RCPedia: Rtcs

Summary

Retrocopy Name	PSMB3P3	Plot displaying the genomic locations of a retrocopy (in chr15) and its respective parental gene (in chr17). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr15:45610649-45610812 UCSC
Coordinates (T2T)	chr15:43418811-43418974 UCSC
Coordinates (hg19)	chr15:45902847-45903010 UCSC
Strand	-
Parental Sequence	NM_002795.4_2
Parental seq. overlap	151 bp
Parental seq. overlap (%)	19.8%
Genomic Region	Intergenic
Retrocopy Summary	PSMB3P3, located on chr15:45610649-45610812, is a retrocopy of the parental gene PSMB3. 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	PSMB3
Full Name	proteasome 20S subunit beta 3
Also known as	HC10-II
Coordinate	chr17:38752741-38764225
Strand	+
Gene summary	The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure 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. 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 a member of the proteasome B-type family, also known as the T1B family, that is a 20S core beta subunit. The 26 S proteasome may be involved in trinucleotide repeat expansion, a phenomenon which is associated with many hereditary neurological diseases. Pseudogenes have been identified on chromosomes 2 and 12. Alternative splicing results in multiple transcript variants [provided by RefSeq, Sep 2013]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	PSMB3P3
Bonobo	Pan paniscus	PSMB3P3
Gorilla	Gorilla gorilla	PSMB3P3
Orangutan	Pongo abelii	PSMB3P3
Gibbon	Nomascus leucogenys	PSMB3P1
Green monkey	Chlorocebus sabaeus	PSMB3P2
Crab-eating macaque	Macaca fascicularis	PSMB3P1
Rhesus	Macaca mulatta	PSMB3P1
Baboon	Papio anubis	PSMB3P1
Golden snub-nosed monkey	Rhinopithecus roxellana	PSMB3P1
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

Related Sequence

>PSMB3P3
CATCTCTCAAGCCATGCTGGATGCTGCGGACCAGGATGCAGTGTCAGACATGGGAGTTATTGTCCACATCATTGAAAAGGACAAAATCACCACCAGGATTGAAGGCCTGAATGGACTAACCCTGTTCGCAGAGCCCACTTTTTTTTTTTTAATAAAATAGCCTT

>NM_002795.4_2
AGCAGTGAGAGCGGTTGCGCAGTGAAGGCTAGACCCGGTTTACTGGAATTGCTCTGGCGATCGAGGGATCCTAGTACACCGCAATCATGTCTATTATGTCCTATAACGGAGGGGCCGTCATGGCCATGAAGGGGAAGAACTGTGTGGCCATCGCTGCAGACAGGCGCTTCGGGATCCAGGCCCAGATGGTGACCACGGACTTCCAGAAGATCTTTCCCATGGGTGACCGGCTGTACATCGGTCTGGCCGGGCTCGCCACTGACGTCCAGACAGTTGCCCAGCGCCTCAAGTTCCGGCTGAACCTGTATGAGTTGAAGGAAGGTCGGCAGATCAAACCTTATACCCTCATGAGCATGGTGGCCAACCTCTTGTATGAGAAACGGTTTGGCCCTTACTACACTGAGCCAGTCATTGCCGGGTTGGACCCGAAGACCTTTAAGCCCTTCATTTGCTCTCTAGACCTCATCGGCTGCCCCATGGTGACTGATGACTTTGTGGTCAGTGGCACCTGCGCCGAACAAATGTACGGAATGTGTGAGTCCCTCTGGGAGCCCAACATGGATCCGGATCACCTGTTTGAAACCATCTCCCAAGCCATGCTGAATGCTGTGGACCGGGATGCAGTGTCAGGCATGGGAGTCATTGTCCACATCATCGAGAAGGACAAAATCACCACCAGGACACTGAAGGCCCGAATGGACTAACCCTGTTCCCAGAGCCCACTTTTTTTTCTTTTTTTGAAATAAAATAGCCTGTCTTTCA

>NM_002795.4_2 

AGCAGTGAGAGCGGTTGCGCAGTGAAGGCTAGACCCGGTTTACTGGAATTGCTCTGGCGATCGAGGGATCCTAGTACACCGCAATCATGTCTATTATGTCCTATAACGGAGGGGCCGTCATGGCCATGAAGGGGAAGAACTGTGTGGCCATCGCTGCAGACAGGCGCTTCGGGATCCAGGCCCAGATGGTGACCACGGACTTCCAGAAGATCTTTCCCATGGGTGACCGGCTGTACATCGGTCTGGCCGGGCTCGCCACTGACGTCCAGACAGTTGCCCAGCGCCTCAAGTTCCGGCTGAACCTGTATGAGTTGAAGGAAGGTCGGCAGATCAAACCTTATACCCTCATGAGCATGGTGGCCAACCTCTTGTATGAGAAACGGTTTGGCCCTTACTACACTGAGCCAGTCATTGCCGGGTTGGACCCGAAGACCTTTAAGCCCTTCATTTGCTCTCTAGACCTCATCGGCTGCCCCATGGTGACTGATGACTTTGTGGTCAGTGGCACCTGCGCCGAACAAATGTACGGAATGTGTGAGTCCCTCTGGGAGCCCAACATGGATCCGGATCACCTGTTTGAAACCATCTCCCAAGCCATGCTGAATGCTGTGGACCGGGATGCAGTGTCAGGCATGGGAGTCATTGTCCACATCATCGAGAAGGACAAAATCACCACCAGGACACTGAAGGCCCGAATGGACTAACCCTGTTCCCAGAGCCCACTTTTTTTTCTTTTTTTGAAATAAAATAGCCTGTCTTTCA

Publications

PMID - Link	Title