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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name RPS4XP20
Plot displaying the genomic locations of a retrocopy (in chr19) and its respective parental gene (in chrY). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr19:34022677-34022872  UCSC
Coordinates (T2T) chr19:36543484-36543679  UCSC
Coordinates (hg19) chr19:34513582-34513777  UCSC
Strand -
Parental Sequence NM_001008.4
Parental seq. overlap 165 bp
Parental seq. overlap (%) 13.9%
Genomic Region Intergenic
Retrocopy Summary RPS4XP20, located on chr19:34022677-34022872, is a retrocopy of the parental gene RPS4Y1. 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 RPS4Y1
Full Name ribosomal protein S4 Y-linked 1
Also known as RPS4Y|S4
Coordinate chrY:2841602-2867268
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, X-linked (RPS4X). 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. 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 LOC112204082P1
Green monkey Chlorocebus sabaeus LOC103246967P2
Rhesus Macaca mulatta RPS4Y1P2
Baboon Papio anubis LOC116272386P3
Golden snub-nosed monkey Rhinopithecus roxellana RPS4Y1P2
Bonobo Pan paniscus Without Homology
Gorilla Gorilla gorilla Without Homology
Orangutan Pongo abelii Without Homology
Gibbon Nomascus leucogenys Without Homology
Crab-eating macaque Macaca fascicularis 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

>RPS4XP20
TTGGTGTGATCACCAACAGAAAGAAGCACCGTGGATCTTTTGATGTGGTTCATGTGAAAGATGCCAATGGCAACAGATTTGCCCCTTGGCTTTCCAACATTTTTGTTACTGGCAAGTGCAACAAACCATGGATTTCTCTTCCCCGAGGAAAGGGTATCCGCCTCACCATTGCTGAAGGGAGAGACAAGAGACTGGT
>NM_001008.4
CTCTTCCGTCGCAGAGTTTCGCCATGGCCCGGGGCCCCAAGAAGCACTTAAAGCGTGTTGCAGCGCCGAAGCATTGGATGCTTGACAAACTAACGGGTGTATTTGCACCTCGTCCATCGACAGGTCCCCACAAGCTGAGGGAATGTCTTCCTCTGATCGTCTTCCTCAGGAATAGACTCAAGTATGCGTTGACTGGAGATGAGGTAAAGAAGATATGTATGCAACGTTTCATCAAAATTGATGGCAAGGTTCGAGTGGATGTCACATACCCTGCTGGATTCATGGATGTCATCAGCATCGAGAAGACAGGTGAACATTTCCGCCTGGTCTATGACACCAAGGGCCGTTTTGCTGTTCACCGCATCACAGTGGAAGAGGCAAAGTACAAGTTGTGCAAAGTGAGGAAGATTACTGTGGGAGTGAAGGGAATCCCTCACCTGGTGACTCATGATGCTCGAACCATCCGCTACCCAGATCCTGTCATCAAGGTGAACGATACTGTGCAGATTGATTTAGGGACTGGCAAGATAATCAACTTTATCAAATTTGATACAGGCAATTTGTGTATGGTGATTGGTGGAGCCAACCTCGGTCGTGTTGGTGTGATCACCAACAGGGAAAGACATCCTGGTTCTTTTGATGTGGTGCATGTGAAGGATGCCAATGGCAACAGCTTTGCCACGAGGCTTTCCAACATTTTTGTCATTGGCAATGGCAATAAACCTTGGATTTCCCTGCCCAGGGGAAAGGGCATTCGACTTACTGTTGCTGAAGAGAGAGATAAGAGGCTGGCCACCAAACAGAGCAGTGGCTAAATTGCAGTAGCAGCATATCTTTTTTTCTTTGCACAAATAAACAGTGAATTCTCGTTTCTTAATGTGTTTTTTCCCCCTTGTGGATAATAGTAGGGTTTGAATTTGCTCATGATTTTGGCACTGTCTTAAGATCTCTAGGAATACCACCTATACTTCCTCTGACCCTCCAGTAAATAAACCTTTGCTTCCCTCATACATGTTACCCACACCATCTCTGTGGGCAGAGTGATGGAGTAGCATTCCAAAACGAAGTACAAAAAACGTATGACATTTCAGAAAGGACGGCATtcttttgtggaagctatgggagatggtcttagttttcttgcttgttcacattattggtagaaattaaatcctgtggctgtaggaaa

Publications

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