RCPedia: Rtcs

Summary

Retrocopy Name	CHMP4BP1	Plot displaying the genomic locations of a retrocopy (in chr14) and its respective parental gene (in chr20). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr14:55298642-55299270 UCSC
Coordinates (T2T)	chr14:49503866-49504494 UCSC
Coordinates (hg19)	chr14:55765360-55765988 UCSC
Strand	+
Parental Sequence	NM_176812.5
Parental seq. overlap	604 bp
Parental seq. overlap (%)	37.7%
Genomic Region	Intragenic (FBXO34)
Retrocopy Summary	CHMP4BP1, located on chr14:55298642-55299270, is a retrocopy of the parental gene CHMP4B. 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	CHMP4B
Full Name	charged multivesicular body protein 4B
Also known as	C20orf178\|CHMP4A\|CTPP3\|CTRCT31\|SNF7\|SNF7-2\|Shax1\|VPS32B\|Vps32-2\|dJ553F4.4
Coordinate	chr20:33811348-33854366
Strand	+
Gene summary	This gene encodes a member of the chromatin-modifying protein/charged multivesicular body protein (CHMP) protein family. The protein is part of the endosomal sorting complex required for transport (ESCRT) complex III (ESCRT-III), which functions in the sorting of endocytosed cell-surface receptors into multivesicular endosomes. The ESCRT machinery also functions in the final abscisson stage of cytokinesis and in the budding of enveloped viruses such as HIV-1. The three proteins of the CHMP4 subfamily interact with programmed cell death 6 interacting protein (PDCD6IP, also known as ALIX), which also functions in the ESCRT pathway. The CHMP4 proteins assemble into membrane-attached 5-nm filaments that form circular scaffolds and promote or stabilize outward budding. These polymers are proposed to help generate the luminal vesicles of multivesicular bodies. Mutations in this gene result in autosomal dominant posterior polar cataracts.[provided by RefSeq, Oct 2009]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	CHMP4BP1
Bonobo	Pan paniscus	CHMP4BP1
Orangutan	Pongo abelii	CHMP4BP1
Gibbon	Nomascus leucogenys	CHMP4BP1
Green monkey	Chlorocebus sabaeus	CHMP4BP1
Crab-eating macaque	Macaca fascicularis	CHMP4BP1
Rhesus	Macaca mulatta	CHMP4BP1
Baboon	Papio anubis	CHMP4BP1
Golden snub-nosed monkey	Rhinopithecus roxellana	CHMP4BP1
Gorilla	Gorilla gorilla	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

Related Sequence

>CHMP4BP1
CGCTGTTCGGGGCTGGAGGGGGTAAGGCCGGCAAGGGCGGCCTGACCCTCCAGGAGGCCATCCAGCGGCTGCGGGACACGGAGGAGATGTTAAGCAAGAAACAGGAGTTCCTGGAGAAGAAAATCGAGCAGAGGCACGGCACCAAAAACAAGCCCGCGGCCCTCCAGGCACTGAAGCGTAAGAAGAGGTATGAGAAGCAGCTGGCGCAGATCGACGGTACATTATCAACCATCGAGTTCCAGCAGCAGGCCCTGGAGAATGCCAACACCAATACCGAGGTGCTCAAGAACATGGGCTCTGCAGCCAAGGCCAAGAAGGCGGCCCACGACAACATGGACATCGATAAAGTTGATGAGTTAATGCAGGACATTGCTGACCAGCAAGAACTTGGGGAGGAGATTTCAACAGCAATTTCGAAACCTGTAGGGTTTGGAGAAAAGTCTGACGAGGATGAGCTCATGGCGGAATTAGAAGAACTAGAACAGGAGGAACCAGACAAGAATTTGCTGGAAGTCAGTGGCCCCGAAACAGTCCCTCTACCAAATGTTCCCTCTATAGCCCTACCATCAAAACCTGCCAAGAAGAGGAAGACGACGACATGAAGGATTTGGAGAACTGGGCTGGGTCCA

>NM_176812.5
ggagaggcctgcggcggcagggagcggcgggactgggagcgggcgccggagccgacccgagccgagccgagccgagccgagccggagcgggcggcgaaggccggcgcggCGAGCAGCAACCATGTCGGTGTTCGGGAAGCTGTTCGGGGCTGGAGGGGGTAAGGCCGGCAAGGGCGGCCCGACCCCCCAGGAGGCCATCCAGCGGCTGCGGGACACGGAAGAGATGTTAAGCAAGAAACAGGAGTTCCTGGAGAAGAAAATCGAGCAGGAGCTGACGGCCGCCAAGAAGCACGGCACCAAAAACAAGCGCGCGGCCCTCCAGGCACTGAAGCGTAAGAAGAGGTATGAGAAGCAGCTGGCGCAGATCGACGGCACATTATCAACCATCGAGTTCCAGCGGGAGGCCCTGGAGAATGCCAACACCAACACCGAGGTGCTCAAGAACATGGGCTATGCCGCCAAGGCCATGAAGGCGGCCCATGACAACATGGACATCGATAAAGTTGATGAGTTAATGCAGGACATTGCTGACCAGCAAGAACTTGCAGAGGAGATTTCAACAGCAATTTCGAAACCTGTAGGGTTTGGAGAAGAGTTTGACGAGGATGAGCTCATGGCGGAATTAGAAGAACTAGAACAGGAGGAACTAGACAAGAATTTGCTGGAAATCAGTGGACCCGAAACAGTCCCTCTACCAAATGTTCCCTCTATAGCCCTACCATCAAAACCCGCCAAGAAGAAAGAAGAGGAGGACGACGACATGAAGGAATTGGAGAACTGGGCTGGATCCATGTAATGGGGTCCAGCGCTGGCTGGGCCCAGACAGACTGTGGTGGCCTGCGCAGCGAGCAGGCGTGTGCGTGTGTGGGGCAGGCAGGATGTGGTGCAGGCAGGTTCCATCGCTTTCGACTCTCACTCCAAAGCAGTAGGGCCGCGTTGCTGCTCACTCTCTGCATAGCATGGTCTGCACCTgggagatgggcggggggaggggggcgggcggggtgggaagtgCCTGCTGTTTATAATGTTGAATTTCTGTAAAATAAACTGTATTTGCAAATCCAACATTGAGCTTCTGGACTACGCTGACTCCACTGCTGAATCCTCAATGGAAAGGGTCGACTGGTTGCAGTTGAAATGACCTGAAATGTAGCCTCTGTCCTTGTAAGTCAGTTGACTTGCCGCACATCTCTTTGTGTACTTGTACGGTACTGGCAGAAAAGTCATTTTTCAAAAGCCATAGGCTTTTCCTTGCCCTTAGCTGTAATAATGCATCTGATTTTGATTTCCTCCAGAGCTGTGTTTCTGTCCATCACCTGTGTATTGGCCCTGTGTTTACCACTCTGGCCCACTCCTCACCCCCTTGCTCCCCTGGTCTTCTGGAGTTTGTGACATTGATTTGAAATGGATGGTGTTCTCTTGAGAGCAAGTGAGATTGTTAGAATTAAGTTCCAACTATACAGTTTTCTAACATAGCTATAAGGTCCTTGTTGCTGTTTGTGATAACTGATAGATAACTCATTGGAAACGTGCATACATTTATATTCAGATGAAATTATGGTTTGCACTGTCTATTAAATATCTCGATTAATTTTCATA

>NM_176812.5 

ggagaggcctgcggcggcagggagcggcgggactgggagcgggcgccggagccgacccgagccgagccgagccgagccgagccggagcgggcggcgaaggccggcgcggCGAGCAGCAACCATGTCGGTGTTCGGGAAGCTGTTCGGGGCTGGAGGGGGTAAGGCCGGCAAGGGCGGCCCGACCCCCCAGGAGGCCATCCAGCGGCTGCGGGACACGGAAGAGATGTTAAGCAAGAAACAGGAGTTCCTGGAGAAGAAAATCGAGCAGGAGCTGACGGCCGCCAAGAAGCACGGCACCAAAAACAAGCGCGCGGCCCTCCAGGCACTGAAGCGTAAGAAGAGGTATGAGAAGCAGCTGGCGCAGATCGACGGCACATTATCAACCATCGAGTTCCAGCGGGAGGCCCTGGAGAATGCCAACACCAACACCGAGGTGCTCAAGAACATGGGCTATGCCGCCAAGGCCATGAAGGCGGCCCATGACAACATGGACATCGATAAAGTTGATGAGTTAATGCAGGACATTGCTGACCAGCAAGAACTTGCAGAGGAGATTTCAACAGCAATTTCGAAACCTGTAGGGTTTGGAGAAGAGTTTGACGAGGATGAGCTCATGGCGGAATTAGAAGAACTAGAACAGGAGGAACTAGACAAGAATTTGCTGGAAATCAGTGGACCCGAAACAGTCCCTCTACCAAATGTTCCCTCTATAGCCCTACCATCAAAACCCGCCAAGAAGAAAGAAGAGGAGGACGACGACATGAAGGAATTGGAGAACTGGGCTGGATCCATGTAATGGGGTCCAGCGCTGGCTGGGCCCAGACAGACTGTGGTGGCCTGCGCAGCGAGCAGGCGTGTGCGTGTGTGGGGCAGGCAGGATGTGGTGCAGGCAGGTTCCATCGCTTTCGACTCTCACTCCAAAGCAGTAGGGCCGCGTTGCTGCTCACTCTCTGCATAGCATGGTCTGCACCTgggagatgggcggggggaggggggcgggcggggtgggaagtgCCTGCTGTTTATAATGTTGAATTTCTGTAAAATAAACTGTATTTGCAAATCCAACATTGAGCTTCTGGACTACGCTGACTCCACTGCTGAATCCTCAATGGAAAGGGTCGACTGGTTGCAGTTGAAATGACCTGAAATGTAGCCTCTGTCCTTGTAAGTCAGTTGACTTGCCGCACATCTCTTTGTGTACTTGTACGGTACTGGCAGAAAAGTCATTTTTCAAAAGCCATAGGCTTTTCCTTGCCCTTAGCTGTAATAATGCATCTGATTTTGATTTCCTCCAGAGCTGTGTTTCTGTCCATCACCTGTGTATTGGCCCTGTGTTTACCACTCTGGCCCACTCCTCACCCCCTTGCTCCCCTGGTCTTCTGGAGTTTGTGACATTGATTTGAAATGGATGGTGTTCTCTTGAGAGCAAGTGAGATTGTTAGAATTAAGTTCCAACTATACAGTTTTCTAACATAGCTATAAGGTCCTTGTTGCTGTTTGTGATAACTGATAGATAACTCATTGGAAACGTGCATACATTTATATTCAGATGAAATTATGGTTTGCACTGTCTATTAAATATCTCGATTAATTTTCATA

Publications

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