RCPedia: Rtcs

Summary

Retrocopy Name	HMGN1P38	Plot displaying the genomic locations of a retrocopy (in chr25) and its respective parental gene (in chr25). Each line represents a retrocopy.
Species	Nomascus leucogenys
Coordinates	chr25:17082571-17083147 UCSC
Strand	+
Parental Sequence	XM_030806380.1
Parental seq. overlap	506 bp
Parental seq. overlap (%)	41.9%
Genomic Region	Intragenic (SCAF4)
Retrocopy Summary	HMGN1P38, located on chr25:17082571-17083147, is a retrocopy of the parental gene HMGN1. 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	HMGN1
Full Name	N/A
Also known as	HMGN1
Coordinate	chr25:24605096-24612372
Strand	-
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Human	Homo sapiens	HMGN1P2
Chimpanzee	Pan troglodytes	HMGN1P35
Bonobo	Pan paniscus	HMGN1P35
Gorilla	Gorilla gorilla	HMGN1P38
Orangutan	Pongo abelii	HMGN1P37
Green monkey	Chlorocebus sabaeus	HMGN1P5
Crab-eating macaque	Macaca fascicularis	HMGN1P9
Rhesus	Macaca mulatta	HMGN1P10
Baboon	Papio anubis	HMGN1P10
Golden snub-nosed monkey	Rhinopithecus roxellana	HMGN1P31
Marmoset	Callithrix jacchus	HMGN1P27
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

>HMGN1P38
GAAGGAAAAGCCCAAGAGGCAATCAGCGTGGCTGTCAGCTAAACCTACTCCTGCAAAAGTGGAAATGAGGCTGAAAAAAGGCAGCAGAAGTATAAATCCTTAGACAAAAAAGTGCAAACAAAAGGGAAAGGGAGGCGGAGCAAAGAGAAAACAGGCTCAAGTGACTAACCAAGAAACTACAGATTTACCTGCAGAAAACGGAGAAACTAAAACCAACGAGAGTCCAGCCTCTGATGAAGCCAGAGAAAGAAGCCAAGTCTACTCAGTACATACCATGTCTTATCAGTGGTCCCTGTCTCCCTTCTCTTCAATCCAGAGTATTTTTATCAACTATTTCGTAAATGCAAGATTTTAGTAGgtctagaaacatttttaaggaGGGAATCTCACTTCATCCCATTTTGTAtgtataaatgctttttttttttaaagaggtaaaatCATTTAccggttgtttattttttggtacaACCAGAACAGAGTGTGGGATGTTGTATTATGGGAGGCTTTGACTGTCTTGGGTGTCAGCTTAACATTCCATAGATGGGGGGGGGGGTTACTTTTTATATCCTAtaat

>XM_030806380.1
GAGGAGTGGCAGCGGCCAGGCAGCGCAGTTTCGCGAAGGCTCTTGGCGCGCCGCGGCCCGCAGGCACCCGGCACGCGCCTTCCCTGCCGCCAGGATGCCCAAGAGGAAGGTCAGTTCCGCCGAAGGCGCCGCCAAGGAAGAGccCAAGAGGAGATCGGCGCGGTTGTCAGCTAAACCTCCTGCAAAAGTGGAAGCGAAGCCGAAAAAGGCAGCAGCGAAGGATAAGTCTTCAGACAAAAAAGTGCaaacaaaagggaaaaggggAGCAAAGGGAAAACAGGCCGAAGTGGCTAACCAAGAAACTAAAGATTTACCTGCAGAAAACGGGGAAACGAAAACTGAGGAGaGTGCAGCCTCTGatgaagcaggagagaaagaagccaagTCTGATTAATACCATATACCATGTCTTATCAGTGGTCCCTGTCTCCCTTCTTGTACAATCCAGAGGAATATTTTTATCAACTATTTTGTAAATGCAAGTTTTTTAGTAgctctagaaacatttttaagaaggaGGGAATCCCACCTCATCccattttttaagtgtaaatgcttttttttaagaggtgaaATCATTTgctggttgtttattttttggtacaACCAGAAAATAGTGTGGGATATTGAATTATGGGAGGCTCTGGCTGTCTCGGATGTCAGCTTAACATTCCATAGATGGGGGGTTAGTTTTTATATCCTATAATACAAAGCATATTAAATGGCAATATGGAGTCAGTCCTGCATTTAATgtcttgaacattttaaattacttctatTCCCATGTTGTTTTTTAGTAGAATTGTTTCCTAAAGAAAACCACTCTTTGATCATGGCTCTCCCTGTCAGAATTGTGTGCACTCTGTAACATCTTTGGTTGTGGTAGTCCTGTTTTCCTAATAACTTTGTGCTGTGAAAGATTACAAATTTGAATATGTAGTGTACGTGCTATTGAGTTGTGAACTGGTGGGCCGTATGTAACAGCTGACCAACATGTGAAGATACTGGTACTTGATAGCCTCTTAAGGAaaatttgcttccaaattttaagctggaaagtcactggaataactttaaaaaagaattacaatacATGGCTTTTTAGAATTTCGTTATGTATGTTAAGATTTGTGTACAAATTGAAATGTCTGTACTGATCCTCAACCAATAAAATctcaattatgaaaata

>XM_030806380.1 

GAGGAGTGGCAGCGGCCAGGCAGCGCAGTTTCGCGAAGGCTCTTGGCGCGCCGCGGCCCGCAGGCACCCGGCACGCGCCTTCCCTGCCGCCAGGATGCCCAAGAGGAAGGTCAGTTCCGCCGAAGGCGCCGCCAAGGAAGAGccCAAGAGGAGATCGGCGCGGTTGTCAGCTAAACCTCCTGCAAAAGTGGAAGCGAAGCCGAAAAAGGCAGCAGCGAAGGATAAGTCTTCAGACAAAAAAGTGCaaacaaaagggaaaaggggAGCAAAGGGAAAACAGGCCGAAGTGGCTAACCAAGAAACTAAAGATTTACCTGCAGAAAACGGGGAAACGAAAACTGAGGAGaGTGCAGCCTCTGatgaagcaggagagaaagaagccaagTCTGATTAATACCATATACCATGTCTTATCAGTGGTCCCTGTCTCCCTTCTTGTACAATCCAGAGGAATATTTTTATCAACTATTTTGTAAATGCAAGTTTTTTAGTAgctctagaaacatttttaagaaggaGGGAATCCCACCTCATCccattttttaagtgtaaatgcttttttttaagaggtgaaATCATTTgctggttgtttattttttggtacaACCAGAAAATAGTGTGGGATATTGAATTATGGGAGGCTCTGGCTGTCTCGGATGTCAGCTTAACATTCCATAGATGGGGGGTTAGTTTTTATATCCTATAATACAAAGCATATTAAATGGCAATATGGAGTCAGTCCTGCATTTAATgtcttgaacattttaaattacttctatTCCCATGTTGTTTTTTAGTAGAATTGTTTCCTAAAGAAAACCACTCTTTGATCATGGCTCTCCCTGTCAGAATTGTGTGCACTCTGTAACATCTTTGGTTGTGGTAGTCCTGTTTTCCTAATAACTTTGTGCTGTGAAAGATTACAAATTTGAATATGTAGTGTACGTGCTATTGAGTTGTGAACTGGTGGGCCGTATGTAACAGCTGACCAACATGTGAAGATACTGGTACTTGATAGCCTCTTAAGGAaaatttgcttccaaattttaagctggaaagtcactggaataactttaaaaaagaattacaatacATGGCTTTTTAGAATTTCGTTATGTATGTTAAGATTTGTGTACAAATTGAAATGTCTGTACTGATCCTCAACCAATAAAATctcaattatgaaaata

Publications

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