RCPedia: Rtcs

Summary

Retrocopy Name	RPL36AP21	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)	chr5:18049549-18049872 UCSC
Coordinates (T2T)	chr5:18051323-18051646 UCSC
Coordinates (hg19)	chr5:18049658-18049981 UCSC
Strand	+
Parental Sequence	NM_021029.6
Parental seq. overlap	284 bp
Parental seq. overlap (%)	37.2%
Genomic Region	Intergenic
Retrocopy Summary	RPL36AP21, located on chr5:18049549-18049872, is a retrocopy of the parental gene RPL36A. 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	RPL36A
Full Name	ribosomal protein L36a
Also known as	L36A\|L44L\|MIG6\|RPL44
Coordinate	chrX:101391011-101396155
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 a ribosomal protein that is a component of the 60S subunit. The protein, which shares sequence similarity with yeast ribosomal protein L44, belongs to the L44E (L36AE) family of ribosomal proteins. Although this gene has been referred to as ribosomal protein L44 (RPL44), its official name is ribosomal protein L36a (RPL36A). This gene and the human gene officially named ribosomal protein L36a-like (RPL36AL) encode nearly identical proteins; however, they are distinct genes. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Naturally occurring read-through transcription occurs between this locus and the heterogeneous nuclear ribonucleoprotein H2 (H') gene. [provided by RefSeq, Jan 2011]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	RPL36ALP1
Bonobo	Pan paniscus	RPL36ALP1
Gorilla	Gorilla gorilla	RPL36ALP2
Orangutan	Pongo abelii	RPL36ALP1
Gibbon	Nomascus leucogenys	LOC100595785P8
Green monkey	Chlorocebus sabaeus	Without Homology
Crab-eating macaque	Macaca fascicularis	Without Homology
Rhesus	Macaca mulatta	Without Homology
Baboon	Papio anubis	Without Homology
Golden snub-nosed monkey	Rhinopithecus roxellana	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

>RPL36AP21
GATGGTCAACGTACCTAAAACCGGAAGAACCTTCTGTAAGAAGTGTGGCAAGCATCAGCCTCACAAAGTGACACAGTATAAGAAGGGTAAGGATTCTTTGTATGCCTAGGGAAAGTGGCACTATGATCGGAAGCAGAGTGGCTATGGTGGGCAGACAAAGCCAATTTTCTGGAAGAAGGCTAAGACCACAAAGAAGATTGTGCTAAGGCTGGACAATGTGTTGAGCCTAACTGCAGATCCAAGAGGATGCTGGCCATTAAGAGATGCAAGCATTTTGAACTGGGAGGAGATAGGAAGAGAAAGGGCCAAGTGATCCAGTTCTAA

>NM_021029.6
CTTTCTTTCCGCGCCGATAGCGCTCACGCAAGCATGGTTAACGTCCCTAAAACCCGCCGGACTTTCTGTAAGAAGTGTGGCAAGCACCAACCCCATAAAGTGACACAGTACAAGAAGGGCAAGGATTCTCTGTACGCCCAGGGAAAGCGGCGTTATGACAGGAAGCAGAGTGGCTATGGTGGGCAAACTAAGCCGATTTTCCGGAAAAAGGCTAAAACTACAAAGAAGATTGTGCTAAGGCTTGAGTGCGTTGAGCCCAACTGCAGATCTAAGAGAATGCTGGCTATTAAAAGATGCAAGCATTTTGAACTGGGAGGAGATAAGAAGAGAAAGGGCCAAGTGATCCAGTTCTAAGTGTCATCTTTTATTATGAAGACAATAAAATCTTGAGTTTATGTTCACTTCATTTGTTTGCTGTTCATCTTTTGGGAGGGAATAAGCTAGAGCCATCAATACAATTCCGCTTGTGGGGAAATTTATGCCTCTTACTGGTACTACTTGTTTTGCATTGAAGCTGACTGGTTGAGTTCACATCATATGTTGCAATTTTCTAATTTGGCACTTCAATCACTAGGGGCCTTATGAGGCAGTTTGTCATTATGCAATGGTTATTGGTTATCATGTGAGTAGACACATTTCAGGCTAATAGGGAGAAGTCAGTAACACATTCATAGTGAATATGAGATGTCTTTGCTAAGAGTTAAGTGTCAGATCTTTGTTATAACAGTTAATTTAATAAAGAATTTTGGCATTGTTCTTCA

>NM_021029.6 

CTTTCTTTCCGCGCCGATAGCGCTCACGCAAGCATGGTTAACGTCCCTAAAACCCGCCGGACTTTCTGTAAGAAGTGTGGCAAGCACCAACCCCATAAAGTGACACAGTACAAGAAGGGCAAGGATTCTCTGTACGCCCAGGGAAAGCGGCGTTATGACAGGAAGCAGAGTGGCTATGGTGGGCAAACTAAGCCGATTTTCCGGAAAAAGGCTAAAACTACAAAGAAGATTGTGCTAAGGCTTGAGTGCGTTGAGCCCAACTGCAGATCTAAGAGAATGCTGGCTATTAAAAGATGCAAGCATTTTGAACTGGGAGGAGATAAGAAGAGAAAGGGCCAAGTGATCCAGTTCTAAGTGTCATCTTTTATTATGAAGACAATAAAATCTTGAGTTTATGTTCACTTCATTTGTTTGCTGTTCATCTTTTGGGAGGGAATAAGCTAGAGCCATCAATACAATTCCGCTTGTGGGGAAATTTATGCCTCTTACTGGTACTACTTGTTTTGCATTGAAGCTGACTGGTTGAGTTCACATCATATGTTGCAATTTTCTAATTTGGCACTTCAATCACTAGGGGCCTTATGAGGCAGTTTGTCATTATGCAATGGTTATTGGTTATCATGTGAGTAGACACATTTCAGGCTAATAGGGAGAAGTCAGTAACACATTCATAGTGAATATGAGATGTCTTTGCTAAGAGTTAAGTGTCAGATCTTTGTTATAACAGTTAATTTAATAAAGAATTTTGGCATTGTTCTTCA

Publications

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