RCPedia: Rtcs

Summary

Retrocopy Name	RPL22L1P14	Plot displaying the genomic locations of a retrocopy (in chr4) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr4:185064966-185065271 UCSC
Coordinates (T2T)	chr4:188408683-188408988 UCSC
Coordinates (hg19)	chr4:185986120-185986425 UCSC
Strand	+
Parental Sequence	NM_001099645.2
Parental seq. overlap	264 bp
Parental seq. overlap (%)	13.9%
Genomic Region	Intergenic
Retrocopy Summary	RPL22L1P14, located on chr4:185064966-185065271, is a retrocopy of the parental gene RPL22L1. 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	RPL22L1
Full Name	ribosomal protein L22 like 1
Also known as	-
Coordinate	chr3:170864875-170870195
Strand	-
Gene summary	Predicted to enable RNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in cytoplasmic translation. Predicted to be located in ribosome. [provided by Alliance of Genome Resources, Apr 2022]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	RPL22L1P1
Bonobo	Pan paniscus	RPL22L1P1
Orangutan	Pongo abelii	RPL22L1P1
Gibbon	Nomascus leucogenys	RPL22L1P1
Green monkey	Chlorocebus sabaeus	RPL22L1P1
Crab-eating macaque	Macaca fascicularis	RPL22L1P1
Rhesus	Macaca mulatta	RPL22L1P1
Baboon	Papio anubis	RPL22L1P1
Golden snub-nosed monkey	Rhinopithecus roxellana	RPL22L1P1
Marmoset	Callithrix jacchus	RPL22L1P3
Gorilla	Gorilla gorilla	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

The Genotype-Tissue Expression project - (GTEx)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

Related Sequence

>RPL22L1P14
TGGCCGGCTCTCAAGATGATGCCGAAGAAAGACAAGAAGCATATGTGGTCAACATGGAAGTTTAATTTGGACCTTACTCATTCAATAGAAGATGGAACTTTTGATTCTGGAAATTTTGAACAGTTTCTAAAAGGTTAAAATCAATGGAAAAACTGAAAATCTCACAGATGTTGTTAACAGTGAATGCTTCAAAAATAAAATCACAGTTGTTTCTGAGAAACAATTTTCTAAAAGGTCCTTAAAATGCCTCACCAAGAAATACCTTAGGGAGAACAATCTTCGTGATTGGCCTTGAGTGGCTGCATC

>NM_001099645.2
CTCTCTGCTCTCGCGGCCGACTCGCAAGATGGCGCCGCAGAAAGACAGGAAGCCCAAGAGGTCAACCTGGAGGTTTAATTTGGACCTTACTCATCCAGTAGAAGATGGAATTTTTGATTCTGGAAATTTTGAGCAATTTCTACGGGAGAAGGTTAAAGTCAATGGCAAAACTGGAAATCTCGGGAATGTTGTTCACATTGAACGCTTCAAGAATAAAATCACAGTTGTTTCTGAGAAACAGTTCTCTAAAAGGTATTTGAAATACCTTACCAAGAAATACCTTAAGAAGAACAATCTTCGTGATTGGCTTCGAGTGGTTGCATCTGACAAGGAGACCTACGAACTTCGTTACTTCCAGATTAGTCAAGATGAAGATGAATCAGAGTCGGAGGACTAGGCAAAGGCTCCCCTTACAGGGCTTTGCTTATTAATAAAATAAATGAAGTATACATGAGAAATACCAAGAAATTGGCTTTTAGTTTATCAGTGAATAAAAAATATTATACTCTTGAACTTTTGTCTCATTTTTTTGAGTATGCTGTTTATATGATTTTGATTTCCCTCTGATAACTATCAACAGTATTTAAATAGCTTATAGCTGGTATAATTTTTTCCCACGATTTCCAAAATCTTTTATGTACTCAGGTAAAAGTAGCGTTATATAGGAAATCttttttttagacactctcgttctgtcacccaggctggagtgcagtgactcagcttcctaaatagctggaattacaggtgtgagccaccatgcccggctaattttttgtacttttagtagagtagggtttggccatgttggccaggctggtttcaaactcctgacctcaagtgatctacccacctcggcttcccaaagtgctgattatagctgtgaaccaccatgcccggccAGGAAATCTTACTGTAGAACAATTTTTTATATAGCTGTATAAAATGTATATGATTGTCTTGACAGTCTCAAATACTGTTTTTAATAGCTTGTAAATGTAATCTCAAGTGCTTAGAACAGTTCTTACATATAAGTTGCTCTGTAGTTTGCTCTTATAGTTAGCCCAAAGACTCTGGGTGTGAGGCCTGCTGTAAACCAATGTTAAACTGCTTATTAGAAAGCCCTAACCACCTGCTTTGTAGGCACCAGAAACTCAAAACCAAATCTCAACTCAGCTACAGAATCTACTGTGGTCCTTGTCTGAAAAAATTAGTTCACTCGGTTGGAATCTTGTCTCAGAGCATCCTCATCTCTTTCTCAAAAGCCCCTACCCCAACACCGGCGTGTTGGTTGTCTATTGAAACTTACAAGTGGATGGACCCTTTCTCCCGAATAAACTGGCCTTTGAAAGCTCTAATCGAAATGGTTTGGCAAAATCCATACTGCAGGAGATTAGGGAGGACAAGAATGATGTGCCTTTTTGTACTGCTGAGCCTGATGGTGGTGCCACTACTTCAGGTACTTAGATGAGTCTTGATGCTAATAGAATTGTGTCGCCAAACATATCTGGACAGTTACAACCTAATCTATGCATTAATTGGTTTGGGAATTGCTTGAAATTATTGTTTAATTCAATGTTTTAATTCGTTTTCCTAAAAATTTAAGTGCCCCCATCATCGTGCAATACCTCAGTGCAGCAACTCCTTGATTCTTGGATGACTGAACTTCCTAACTTGGCTCTGCCCCATTGTTCCCATTTttcatgtttttcacaaatagttaaccaggtacctactactgtgcaccgctgcagagcattgaggatgtatgtgatgagtaaaaacacccagcctgctctgctgtgttagtattatgacggaaactgatcaaatcacatgtgaacaaatttactgctacaaaagggagggcttaataaaaggaatttcatctgggaaggcaaa

>NM_001099645.2 

CTCTCTGCTCTCGCGGCCGACTCGCAAGATGGCGCCGCAGAAAGACAGGAAGCCCAAGAGGTCAACCTGGAGGTTTAATTTGGACCTTACTCATCCAGTAGAAGATGGAATTTTTGATTCTGGAAATTTTGAGCAATTTCTACGGGAGAAGGTTAAAGTCAATGGCAAAACTGGAAATCTCGGGAATGTTGTTCACATTGAACGCTTCAAGAATAAAATCACAGTTGTTTCTGAGAAACAGTTCTCTAAAAGGTATTTGAAATACCTTACCAAGAAATACCTTAAGAAGAACAATCTTCGTGATTGGCTTCGAGTGGTTGCATCTGACAAGGAGACCTACGAACTTCGTTACTTCCAGATTAGTCAAGATGAAGATGAATCAGAGTCGGAGGACTAGGCAAAGGCTCCCCTTACAGGGCTTTGCTTATTAATAAAATAAATGAAGTATACATGAGAAATACCAAGAAATTGGCTTTTAGTTTATCAGTGAATAAAAAATATTATACTCTTGAACTTTTGTCTCATTTTTTTGAGTATGCTGTTTATATGATTTTGATTTCCCTCTGATAACTATCAACAGTATTTAAATAGCTTATAGCTGGTATAATTTTTTCCCACGATTTCCAAAATCTTTTATGTACTCAGGTAAAAGTAGCGTTATATAGGAAATCttttttttagacactctcgttctgtcacccaggctggagtgcagtgactcagcttcctaaatagctggaattacaggtgtgagccaccatgcccggctaattttttgtacttttagtagagtagggtttggccatgttggccaggctggtttcaaactcctgacctcaagtgatctacccacctcggcttcccaaagtgctgattatagctgtgaaccaccatgcccggccAGGAAATCTTACTGTAGAACAATTTTTTATATAGCTGTATAAAATGTATATGATTGTCTTGACAGTCTCAAATACTGTTTTTAATAGCTTGTAAATGTAATCTCAAGTGCTTAGAACAGTTCTTACATATAAGTTGCTCTGTAGTTTGCTCTTATAGTTAGCCCAAAGACTCTGGGTGTGAGGCCTGCTGTAAACCAATGTTAAACTGCTTATTAGAAAGCCCTAACCACCTGCTTTGTAGGCACCAGAAACTCAAAACCAAATCTCAACTCAGCTACAGAATCTACTGTGGTCCTTGTCTGAAAAAATTAGTTCACTCGGTTGGAATCTTGTCTCAGAGCATCCTCATCTCTTTCTCAAAAGCCCCTACCCCAACACCGGCGTGTTGGTTGTCTATTGAAACTTACAAGTGGATGGACCCTTTCTCCCGAATAAACTGGCCTTTGAAAGCTCTAATCGAAATGGTTTGGCAAAATCCATACTGCAGGAGATTAGGGAGGACAAGAATGATGTGCCTTTTTGTACTGCTGAGCCTGATGGTGGTGCCACTACTTCAGGTACTTAGATGAGTCTTGATGCTAATAGAATTGTGTCGCCAAACATATCTGGACAGTTACAACCTAATCTATGCATTAATTGGTTTGGGAATTGCTTGAAATTATTGTTTAATTCAATGTTTTAATTCGTTTTCCTAAAAATTTAAGTGCCCCCATCATCGTGCAATACCTCAGTGCAGCAACTCCTTGATTCTTGGATGACTGAACTTCCTAACTTGGCTCTGCCCCATTGTTCCCATTTttcatgtttttcacaaatagttaaccaggtacctactactgtgcaccgctgcagagcattgaggatgtatgtgatgagtaaaaacacccagcctgctctgctgtgttagtattatgacggaaactgatcaaatcacatgtgaacaaatttactgctacaaaagggagggcttaataaaaggaatttcatctgggaaggcaaa

Publications

PMID - Link	Title
No publications available for this retrocopy

Summary

Parental Gene

Homology

Expression

The Genotype-Tissue Expression project - (GTEx)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

log10(TPM+1) <=> TPM

Related Sequence

Publications