RCPedia: Rtcs

Summary

Retrocopy Name	RPS4XP6	Plot displaying the genomic locations of a retrocopy (in chr5) and its respective parental gene (in chrX). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr5:37085016-37085918 UCSC
Coordinates (T2T)	chr5:37334849-37335751 UCSC
Coordinates (hg19)	chr5:37085118-37086020 UCSC
Strand	+
Parental Sequence	NM_001007.5
Parental seq. overlap	845 bp
Parental seq. overlap (%)	57%
Genomic Region	Intragenic (CPLANE1)
Retrocopy Summary	RPS4XP6, located on chr5:37085016-37085918, is a retrocopy of the parental gene RPS4X. 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	RPS4X
Full Name	ribosomal protein S4 X-linked
Also known as	CCG2\|DXS306\|RPS4\|S4\|SCAR\|SCR10
Coordinate	chrX:72272042-72277248
Strand	-
Gene summary	Cytoplasmic ribosomes, organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes ribosomal protein S4, a component of the 40S subunit. Ribosomal protein S4 is the only ribosomal protein known to be encoded by more than one gene, namely this gene and ribosomal protein S4, Y-linked (RPS4Y). The 2 isoforms encoded by these genes are not identical, but are functionally equivalent. Ribosomal protein S4 belongs to the S4E family of ribosomal proteins. This gene is not subject to X-inactivation. It has been suggested that haploinsufficiency of the ribosomal protein S4 genes plays a role in Turner syndrome; however, this hypothesis is controversial. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	RPS4XP3
Bonobo	Pan paniscus	RPS4XP3
Gorilla	Gorilla gorilla	RPS4XP17
Orangutan	Pongo abelii	RPS4XP5
Gibbon	Nomascus leucogenys	RPS4XP7
Green monkey	Chlorocebus sabaeus	LOC103232177P4
Crab-eating macaque	Macaca fascicularis	RPS4XP8
Rhesus	Macaca mulatta	RPS4XP8
Baboon	Papio anubis	LOC116271871P6
Golden snub-nosed monkey	Rhinopithecus roxellana	RPS4XP3
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

>RPS4XP6
ACACCGGAAGAGAGGTCGTCTTTCCTTGCCTAATGCAGCCATGGCTGGTGGTCCCAAGAAGCATCTGAAGTAGGTAGCAACTCCAAAGCATTGGATGCTGGATAAATTGACCAGTGTGTTTGCTCCTTGTCCATCCACCAGTCCTCACAAGTTGAGAGAGTGTCTCCCCCTCATCATTTTCCTAAGGAACAGACTTAAGTATGCCCTGACAGGAGATGAAGTAAAGATTTGCATGCAGGGGTTCATTAAGGTTGATGGCAAGGTACGAACTGATATAACCTACCCTGCTGGATTCATGGATGTCATCAGCATTGACAAGACGGGAGATAATTTCCATCTGATCTATGACACCAAGGGTCGCTTTGCTGTACATCGTATTACACCCGAGGAGGCTAAGTACAAATTGGGTAAAGTGAGAAAAATCTTTGTGGGCACAAAAGGAATCCCTCATCTGGTGACTCATGATGCTCACAGCATCCGCTACCTTGATCCCCTCATCAAGGTAAATGATACCATTCAGACTGATTTGGAGACTGGCAAGATTACTGTTTTCATCAAGTTCAACACTGGTACACTGGTAACCTGTGTATGGTGACTGGAGGTGCTAACCTGGGAATAACTGGTGTGATCACCAACAGAGAGAGGCACCCTGGATCTTTTGACGTGGTTCACATGAAAGATGTCAATGGCAACAGCTTTGCTACTCGACTTTCCAACATTTTTGTTATTGGCAAGGGCAACAAACCATGGATTTCTCTTCCCCGAGGAAAGGGTATCTGCCTCACTATTGCTGAAGAGAGAGACAAAAGACTGGGGGCCAAACAGAGCAGTGGGTGAAATGGTCCCTGGGTGACGTGTTAAATCTTTGTACATAATTAAAAATAATGTGGCAGGAATTAATAG

>NM_001007.5
AATTTCTACGCGCACCGGAAGACGGAGGTCCTCTTTCCTTGCCTAACGCAGCCATGGCTCGTGGTCCCAAGAAGCATCTGAAGCGGGTGGCAGCTCCAAAGCATTGGATGCTGGATAAATTGACCGGTGTGTTTGCTCCTCGTCCATCCACCGGTCCCCACAAGTTGAGAGAGTGTCTCCCCCTCATCATTTTCCTGAGGAACAGACTTAAGTATGCCCTGACAGGAGATGAAGTAAAGAAGATTTGCATGCAGCGGTTCATTAAAATCGATGGCAAGGTCCGAACTGATATAACCTACCCTGCTGGATTCATGGATGTCATCAGCATTGACAAGACGGGAGAGAATTTCCGTCTGATCTATGACACCAAGGGTCGCTTTGCTGTACATCGTATTACACCTGAGGAGGCCAAGTACAAGTTGTGCAAAGTGAGAAAGATCTTTGTGGGCACAAAAGGAATCCCTCATCTGGTGACTCATGATGCCCGCACCATCCGCTACCCCGATCCCCTCATCAAGGTGAATGATACCATTCAGATTGATTTGGAGACTGGCAAGATTACTGATTTCATCAAGTTCGACACTGGTAACCTGTGTATGGTGACTGGAGGTGCTAACCTAGGAAGAATTGGTGTGATCACCAACAGAGAGAGGCACCCTGGATCTTTTGACGTGGTTCACGTGAAAGATGCCAATGGCAACAGCTTTGCCACTCGACTTTCCAACATTTTTGTTATTGGCAAGGGCAACAAACCATGGATTTCTCTTCCCCGAGGAAAGGGTATCCGCCTCACCATTGCTGAAGAGAGAGACAAAAGACTGGCGGCCAAACAGAGCAGTGGGTGAAATGGGTCCCTGGGTGACATGTCAGATCTTTGTACGTAATTAAAAATATTGTGGCAGGATTAATAGCATTTTGGTTTTGTGGGTTGTTTTTTTTTTTAATTCAGTTTCCTGCTATTTTACTGTATAACATGAACAGTGATTAAGTTCTCAGGCAGGCTTAGGCAGTCTGTTATTGGCTGGGCTTAGTTAGTGGTGGGAAGTAGAAGATACCAGACTTGGGAAAGGAACAGCAACTAACCAAGGAGTAGAAAGAGCCAAGAAATCCCGGAGTATTTATCTCCCCCGCCTTGACTTGGCCAAGAACTTCTCTACACAGTGGACCCCTCTGCCCTGTTAAGTTCCCTTGGCTTTCTAAAAATCTGCCCTCATTTTCTTCTCCAGTCTGTATTGCACTAGCCCATCCACAAGCCTGGCTCATCTGTTTTTCCCACTCCTGTGCCCATCTTGCCAAACGCAGGATGAAAATCTCCAGTTGCCATTAAAGGTGGTCATAAATGGGCTGTTGATGTTGCAAAGCATTGCAGTTCCTTGGACTTAGTGCCCTTATTCTCCAGCTGCCGCTGCAGTCCTCAACTCTGTTTTTCAGAGGACAGAGATGTAGAACATAAACTTGTTCTTGCTTGTCCAAA

>NM_001007.5 

AATTTCTACGCGCACCGGAAGACGGAGGTCCTCTTTCCTTGCCTAACGCAGCCATGGCTCGTGGTCCCAAGAAGCATCTGAAGCGGGTGGCAGCTCCAAAGCATTGGATGCTGGATAAATTGACCGGTGTGTTTGCTCCTCGTCCATCCACCGGTCCCCACAAGTTGAGAGAGTGTCTCCCCCTCATCATTTTCCTGAGGAACAGACTTAAGTATGCCCTGACAGGAGATGAAGTAAAGAAGATTTGCATGCAGCGGTTCATTAAAATCGATGGCAAGGTCCGAACTGATATAACCTACCCTGCTGGATTCATGGATGTCATCAGCATTGACAAGACGGGAGAGAATTTCCGTCTGATCTATGACACCAAGGGTCGCTTTGCTGTACATCGTATTACACCTGAGGAGGCCAAGTACAAGTTGTGCAAAGTGAGAAAGATCTTTGTGGGCACAAAAGGAATCCCTCATCTGGTGACTCATGATGCCCGCACCATCCGCTACCCCGATCCCCTCATCAAGGTGAATGATACCATTCAGATTGATTTGGAGACTGGCAAGATTACTGATTTCATCAAGTTCGACACTGGTAACCTGTGTATGGTGACTGGAGGTGCTAACCTAGGAAGAATTGGTGTGATCACCAACAGAGAGAGGCACCCTGGATCTTTTGACGTGGTTCACGTGAAAGATGCCAATGGCAACAGCTTTGCCACTCGACTTTCCAACATTTTTGTTATTGGCAAGGGCAACAAACCATGGATTTCTCTTCCCCGAGGAAAGGGTATCCGCCTCACCATTGCTGAAGAGAGAGACAAAAGACTGGCGGCCAAACAGAGCAGTGGGTGAAATGGGTCCCTGGGTGACATGTCAGATCTTTGTACGTAATTAAAAATATTGTGGCAGGATTAATAGCATTTTGGTTTTGTGGGTTGTTTTTTTTTTTAATTCAGTTTCCTGCTATTTTACTGTATAACATGAACAGTGATTAAGTTCTCAGGCAGGCTTAGGCAGTCTGTTATTGGCTGGGCTTAGTTAGTGGTGGGAAGTAGAAGATACCAGACTTGGGAAAGGAACAGCAACTAACCAAGGAGTAGAAAGAGCCAAGAAATCCCGGAGTATTTATCTCCCCCGCCTTGACTTGGCCAAGAACTTCTCTACACAGTGGACCCCTCTGCCCTGTTAAGTTCCCTTGGCTTTCTAAAAATCTGCCCTCATTTTCTTCTCCAGTCTGTATTGCACTAGCCCATCCACAAGCCTGGCTCATCTGTTTTTCCCACTCCTGTGCCCATCTTGCCAAACGCAGGATGAAAATCTCCAGTTGCCATTAAAGGTGGTCATAAATGGGCTGTTGATGTTGCAAAGCATTGCAGTTCCTTGGACTTAGTGCCCTTATTCTCCAGCTGCCGCTGCAGTCCTCAACTCTGTTTTTCAGAGGACAGAGATGTAGAACATAAACTTGTTCTTGCTTGTCCAAA

Publications

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