RCPedia: Rtcs

Summary

Retrocopy Name	ARF1P3	Plot displaying the genomic locations of a retrocopy (in chr8) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Pan paniscus
Coordinates	chr8:120839961-120840250 UCSC
Strand	+
Parental Sequence	XM_003804759.3
Parental seq. overlap	247 bp
Parental seq. overlap (%)	12.9%
Genomic Region	Intergenic
Retrocopy Summary	ARF1P3, located on chr8:120839961-120840250, is a retrocopy of the parental gene ARF1. 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	ARF1
Full Name	N/A
Also known as	-
Coordinate	chr1:203484803-203501395
Strand	+
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Human	Homo sapiens	ARF1P3
Chimpanzee	Pan troglodytes	ARF1P2
Gorilla	Gorilla gorilla	ARF1P2
Orangutan	Pongo abelii	ARF1P2
Gibbon	Nomascus leucogenys	ARF1P5
Green monkey	Chlorocebus sabaeus	ARF1P1
Crab-eating macaque	Macaca fascicularis	ARF1P5
Rhesus	Macaca mulatta	ARF1P5
Baboon	Papio anubis	ARF1P5
Golden snub-nosed monkey	Rhinopithecus roxellana	ARF1P4
Marmoset	Callithrix jacchus	ARF1P13
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

>ARF1P3
GAACCAATGCCTGGCTGGGGGAGCTGCCACTGAGGTGTCCCTGGCCAGTGTCCTTCCACCCACTCGCAAGCATGGGGGACATCTTCACCAACTTCTTAAAGGGCTTTTTTGGCACAAAAGAAGTGCCCATCATCATGGTGGGCCTGGACGCTGCAAGGAAGACGCCAATCCTGTACAAGCTGAAGTTGGGCGAGATTATGACCACCGTCCCCACCTTAGACTTCAGCGTGGAGAATGCGGAGTACAAGAACATCAGCTTCAGCCTGTGGGATGTGGGTGGCCAGGACAAG

>XM_003804759.3
TGGGCGGAGTTCCCGGCGTCTCCGCCCCTTACCCGGCGTGCCCCGCGCCCGCAGGCGCTGACGTGGCCGCCGTCAGAGCCGCCATCTTGTGGGAGCAAAACCAACGCCTGGCTCGGAGCAGCAGCCTCTGAGGTGTCCCTGGCCAGTGTCCTTCCACCTGTCCACAAGCATGGGGAACATCTTCGCCAACCTCTTCAAGGGCCTTTTTGGCAAAAAAGAAATGCGCATCCTCATGGTGGGCCTGGATGCTGCAGGGAAGACCACGATCCTCTACAAGCTTAAGCTGGGTGAGATCGTGACCACCATTCCCACCATAGGCTTCAACGTGGAAACCGTGGAGTACAAGAACATCAGCTTCACTGTGTGGGACGTGGGTGGCCAGGACAAGATCCGGCCCCTGTGGCGCCACTACTTCCAGAACACACAAGGCCTGATCTTCGTGGTGGACAGCAATGACAGAGAGCGTGTGAACGAGGCCCGTGAGGAGCTCATGAGGATGCTGGCCGAGGACGAGCTCCGGGATGCTGTCCTCCTGGTGTTCGCCAACAAGCAGGACCTCCCCAACGCCATGAATGCGGCTGAGATCACAGACAAGCTGGGGCTGCACTCCCTACGCCACAGAAACTGGTACATTCAGGCCACCTGCGCCACCAGCGGTGACGGGCTCTATGAAGGACTGGACTGGCTGTCCAATCAGCTCCGGAACCAGAAGTGAACGTGACCCCCCTCCCTCTCACTCCTCTTGCCCTCTGCTTTACTCTCATGTGGCAAACGTGCGGCTCGTGGTGTGAGTGCCAGAAGCTGCCTCCGTGGTTTGGTCACCGTGTGCATCGCACCGTGCTGTAAATGTGGCAGACACAGCCTGCGGCCAGGCTTTTTATTTAATGTAAATAGTTTTTGTTTCCAATGAGGCAGTTTCTGGTACTCCTATGCAATATTACTCAGCTTTTTTTATTGTAAAAAGAAAAATCAACTCACTGTTCAGTGCTGAGAGGGGATGTAGGCCCATGGGCACCTGGCCTCCAGGAGTCGCTGTGTTGGGAGAGCCGGCCACGCCCTTGGCTTTAGAGCTGTGTTGAAATCCATTTTGGTGGTTGGTTTTTAACCCAAACTCAGTGCATTTTTTAAAATAGTTAAGAATCCAAGTCGAGAACACTTGAACACACAGAAGGGAGACCCTGCCTAGCATAGATTTGCAGTTACGGCCTGGATGCCAGTCGCCAGCCCAGCTGTTCCCCTCGGGAACATGAGGTGGTGGTGGCGCAGCAGACCGCGATCAATTCTGCATGGTCACAGTAGAGATCCCCGCAACTCGCTCGTCCTTGGGTCACCCTGCATTCCATAGCCATGTGCTTGTCCCTGTGCTCCCACGGATCCCAGGGGCCAGGCTGGGAGCCCACAGCCACCCCACTCTCCCGCAGGCCGCCCTACCCACCTTCAGGCAGCCTATGGGACGCAGGGCCCCATCTGTCCCTCGGTCACCGTGTGGCCAGAGTGGGTCCGTCGTCCCCAACACTCGTGCTCGCTCAGACACTTTGGCAGGATGTCTGGGGCCTCACCAGCAGGAGCGCGTGCAAGCCGGGCAGGCAGTCCACCTAGACCCACAGCCCCTCGGGAGCACCCCACCTCTGTGTGTGATGTAGCTTTCTCTCCCTCAGCCTGCAAGGGTCCGATTTGCCATCGAAAAAGACAACCTCTACTTTTTTCTTTTGTATTTTGATAAACACTGAAGCTGGAGCTGTTAAATTTATCTTGGGGAAACCTCAGAACTGGTCTATTTGGTGTCGTGGAACCTCTTACTGCTTTCAATACACGATTAGTAATCAACTGTTTTGTATACTTGTTTTCAGTTTTCATTTCGACAAACAAGCACTGTAATTATAGCTATTAGAATAAAATCTCTTAACTATTTCA

>XM_003804759.3 

TGGGCGGAGTTCCCGGCGTCTCCGCCCCTTACCCGGCGTGCCCCGCGCCCGCAGGCGCTGACGTGGCCGCCGTCAGAGCCGCCATCTTGTGGGAGCAAAACCAACGCCTGGCTCGGAGCAGCAGCCTCTGAGGTGTCCCTGGCCAGTGTCCTTCCACCTGTCCACAAGCATGGGGAACATCTTCGCCAACCTCTTCAAGGGCCTTTTTGGCAAAAAAGAAATGCGCATCCTCATGGTGGGCCTGGATGCTGCAGGGAAGACCACGATCCTCTACAAGCTTAAGCTGGGTGAGATCGTGACCACCATTCCCACCATAGGCTTCAACGTGGAAACCGTGGAGTACAAGAACATCAGCTTCACTGTGTGGGACGTGGGTGGCCAGGACAAGATCCGGCCCCTGTGGCGCCACTACTTCCAGAACACACAAGGCCTGATCTTCGTGGTGGACAGCAATGACAGAGAGCGTGTGAACGAGGCCCGTGAGGAGCTCATGAGGATGCTGGCCGAGGACGAGCTCCGGGATGCTGTCCTCCTGGTGTTCGCCAACAAGCAGGACCTCCCCAACGCCATGAATGCGGCTGAGATCACAGACAAGCTGGGGCTGCACTCCCTACGCCACAGAAACTGGTACATTCAGGCCACCTGCGCCACCAGCGGTGACGGGCTCTATGAAGGACTGGACTGGCTGTCCAATCAGCTCCGGAACCAGAAGTGAACGTGACCCCCCTCCCTCTCACTCCTCTTGCCCTCTGCTTTACTCTCATGTGGCAAACGTGCGGCTCGTGGTGTGAGTGCCAGAAGCTGCCTCCGTGGTTTGGTCACCGTGTGCATCGCACCGTGCTGTAAATGTGGCAGACACAGCCTGCGGCCAGGCTTTTTATTTAATGTAAATAGTTTTTGTTTCCAATGAGGCAGTTTCTGGTACTCCTATGCAATATTACTCAGCTTTTTTTATTGTAAAAAGAAAAATCAACTCACTGTTCAGTGCTGAGAGGGGATGTAGGCCCATGGGCACCTGGCCTCCAGGAGTCGCTGTGTTGGGAGAGCCGGCCACGCCCTTGGCTTTAGAGCTGTGTTGAAATCCATTTTGGTGGTTGGTTTTTAACCCAAACTCAGTGCATTTTTTAAAATAGTTAAGAATCCAAGTCGAGAACACTTGAACACACAGAAGGGAGACCCTGCCTAGCATAGATTTGCAGTTACGGCCTGGATGCCAGTCGCCAGCCCAGCTGTTCCCCTCGGGAACATGAGGTGGTGGTGGCGCAGCAGACCGCGATCAATTCTGCATGGTCACAGTAGAGATCCCCGCAACTCGCTCGTCCTTGGGTCACCCTGCATTCCATAGCCATGTGCTTGTCCCTGTGCTCCCACGGATCCCAGGGGCCAGGCTGGGAGCCCACAGCCACCCCACTCTCCCGCAGGCCGCCCTACCCACCTTCAGGCAGCCTATGGGACGCAGGGCCCCATCTGTCCCTCGGTCACCGTGTGGCCAGAGTGGGTCCGTCGTCCCCAACACTCGTGCTCGCTCAGACACTTTGGCAGGATGTCTGGGGCCTCACCAGCAGGAGCGCGTGCAAGCCGGGCAGGCAGTCCACCTAGACCCACAGCCCCTCGGGAGCACCCCACCTCTGTGTGTGATGTAGCTTTCTCTCCCTCAGCCTGCAAGGGTCCGATTTGCCATCGAAAAAGACAACCTCTACTTTTTTCTTTTGTATTTTGATAAACACTGAAGCTGGAGCTGTTAAATTTATCTTGGGGAAACCTCAGAACTGGTCTATTTGGTGTCGTGGAACCTCTTACTGCTTTCAATACACGATTAGTAATCAACTGTTTTGTATACTTGTTTTCAGTTTTCATTTCGACAAACAAGCACTGTAATTATAGCTATTAGAATAAAATCTCTTAACTATTTCA

Publications

PMID - Link	Title