RCPedia: Rtcs

Summary

Retrocopy Name	POU5F1P2	Plot displaying the genomic locations of a retrocopy (in chr9) and its respective parental gene (in chr4). Each line represents a retrocopy.
Species	Macaca mulatta
Coordinates	chr9:69910235-69910910 UCSC
Strand	+
Parental Sequence	NM_001114955.1
Parental seq. overlap	614 bp
Parental seq. overlap (%)	56.1%
Genomic Region	Intragenic (HERC4)
Retrocopy Summary	POU5F1P2, located on chr9:69910235-69910910, is a retrocopy of the parental gene POU5F1. 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	POU5F1
Full Name	N/A
Also known as	OCT3\|OCT3/4\|OCT4\|Oct-4
Coordinate	chr4:138762445-138768342
Strand	+
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Human	Homo sapiens	POU5F1P5
Chimpanzee	Pan troglodytes	POU5F1P6
Bonobo	Pan paniscus	POU5F1P6
Gorilla	Gorilla gorilla	POU5F1P5
Orangutan	Pongo abelii	POU5F1P3
Gibbon	Nomascus leucogenys	POU5F1P2
Green monkey	Chlorocebus sabaeus	POU5F1P2
Crab-eating macaque	Macaca fascicularis	POU5F1P2
Baboon	Papio anubis	POU5F1P2
Golden snub-nosed monkey	Rhinopithecus roxellana	POU5F1P2
Marmoset	Callithrix jacchus	POU5F1P3
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

>POU5F1P2
CAGTCCCAGGACATCTCAAAGCTCTGCAGAAAGAACTTGAGCAATTTGCCAAGTTCCTGAAGCAGAAGAGGATCACCCTGGGATATGCACAGGCCTGTGTGGGGCTTACCCTGGGGGTTCTATTTGGGTAGGTGTTCAGCCCAACAACCATCTGCCTCTTTGAGGCTCAGCAGCTTAGCTTCAAGAACATGAGTAAGCGGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAAAATATTCAGGAGATGCAAAGCAGAAACTCTTGTGCAGGCCTGAAATAGAAAGCGAACCAGTATTGAGAACCTGGAGAATTTGTTCCTGCAGCACCCGGAACCCACACTGCAGCAGATCAGTCACATCGCCCAGCAGCTTGGGCTCTAGAAGGATGTGATCTGAGTGTGGTTCTGTAACTGGTGCCAGAAGGGCAAGTGATCAAGCAGTGATTATGCACCATGAGAGGATTTTGAGGCTGCTGGGTCTCCTTTCTCAGGGGCATCAGTGTCCTTTCCTCTGGCCTCAGGGCCCCATTTTGATACCCCAGGCTATGGGAGCCCTCATTGCACTGCACTGCACTGCACTGTATTCCTCATTCCCTTTCCTTGAGGGAGAAGCCTTTCCCCCTGTTTCCATTGCCACTCTGGGCTCTCCCATGCATTCAAACTGA

>NM_001114955.1
ATGGCGGGACACCTGGCTTCGGATTTCGCCTTCTCGCCCCCTCCAGGAGGTGGAGGTGATGGGCCAGGGGGGCCGGAGCCGGGCTGGGTTGATCCTCGGACCTGGCTAAGCTTCCAAGGCCCTCCTGGAGGGCCAGGAATCGGGCCGGGGGTTGGGCCAGGCTCTGAGGTGTGGGGGATTCCCCCGTGCCCCCCGCCATATGAGTTCTGTGGGGGGATGGCGTACTGTGGGCCTCAGGTTGGAGTGGGGCTAGTGCCCCAAGGTGGCTTGGAGACCTCTCAGCCTGAGGGCGAAGCAGGAGCCGGGGTGGAGAGCAACTCCGATGGGGCCTCCCCAGAGCCCTGCACCGTCCCCACTGGTGCCGTGAAGCTGGAGAAGGAGAAGCTGGAGCAAAACCCGGAGGAGTCCCAGGACATCAAAGCTCTGCAGAAAGAACTCGAGCAATTTGCCAAGCTCCTGAAGCAGAAGAGGATCACCCTGGGATATACACAGGCCGATGTGGGGCTCACCCTGGGGGTTCTATTTGGGAAGGTGTTCAGCCAAACGACCATCTGCCGCTTTGAGGCTCTGCAGCTTAGCTTCAAGAACATGTGTAAGCTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAAAATCTTCAGGAGATATGCAAAGCAGAAACCCTGGTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAACCGAGTGAGAGGCAGCCTGGAGAATCTGTTCCTGCAGTGCCCGAAACCCACCCTGCAGCAGATCAGCCACATCGCCCAGCAGCTTGGGCTCGAGAAGGATGTGGTCCGAGTGTGGTTCTGTAACCGGCGCCAGAAGGGCAAGCGATCGAGCAGTGACTATGCACAACGAGAGGATTTTGAGGCTGCTGGGTCTCCTTTCTCAGGGGGACCAGTGTCCTTTCCTCTGGCCCCAGGGCCCCATTTTGGTACCCCAGGCTATGGGAGCCCTCACTTCACTGCACTGTACTCCTCGGTCCCTTTCCCTGAGGGGGAAGCCTTTCCCCCTGTCTCCGTCACCACTCTGGGCTCTCCCATGCATTCAAACTGA

>NM_001114955.1 

ATGGCGGGACACCTGGCTTCGGATTTCGCCTTCTCGCCCCCTCCAGGAGGTGGAGGTGATGGGCCAGGGGGGCCGGAGCCGGGCTGGGTTGATCCTCGGACCTGGCTAAGCTTCCAAGGCCCTCCTGGAGGGCCAGGAATCGGGCCGGGGGTTGGGCCAGGCTCTGAGGTGTGGGGGATTCCCCCGTGCCCCCCGCCATATGAGTTCTGTGGGGGGATGGCGTACTGTGGGCCTCAGGTTGGAGTGGGGCTAGTGCCCCAAGGTGGCTTGGAGACCTCTCAGCCTGAGGGCGAAGCAGGAGCCGGGGTGGAGAGCAACTCCGATGGGGCCTCCCCAGAGCCCTGCACCGTCCCCACTGGTGCCGTGAAGCTGGAGAAGGAGAAGCTGGAGCAAAACCCGGAGGAGTCCCAGGACATCAAAGCTCTGCAGAAAGAACTCGAGCAATTTGCCAAGCTCCTGAAGCAGAAGAGGATCACCCTGGGATATACACAGGCCGATGTGGGGCTCACCCTGGGGGTTCTATTTGGGAAGGTGTTCAGCCAAACGACCATCTGCCGCTTTGAGGCTCTGCAGCTTAGCTTCAAGAACATGTGTAAGCTGCGGCCCTTGCTGCAGAAGTGGGTGGAGGAAGCTGACAACAATGAAAATCTTCAGGAGATATGCAAAGCAGAAACCCTGGTGCAGGCCCGAAAGAGAAAGCGAACCAGTATCGAGAACCGAGTGAGAGGCAGCCTGGAGAATCTGTTCCTGCAGTGCCCGAAACCCACCCTGCAGCAGATCAGCCACATCGCCCAGCAGCTTGGGCTCGAGAAGGATGTGGTCCGAGTGTGGTTCTGTAACCGGCGCCAGAAGGGCAAGCGATCGAGCAGTGACTATGCACAACGAGAGGATTTTGAGGCTGCTGGGTCTCCTTTCTCAGGGGGACCAGTGTCCTTTCCTCTGGCCCCAGGGCCCCATTTTGGTACCCCAGGCTATGGGAGCCCTCACTTCACTGCACTGTACTCCTCGGTCCCTTTCCCTGAGGGGGAAGCCTTTCCCCCTGTCTCCGTCACCACTCTGGGCTCTCCCATGCATTCAAACTGA

Publications

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