RCPedia: Rtcs

Summary

Retrocopy Name	UBBP2	Plot displaying the genomic locations of a retrocopy (in chr1) and its respective parental gene (in chr19). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr1:217850425-217850633 UCSC
Coordinates (T2T)	chr1:217091222-217091431 UCSC
Coordinates (hg19)	chr1:218023767-218023975 UCSC
Strand	-
Parental Sequence	NM_003333.5
Parental seq. overlap	174 bp
Parental seq. overlap (%)	6.2%
Genomic Region	Intragenic (SPATA17)
Retrocopy Summary	UBBP2, located on chr1:217850425-217850633, is a retrocopy of the parental gene UBA52. 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	UBA52
Full Name	ubiquitin A-52 residue ribosomal protein fusion product 1
Also known as	CEP52\|HUBCEP52\|L40\|RPL40
Coordinate	chr19:18563766-18577550
Strand	+
Gene summary	Ubiquitin is a highly conserved nuclear and cytoplasmic protein that has a major role in targeting cellular proteins for degradation by the 26S proteosome. It is also involved in the maintenance of chromatin structure, the regulation of gene expression, and the stress response. Ubiquitin is synthesized as a precursor protein consisting of either polyubiquitin chains or a single ubiquitin moiety fused to an unrelated protein. This gene encodes a fusion protein consisting of ubiquitin at the N terminus and ribosomal protein L40 at the C terminus, a C-terminal extension protein (CEP). Multiple processed pseudogenes derived from this gene are present in the genome. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	UBBP1
Bonobo	Pan paniscus	UBA52P1
Gorilla	Gorilla gorilla	RPS27AP3
Orangutan	Pongo abelii	LOC100451913P1
Gibbon	Nomascus leucogenys	UBBP1
Green monkey	Chlorocebus sabaeus	UBA52P12
Crab-eating macaque	Macaca fascicularis	UBA52P2
Rhesus	Macaca mulatta	UBA52P2
Baboon	Papio anubis	LOC100998924P1
Golden snub-nosed monkey	Rhinopithecus roxellana	UBA52P8
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

>UBBP2
ATGCAGATCTTCGTGAAGACCCTGACTGGCAAGACCATCACCCTTGAAGTGGAGCCCAGTGACACCATCGAAAATGTGAAGGCCAATATCCAGGATAAGGAAGGCATCCTCCCCGACCAGCAGAGGCTCATCTTTGCAGGCATGCAGCTAGAAGAGGCTGTACTCTTTCTGACTACAACATCCAGAAAGAGTTGACCCTGTACCTGGTC

>NM_003333.5
CTTCTTTTTCTTCAGCGAGGCGGCCGAGCTGACGCAAACATGCAGATCTTTGTGAAGACCCTCACTGGCAAAACCATCACCCTTGAGGTCGAGCCCAGTGACACCATTGAGAATGTCAAAGCCAAAATTCAAGACAAGGAGGGTATCCCACCTGACCAGCAGCGTCTGATATTTGCCGGCAAACAGCTGGAGGATGGCCGCACTCTCTCAGACTACAACATCCAGAAAGAGTCCACCCTGCACCTGGTGTTGCGCCTGCGAGGTGGCATTATTGAGCCTTCTCTCCGCCAGCTTGCCCAGAAATACAACTGCGACAAGATGATCTGCCGCAAGTGCTATGCTCGCCTTCACCCTCGTGCTGTCAACTGCCGCAAGAAGAAGTGTGGTCACACCAACAACCTGCGTCCCAAGAAGAAGGTCAAATAAGGTGGTTCTTTCCTTGAAGGGCAGCCTCCTGCCCAGGCCCCGTGGCCCTGGAGCCTCAATAAAGTGTCCCTTTCATTGACTGGAGCAGCAATTGGTGTCCTCATGGCTGATCTGTCCAGGGAGGTGGCTGAAGAGTGGGCATCTCCCTTAGGGACTCTACTCAGCACTCCATTCTGTGCCACCTGTGGGGTCTTCTGTCCTAGATTCTGTCACATCGGCATTGGTCCCTGCCCTATGCCCCTGACTCTGGATTTGTCATCTGTAAAACTGGAGTAAAAACCTCAGTCGTGTAATTGGTGGGACTGAGGATCAGTTTTGTCATTGCTGGGATCCTGTCAGGCACTTTGAGGTGTCCCTCAGGCCTTGGCCCTGAAGTGTCTAGGTGTGTGGAGATGGGTAGAAAATTAGGTACACCCAATGGTGTAGAACGTTGATTCTCAAAtttttttattttatacaaatggggtctcactatgttgtccaggctggtcttgaactcctgggctcaagccatccgcccatctcagcccctcaaagtgttgggattacaagcaagaactgccatgcctgaccCAGTTCTCAgttttttgtttgtttgtttgtttgtttgttttgagacggagtcttgctctgtcgcccaggctggagtgcagtggcgcagtctcggcttactacaacctctgcctccggggttcacatccttctcctgcctcagcctcccgagtagctgggactacaggtgcccgccacaactcctggctaattttttgtatttttagtagagacggggtttcactgggttagccaggttggtctcgatctcctgaccttgtgatccattcgccttggcctcccagaatgctggtattacaggcgtgagccagcacgcctggccCAGTTACTCAGTTTTGAATCTGAGGCCGTGACATCACTCATGGTCTGCAGTCAGTGCTCTGCCCCTGAGCTGTACCCTCTCCTATGATAATCACTCTTAAGAAGGGCAACCCTTGGTGTTTTCCCCTTAAGgtcacccaggctggaatgcagtggtgtggtcatggctccctgtaccctggaactcaggcttgggtgatcctctctcctttgcctccgaagtagccaggactacaggtgtgcacccaccaccacactcagataattgctttggtgtttttAAAGCTTGTAATGATCAGTAGGCTGAGGTGGGCAAATCATAAGGTCAAGAGTTTTTTAGATGGGGTGAGCACAGACCAATTCCTGTTTTATTTACTGATTTAAAAttttgagacagtctcactgtcacccaggttggggtgcagtggtaggatcatagcttgctgcagccttgatctcccaggatcttgcctcagcctcccgagtagctgggactgcatgcttgtgccaccacactcggttaatattttgtagagatggggtcttgctatgttgcccaggctggcttcaaactcctgaacttaaAAGCCTCCTGTTTAGTTTTGGttttttatcactttttttttttttttttgagatggagccttgctcccatcgtgcaggctggagtgcggtggcgcagtctcggctcactgcagcttctgcctctcgggttcaagcgattctcctttctcagcctcttgagtagctggaattaccagtgtgcgccaccaccaccacgcctggctagtttttctgtttttagtagagacagggttttgctatgttggccaggctggtcttgaactactgacctcttgtgatctacctgtcttggccttccaaagtgctaggattacaagcgtaagccacagcgcctggccTTGCTACATTTTTTTttttttttttttttttacagacatggtctcgctatgttgcccagaatggttttgcactgggtccaagcagttctgccgcagcctcccaaagtgctgggattacaggggtgaggcaccTTGCTGGCCCCTGTTTTGATTAGGGTGCAGTGCTGGTGAAGCCGGTGCACGAGGCCAGTGATGCATCCTAATGAGGGGTGGAGTTGGCGGGACTTCCTGGGCCAGTTTGGGGACTTTCACAAAAGACCCCCATGACTCAGGGTTTTGAGTTCTTAACTGATCGAATGAaggattcaaaattaaccactccaaggggggattgaaggaagaaccactcttaatggacaaaaagaaagaaaggggagggagtaacagggatatgagctctagccgcccaagctagcaatggcaacccttctgggtccccttccagcatgtggaagctttcctttcgcttcattcaataaacagctgctgctcactctcctggtccgtggactctttttgaactgttaacactccccgcaaaggtccgcagcttcattcttcaaagttagcgagaccaggaacc

>NM_003333.5 

CTTCTTTTTCTTCAGCGAGGCGGCCGAGCTGACGCAAACATGCAGATCTTTGTGAAGACCCTCACTGGCAAAACCATCACCCTTGAGGTCGAGCCCAGTGACACCATTGAGAATGTCAAAGCCAAAATTCAAGACAAGGAGGGTATCCCACCTGACCAGCAGCGTCTGATATTTGCCGGCAAACAGCTGGAGGATGGCCGCACTCTCTCAGACTACAACATCCAGAAAGAGTCCACCCTGCACCTGGTGTTGCGCCTGCGAGGTGGCATTATTGAGCCTTCTCTCCGCCAGCTTGCCCAGAAATACAACTGCGACAAGATGATCTGCCGCAAGTGCTATGCTCGCCTTCACCCTCGTGCTGTCAACTGCCGCAAGAAGAAGTGTGGTCACACCAACAACCTGCGTCCCAAGAAGAAGGTCAAATAAGGTGGTTCTTTCCTTGAAGGGCAGCCTCCTGCCCAGGCCCCGTGGCCCTGGAGCCTCAATAAAGTGTCCCTTTCATTGACTGGAGCAGCAATTGGTGTCCTCATGGCTGATCTGTCCAGGGAGGTGGCTGAAGAGTGGGCATCTCCCTTAGGGACTCTACTCAGCACTCCATTCTGTGCCACCTGTGGGGTCTTCTGTCCTAGATTCTGTCACATCGGCATTGGTCCCTGCCCTATGCCCCTGACTCTGGATTTGTCATCTGTAAAACTGGAGTAAAAACCTCAGTCGTGTAATTGGTGGGACTGAGGATCAGTTTTGTCATTGCTGGGATCCTGTCAGGCACTTTGAGGTGTCCCTCAGGCCTTGGCCCTGAAGTGTCTAGGTGTGTGGAGATGGGTAGAAAATTAGGTACACCCAATGGTGTAGAACGTTGATTCTCAAAtttttttattttatacaaatggggtctcactatgttgtccaggctggtcttgaactcctgggctcaagccatccgcccatctcagcccctcaaagtgttgggattacaagcaagaactgccatgcctgaccCAGTTCTCAgttttttgtttgtttgtttgtttgtttgttttgagacggagtcttgctctgtcgcccaggctggagtgcagtggcgcagtctcggcttactacaacctctgcctccggggttcacatccttctcctgcctcagcctcccgagtagctgggactacaggtgcccgccacaactcctggctaattttttgtatttttagtagagacggggtttcactgggttagccaggttggtctcgatctcctgaccttgtgatccattcgccttggcctcccagaatgctggtattacaggcgtgagccagcacgcctggccCAGTTACTCAGTTTTGAATCTGAGGCCGTGACATCACTCATGGTCTGCAGTCAGTGCTCTGCCCCTGAGCTGTACCCTCTCCTATGATAATCACTCTTAAGAAGGGCAACCCTTGGTGTTTTCCCCTTAAGgtcacccaggctggaatgcagtggtgtggtcatggctccctgtaccctggaactcaggcttgggtgatcctctctcctttgcctccgaagtagccaggactacaggtgtgcacccaccaccacactcagataattgctttggtgtttttAAAGCTTGTAATGATCAGTAGGCTGAGGTGGGCAAATCATAAGGTCAAGAGTTTTTTAGATGGGGTGAGCACAGACCAATTCCTGTTTTATTTACTGATTTAAAAttttgagacagtctcactgtcacccaggttggggtgcagtggtaggatcatagcttgctgcagccttgatctcccaggatcttgcctcagcctcccgagtagctgggactgcatgcttgtgccaccacactcggttaatattttgtagagatggggtcttgctatgttgcccaggctggcttcaaactcctgaacttaaAAGCCTCCTGTTTAGTTTTGGttttttatcactttttttttttttttttgagatggagccttgctcccatcgtgcaggctggagtgcggtggcgcagtctcggctcactgcagcttctgcctctcgggttcaagcgattctcctttctcagcctcttgagtagctggaattaccagtgtgcgccaccaccaccacgcctggctagtttttctgtttttagtagagacagggttttgctatgttggccaggctggtcttgaactactgacctcttgtgatctacctgtcttggccttccaaagtgctaggattacaagcgtaagccacagcgcctggccTTGCTACATTTTTTTttttttttttttttttacagacatggtctcgctatgttgcccagaatggttttgcactgggtccaagcagttctgccgcagcctcccaaagtgctgggattacaggggtgaggcaccTTGCTGGCCCCTGTTTTGATTAGGGTGCAGTGCTGGTGAAGCCGGTGCACGAGGCCAGTGATGCATCCTAATGAGGGGTGGAGTTGGCGGGACTTCCTGGGCCAGTTTGGGGACTTTCACAAAAGACCCCCATGACTCAGGGTTTTGAGTTCTTAACTGATCGAATGAaggattcaaaattaaccactccaaggggggattgaaggaagaaccactcttaatggacaaaaagaaagaaaggggagggagtaacagggatatgagctctagccgcccaagctagcaatggcaacccttctgggtccccttccagcatgtggaagctttcctttcgcttcattcaataaacagctgctgctcactctcctggtccgtggactctttttgaactgttaacactccccgcaaaggtccgcagcttcattcttcaaagttagcgagaccaggaacc

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