTTTGAGATGGCAGTAGCCAAGGTCATGCAGAAGGACAGTGAGAAAAACATGTCCATCAAGAAATTATGGAAGTGAGTGGACAGCCTTTGTGTGTATCTCTCCAATAAAGCTCTGTGGGCCAAGTC

Publications

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