RCPedia: Rtcs

Summary

Retrocopy Name	VPS26CP1	Plot displaying the genomic locations of a retrocopy (in chr2) and its respective parental gene (in chr21). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr2:206686246-206687363 UCSC
Coordinates (T2T)	chr2:207168344-207169461 UCSC
Coordinates (hg19)	chr2:207550970-207552087 UCSC
Strand	-
Parental Sequence	NM_006052.2
Parental seq. overlap	934 bp
Parental seq. overlap (%)	30.4%
Genomic Region	Intragenic (DYTN)
Retrocopy Summary	VPS26CP1, located on chr2:206686246-206687363, is a retrocopy of the parental gene VPS26C. 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	VPS26C
Full Name	VPS26 endosomal protein sorting factor C
Also known as	DCRA\|DSCR3\|DSCRA
Coordinate	chr21:37223420-37268108
Strand	-
Gene summary	The region of chromosome 21 between genes CBR and ERG (CBR-ERG region), which spans 2.5 Mb on 21q22.2, has been defined by analysis of patients with partial trisomy 21. It contributes significantly to the pathogenesis of many characteristics of Down syndrome, including morphological features, hypotonia, and cognitive disability. The DSCR3 (Down syndrome critical region gene 3) gene is found in this region and is predictated to contain eight exons. DSCR3 is expressed in most tissues examined. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	VPS26CP1
Bonobo	Pan paniscus	VPS26CP1
Gorilla	Gorilla gorilla	VPS26CP1
Orangutan	Pongo abelii	VPS26CP1
Gibbon	Nomascus leucogenys	VPS26CP2
Green monkey	Chlorocebus sabaeus	DSCR3P1
Crab-eating macaque	Macaca fascicularis	DSCR3P1
Rhesus	Macaca mulatta	VPS26CP1
Baboon	Papio anubis	VPS26CP1
Golden snub-nosed monkey	Rhinopithecus roxellana	VPS26CP1
Marmoset	Callithrix jacchus	VPS26CP1
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)

Related Sequence

>VPS26CP1
GGGACCTCCCTGGACATCAAGATGGAAGAGCAAATAGTTTCTCATGCTGGAGAAATGCTCTCCAGTGTGGTGGTCGTATCTTGTAAGGATTCAGTCCCACATCAAGTAGTGTCTTTGACAATGGAAGGAATTGCAATCCCCCAGCTCAGTGCCAAAAGTGTGGGCAGTTTTGAAGCTTTTTATAATTCCATTAAACCTATCCAGATTATCAACAGTGCCATAGAAAGGATGAAGCCAGGGAAATTTCCCTATGGCAAAACAAATTTATTTCGCATTTCTTCTGTATGTGAGGGGTAACAAAGTTCTGTATGAGACTTATTATCAGACATTCAGTATACACTACGCTGTGACATGAGGCAGTCTCTGTTGACCAAGGACTTGACAAAGGCCGGTGAATTTACCATCCACTCTGCTCCTCAGGAGGGGAAGTTGACTCCAAGTCCTGTGGACTTCACAGATTATACCTGCAACCTTACAGAATATCAAAGAGAGAGCCTTGCTCCCCAGATTTCTCATTCGAGAACACCCCAACTCAATGAATTGTGTCATCGTGCAGCTGCTTACAGGAGAGCTGGTGGTGAAAAGGCATGGGGCTGCAACTGGTGCACATGGAGACCTGTGGGTGTGCAAAAAGCTATGCCAATGATGCCACAGAGTTTCCTTATATTCAGATGCCCATGGGGACATTTGTAGGGGCCTCTCTGTCCCTATATACATGGTCTTCTCCAGGCTGTTTACCTGCCGCATGCTGAAGACCAACTTCAAAGTGGAATTTGAGGCCACCATCGACATGCGTCTTCATGCTAACCACCTGGTCACAGAGAACTTCCTATTGCAGCTCTGCAGGACTCAGCCCAGGAGGAGGGAAGCACAGAAAACAGGGGTGGCCTTGTGGATATCCTGCTGGTTATCGTTCATGGGGAACTAAAGCCAGCAGTATATACTTGTTTTTGTGATTATTCTGTATCAGAAATGAAATGGACTCCTTAAATTACAATTATTTTTCCTCCTCATTTCTTCGAGGCTTCTACTTCCAAAAGTCACCTTTAATCATATCTTTTCTTTGAAATTCAACAGAATTTCTTAATGCTGTTTGCAAGATCATTTCACAGAAAACG

>NM_006052.2
ACGCGCAGCCGGAAGTGGCGGCTGCTGCGGAGAATTGGAGATGGGGACCGCCCTGGACATCAAGATTAAAAGAGCGAATAAAGTTTATCACGCCGGGGAAGTGCTCTCTGGCGTGGTGGTCATATCGAGTAAGGATTCAGTCCAACACCAGGGAGTGTCTTTGACCATGGAAGGAACTGTAAACCTCCAGCTCAGTGCCAAAAGTGTGGGTGTGTTTGAAGCTTTTTATAATTCTGTTAAGCCTATCCAGATTATCAACAGCACCATAGAAATGGTGAAGCCGGGGAAATTTCCCAGCGGCAAAACAGAAATCCCTTTTGAATTTCCTCTGCACTTGAAGGGTAACAAAGTTCTGTATGAGACGTATCATGGCGTGTTTGTCAACATTCAGTATACACTGCGCTGTGACATGAAGCGGTCTCTGTTGGCCAAGGACTTGACAAAGACCTGTGAATTTATCGTTCACTCCGCTCCTCAGAAGGGGAAGTTTACTCCCAGTCCCGTGGACTTCACGATTACACCTGAAACCTTACAGAACGTCAAAGAGAGAGCTTTGCTTCCCAAATTTCTCCTTCGAGGACATCTCAACTCAACAAACTGTGTCATCACGCAGCCACTAACGGGAGAGCTGGTGGTGGAGAGCTCGGAAGCCGCCATCAGAAGCGTGGAGCTGCAGCTGGTGCGCGTGGAGACGTGCGGGTGTGCAGAAGGCTATGCCCGCGACGCCACGGAGATTCAGAACATTCAGATCGCCGACGGGGATGTGTGCAGGGGCCTCTCTGTCCCCATCTACATGGTCTTCCCTAGGCTGTTCACCTGCCCTACACTGGAGACCACCAACTTCAAAGTGGAATTTGAGGTTAACATCGTGGTGCTGCTTCACCCTGACCACCTCATCACGGAGAACTTCCCGCTGAAGCTCTGCAGGATATAGCCCGGAGGAGGGAAGCATAGAGAACGGGAGTGGCCATCTGGAAATCCAGCTGGTTATCCAAATCCTAAGGGGAGCTACAGCCAGCGGCATATACTTGTTTTTGTGATTATTCTGTATCAGAAATGAAACAGACCCTCAAATTAACTTTCCTTCCTCATTTCTTGAGGCTTCTGCTTCCAACAGGCACCTCTAATCAGACCTTTTCTTTGAAATTCAACAAGATTTCTTAATGCTATTTGCCAAGACCATTTCACAGAAAACATTGACTGTGGCTCTTGCCTTATCTGTTCCTTTTTAGGTACAGTAAAACAATTGTGACAGCAGTTTGAGCTTGCTGGAGAGTGGCATCATGGGGACAAAAGGAAACCTCTGACTTGCTAATGGATGTAGCCAGGGACTCCCCATAGCAAAGGGTCTGTGGCCAGTTGACATCCAGGATGGCTGCAAGCGCACTTGATGGTCAGGAAGTTTGCAGATACTCGCCAAGGCAGAGCGCAAAGTGCTAGCCACTGGAAATGCATGACTTCCCTCCACCCCTACTCTATTCTGTAGttttttggttttgtttctgagacggagtctcagtctgtcacccaggctggagtgatctcagctcactgcaacctccacctcccaggttcaagcgactctcctgcctcagcctcccgagtagttgggattacaggtgactgccaccgtgcccggctaatgtttgtatttttagtagagacggggcttcaccatcttggccaggctggtcttgaactcctgacctcgtgacccacccgccttggcctcccaaagtgctgggattacaggtgtgagccaccacacccagccTCTGTAGTTCTTTTTACAACATTTTTCATTATAACTTTAAATTTTTTAAGCAACTGGAAAAGTGTTCCTTGCTCTCTTGGGGGGATTTGGCTGGTGCCGAAGTGTTTCTGAAGTCTCAAGAACTGCCATAAAATCTCACGCTGCCATTTCCCTGAACAGATACATACATAGAGAGAGACAGTTTTCCAAActgtgtcacgcaggctgagtgcactggcaggatcacagctcacggcagcctcaacctccctggctcaagcgatccctcccctcagcctcctgagtagctgagactacaggtgagtgccaccacactcagctaattttcaaattttttgtagacagggtctccctatgttgcccaggctggtcttgaactcctagactcaagtgatcctcctgtcttggcctcccaaagtgctgagattacaggtgtgagccactgtgcccagcAGTTTCCCAGAATATATTTAAATGCAAAGTTACATGAGGGGAAAACATGTATGTTTGCTCCTGTTGTTACTGGGTAGGTTCTGAACAGCAGAAACCCATGTGCAGGGTGGGCTGGTGAAGGCCCCTCTCCGCAAGGTGGTAGCAGGAAAAGGTCCTTGACTTGATGAATTTGGTCTGCCTCTGAGCCACTGGAGGAAGCTGTTTTGAGCCAGGGTTTTTTGGCCTAAAGCCAGCATTTCCTCAGTCTCCCTTTGTGGTTCGAAGGATATGGACTATTGCAATACATTTCTTCCTTCAAATCCTGCCACTGTTTTGTTGGCCCACAACTAATAGGACCTCAAAATAAGCCATGCTGCTTTGCACACACACTAGCCTTCTTTTGTACTTTTCATTCTGGATGGGCTTGGCCAAAACAGGCTCAGGCCAAAGACCTCCCAAGCTGTATGTACTTCCAGTATCCTGAAACAGTGTTTGGTGACATAATGCCAAGGGTAAACAAGCCTGATTTAGGCACTGCTTTATCCAGGGGCTTCACCCATGAAATTAATAAAACTTATCTGAGTCACTTGAAACTTGGTTCCCAGAAAACACATTTCTGGTTTATAATCTCCTTTTATGCTCACCTGACATTAATTATCTATCCTTGATGATGTGTTTAAACTGAGTAGCAGAAAACAGAGGCCACACTTTCTGGGAAATTTTAAAGGAAGAAACCATTTTTAATGAGATGAAAATATTTAACGAATTTAAAAAGCTAATGACAATTTTGAGAAAAGGTTTGGGATGTATATTGCTATGTAATTTAATAAACTGATTTTATGGATATAAA

>NM_006052.2 

ACGCGCAGCCGGAAGTGGCGGCTGCTGCGGAGAATTGGAGATGGGGACCGCCCTGGACATCAAGATTAAAAGAGCGAATAAAGTTTATCACGCCGGGGAAGTGCTCTCTGGCGTGGTGGTCATATCGAGTAAGGATTCAGTCCAACACCAGGGAGTGTCTTTGACCATGGAAGGAACTGTAAACCTCCAGCTCAGTGCCAAAAGTGTGGGTGTGTTTGAAGCTTTTTATAATTCTGTTAAGCCTATCCAGATTATCAACAGCACCATAGAAATGGTGAAGCCGGGGAAATTTCCCAGCGGCAAAACAGAAATCCCTTTTGAATTTCCTCTGCACTTGAAGGGTAACAAAGTTCTGTATGAGACGTATCATGGCGTGTTTGTCAACATTCAGTATACACTGCGCTGTGACATGAAGCGGTCTCTGTTGGCCAAGGACTTGACAAAGACCTGTGAATTTATCGTTCACTCCGCTCCTCAGAAGGGGAAGTTTACTCCCAGTCCCGTGGACTTCACGATTACACCTGAAACCTTACAGAACGTCAAAGAGAGAGCTTTGCTTCCCAAATTTCTCCTTCGAGGACATCTCAACTCAACAAACTGTGTCATCACGCAGCCACTAACGGGAGAGCTGGTGGTGGAGAGCTCGGAAGCCGCCATCAGAAGCGTGGAGCTGCAGCTGGTGCGCGTGGAGACGTGCGGGTGTGCAGAAGGCTATGCCCGCGACGCCACGGAGATTCAGAACATTCAGATCGCCGACGGGGATGTGTGCAGGGGCCTCTCTGTCCCCATCTACATGGTCTTCCCTAGGCTGTTCACCTGCCCTACACTGGAGACCACCAACTTCAAAGTGGAATTTGAGGTTAACATCGTGGTGCTGCTTCACCCTGACCACCTCATCACGGAGAACTTCCCGCTGAAGCTCTGCAGGATATAGCCCGGAGGAGGGAAGCATAGAGAACGGGAGTGGCCATCTGGAAATCCAGCTGGTTATCCAAATCCTAAGGGGAGCTACAGCCAGCGGCATATACTTGTTTTTGTGATTATTCTGTATCAGAAATGAAACAGACCCTCAAATTAACTTTCCTTCCTCATTTCTTGAGGCTTCTGCTTCCAACAGGCACCTCTAATCAGACCTTTTCTTTGAAATTCAACAAGATTTCTTAATGCTATTTGCCAAGACCATTTCACAGAAAACATTGACTGTGGCTCTTGCCTTATCTGTTCCTTTTTAGGTACAGTAAAACAATTGTGACAGCAGTTTGAGCTTGCTGGAGAGTGGCATCATGGGGACAAAAGGAAACCTCTGACTTGCTAATGGATGTAGCCAGGGACTCCCCATAGCAAAGGGTCTGTGGCCAGTTGACATCCAGGATGGCTGCAAGCGCACTTGATGGTCAGGAAGTTTGCAGATACTCGCCAAGGCAGAGCGCAAAGTGCTAGCCACTGGAAATGCATGACTTCCCTCCACCCCTACTCTATTCTGTAGttttttggttttgtttctgagacggagtctcagtctgtcacccaggctggagtgatctcagctcactgcaacctccacctcccaggttcaagcgactctcctgcctcagcctcccgagtagttgggattacaggtgactgccaccgtgcccggctaatgtttgtatttttagtagagacggggcttcaccatcttggccaggctggtcttgaactcctgacctcgtgacccacccgccttggcctcccaaagtgctgggattacaggtgtgagccaccacacccagccTCTGTAGTTCTTTTTACAACATTTTTCATTATAACTTTAAATTTTTTAAGCAACTGGAAAAGTGTTCCTTGCTCTCTTGGGGGGATTTGGCTGGTGCCGAAGTGTTTCTGAAGTCTCAAGAACTGCCATAAAATCTCACGCTGCCATTTCCCTGAACAGATACATACATAGAGAGAGACAGTTTTCCAAActgtgtcacgcaggctgagtgcactggcaggatcacagctcacggcagcctcaacctccctggctcaagcgatccctcccctcagcctcctgagtagctgagactacaggtgagtgccaccacactcagctaattttcaaattttttgtagacagggtctccctatgttgcccaggctggtcttgaactcctagactcaagtgatcctcctgtcttggcctcccaaagtgctgagattacaggtgtgagccactgtgcccagcAGTTTCCCAGAATATATTTAAATGCAAAGTTACATGAGGGGAAAACATGTATGTTTGCTCCTGTTGTTACTGGGTAGGTTCTGAACAGCAGAAACCCATGTGCAGGGTGGGCTGGTGAAGGCCCCTCTCCGCAAGGTGGTAGCAGGAAAAGGTCCTTGACTTGATGAATTTGGTCTGCCTCTGAGCCACTGGAGGAAGCTGTTTTGAGCCAGGGTTTTTTGGCCTAAAGCCAGCATTTCCTCAGTCTCCCTTTGTGGTTCGAAGGATATGGACTATTGCAATACATTTCTTCCTTCAAATCCTGCCACTGTTTTGTTGGCCCACAACTAATAGGACCTCAAAATAAGCCATGCTGCTTTGCACACACACTAGCCTTCTTTTGTACTTTTCATTCTGGATGGGCTTGGCCAAAACAGGCTCAGGCCAAAGACCTCCCAAGCTGTATGTACTTCCAGTATCCTGAAACAGTGTTTGGTGACATAATGCCAAGGGTAAACAAGCCTGATTTAGGCACTGCTTTATCCAGGGGCTTCACCCATGAAATTAATAAAACTTATCTGAGTCACTTGAAACTTGGTTCCCAGAAAACACATTTCTGGTTTATAATCTCCTTTTATGCTCACCTGACATTAATTATCTATCCTTGATGATGTGTTTAAACTGAGTAGCAGAAAACAGAGGCCACACTTTCTGGGAAATTTTAAAGGAAGAAACCATTTTTAATGAGATGAAAATATTTAACGAATTTAAAAAGCTAATGACAATTTTGAGAAAAGGTTTGGGATGTATATTGCTATGTAATTTAATAAACTGATTTTATGGATATAAA

Publications

PMID - Link	Title
No publications available for this retrocopy