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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name PSMC5P2
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Plot displaying the genomic locations of a retrocopy (in chr18) and its respective parental gene (in chr17). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr18:63415314-63415560  UCSC
Coordinates (T2T) chr18:63620355-63620601  UCSC
Coordinates (hg19) chr18:61082547-61082793  UCSC
Strand -
Parental Sequence NM_001199163.2
Parental seq. overlap 217 bp
Parental seq. overlap (%) 15%
Genomic Region Intragenic (VPS4B)
Retrocopy Summary PSMC5P2, located on chr18:63415314-63415560, 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 PSMC5P2
Bonobo Pan paniscus PSMC5P2
Orangutan Pongo abelii PSMC5P2
Gibbon Nomascus leucogenys PSMC5P1
Green monkey Chlorocebus sabaeus PSMC5P1
Baboon Papio anubis PSMC5P2
Golden snub-nosed monkey Rhinopithecus roxellana PSMC5P2
Gorilla Gorilla gorilla Without Homology
Crab-eating macaque Macaca fascicularis Without Homology
Rhesus Macaca mulatta 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

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 Medulla00.51
log10(TPM+1)

Related Sequence

>PSMC5P2
GCTGGACATTTTGAAGATCCATTCTCTGAAAAGGAACCTGACCCAGGGGATCAACCAGAGAAAAATTGCCAAGCTTATGCCAGGAGCATCAGGGGCTGAAGTGAAAGTCATATACAGAGAAAGCAGCATATATGCCCTGAGGGAACGGCGAGTGCATGTCACCCAGGAGGACTTTGAGATAGCAGTAGCCAGCGTCATGCAGAAGGATAGAGAGTAAAACATGTCCATCAAGAAACTATGGAAGTGC
>NM_001199163.2
AGAAGCGGAGTGAGTGAGGGAAGCGATGGGCGCGGGAATGGCCGGCCCACGGGTCGCAGGAGACGGGACGCCAGTCCTTTGGCTCCGTTCCGCTGGCTCCTTCGTCAGTACTGACACCTCGGGCTTGTAGAGCACTTCACGCAGTGCAAAGCGCCCCCCGTCTATATCATATCGCCTCTCGGTCCTCCTAAAAGTCGTATGAGATGGAGCTGGAGGAGGGGAAGGCAGGCAGCGGACTCCGCCAATATTATCTGTCCAAGATTGAAGAACTCCAGCTGATTGTGAATGATAAGAGCCAAAACCTCCGGAGGCTGCAGGCACAGAGGAACGAACTAAATGCTAAAGTTCGCCTATTGCGGGAGGAGCTACAGCTGCTGCAGGAGCAGGGCTCCTATGTGGGGGAAGTAGTCCGGGCCATGGATAAGAAGAAAGTGTTGGTCAAGGTACATCCTGAAGGTAAATTTGTTGTAGACGTGGACAAAAACATTGACATCAATGATGTGACACCCAATTGCCGGGTGGCTCTAAGGAATGACAGCTACACTCTGCACAAGATCCTGCCCAACAAGGTAGACCCATTAGTGTCACTGATGATGGTGGAGAAAGTACCAGATTCAACTTATGAGATGATTGGTGGACTGGACAAACAGATCAAGGAGATCAAAGAAGTGATCGAGCTGCCTGTTAAGCATCCTGAGCTCTTCGAAGCACTGGGCATTGCTCAGCCCAAGGGAGTGCTGCTGTATGGACCTCCAGGCACTGGGAAGACACTGTTGGCCCGGGCTGTGGCTCATCATACGGACTGTACCTTTATTCGTGTCTCTGGCTCTGAACTGGTACAGAAATTCATAGGGGAAGGGGCAAGAATGGTGAGGGAGCTGTTTGTCATGGCACGGGAACATGCTCCATCTATCATCTTCATGGACGAAATCGACTCCATCGGCTCCTCGCGGCTGGAGGGGGGTTCTGGAGGGGACAGTGAAGTGCAGCGCACGATGCTGGAGTTGCTCAACCAGCTCGACGGCTTTGAGGCCACCAAGAACATCAAGGTTATCATGGCTACTAATAGGATTGATATCCTGGACTCGGCACTGCTTCGCCCAGGGCGCATTGACAGAAAAATTGAATTCCCACCCCCCAATGAGGAGGCCCGGCTGGACATTTTGAAGATTCATTCTCGGAAGATGAACCTGACCCGGGGGATCAACCTGAGAAAAATTGCTGAGCTCATGCCAGGAGCATCAGGGGCTGAAGTGAAGGGCGTGTGCACAGAAGCTGGCATGTATGCCCTGCGAGAACGGCGAGTCCATGTCACTCAGGAGGACTTTGAGATGGCAGTAGCCAAGGTCATGCAGAAGGACAGTGAGAAAAACATGTCCATCAAGAAATTATGGAAGTGAGTGGACAGCCTTTGTGTGTATCTCTCCAATAAAGCTCTGTGGGCCAAGTC

Publications

PMID - Link Title
No publications available for this retrocopy