RCPedia: Rtcs

Summary

Retrocopy Name	HMGB1P5	Plot displaying the genomic locations of a retrocopy (in scaffold_m13_p_6) and its respective parental gene (in scaffold_m13_p_11). Each line represents a retrocopy.
Species	Rousettus aegyptiacus
Coordinates	scaffold_m13_p_6:87322415-87322841 UCSC
Strand	-
Parental Sequence	HMGB1_x5
Parental seq. overlap	364 bp
Parental seq. overlap (%)	16.6%
Genomic Region	Intergenic
Retrocopy Summary	HMGB1P5, located on scaffold_m13_p_6:87322415-87322841, is a retrocopy of the parental gene HMGB1. 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	HMGB1
Full Name	N/A
Also known as	NULL
Coordinate	scaffold_m13_p_11:3496361-3502206
Strand	-
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Pig	Sus scrofa	HMGB1P3
Cow	Bos taurus	HMGB1P8
Sheep	Ovis aries	HMGB1P9
Dog	Canis familiaris	HMGB1P7
Velvety free-tailed bat	Molossus molossus	HMGB1P24
Greater horseshoe bat	Rhinolophus ferrumequinum	HMGB1P25
Human	Homo sapiens	Without Homology
Chimpanzee	Pan troglodytes	Without Homology
Bonobo	Pan paniscus	Without Homology
Gorilla	Gorilla gorilla	Without Homology
Orangutan	Pongo abelii	Without Homology
Gibbon	Nomascus leucogenys	Without Homology
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
Dolphin	Tursiops truncatus	Without Homology
Horse	Equus caballus	Without Homology
Panda	Ailuropoda melanoleuca	Without Homology
Cat	Felis catus	Without Homology
Pale spear-nosed bat	Phyllostomus discolor	Without Homology
Greater mouse-eared bat	Myotis myotis	Without Homology
Kuhl's pipistrelle	Pipistrellus kuhlii	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

>HMGB1P5
CAGCCACTGCAGTACATCGAGGTCCACAGAGACAGCACCAGGGCAAGTGAGAGCCAGACAGGAACTGGGTGACTCTGAGCCTCACCGAAGAAAAATAACTATATATGGGCAAAGGAGATCCTAAGAAGCCGAGAGGCAAGATATCATCATATACATTCTTTGTGAAAATTTGCTGGGAAGAGCACAAGAAGAAGCACCCAGATGCCTCAGTCAACTCCTCAGGGTTTTCTAAGAAGTGTTCAGATTGGTGAAAAATCATGTCTGCTAAAGAGAAAGGAAAATTTTAAGATGTGGCAAAAGTGAACAAGGCCCATTATGAAAGAGCATGAAAGCATATCCTTCCTGAAGGGGAAATAAAAATGTTCAAGGATCTCAGTGTACCCAAGAGGCCTCCTTTGGCCTTCTTCTTGTTTTGTTCTGAGTATCA

>HMGB1_x5
GTTACAGAGCGGAGAGAGTGAGGAGGCTGCGTCTGGCTCCCGCTCTCACAGCCATTGCAGTACATTGAGCTCCATAGAGACAGCGCCGGGGCAAGTGCGAGCCGGACGGGCACTGGGCGACTCTGTGCTCGCGGAGGAAAAATAAGTCAACATGGGCAAAGGAGATCCTAAGAAGCCCAGAGGCAAAATGTCATCATATGCATTCTTTGTGCAAACTTGCCGGGAGGAGCACAAGAAGAAGCACCCAGATGCTTCAGTCAACTTCTCAGAGTTTTCTAAGAAGTGCTCAGAGAGGTGGAAGACCATGTCTGCTAAAGAGAAGGGAAAATTCGAAGACATGGCAAAGGCGGACAAGGCCCGCTACGAAAGAGAAATGAAAACTTATATCCCCCCCAAAGGGGAAACAAAAAAGAAGTTCAAGGACCCCAATGCACCCAAGAGGCCTCCTTCGGCCTTTTTCTTGTTTTGTTCTGAGTATCGCCCCAAAATCAAAGGAGAGCACCCCGGCCTGTCCATTGGCGACGTCGCAAAGAAGCTGGGGGAGATGTGGAATAACACCGCCGCGGACGACAAGCAGCCTTACGAGAAGAAGGCCGCCAAGCTGAAGGAGAAaggaggaggaggaggatgaagacgaggaggatgaggacgaggacgaggaggaggacgacgaATGAGTCGCTGGCGCAGTTTTCTTGTCTATAAAGCATTTAACCCCCCTGTACACAACTCACTCCTTTTAAAGAAAAAAAAATTGAAATGTAAGGCTGTGTAAGATTTGTTTTTAAACTGTACAGTGTCTTTTTTTGTATAGTTAACACACTACCGAATGTGTCTTTAGGTAGCCCTGTCCTGGTGGTATTTCAGTAGCCACTGACCTTGCCTGGTACAGTATGGGGGTTGTAAATTGGCATGGAAACTTAAAGCAGGTTCTTGTTGGTGCACAGCACAAATTAGTTATATATGGGGATGGTAGTTTTTCATCTTCAGTTGTCTCTGATGCAGCTTATACGAAATAATTGTCGTTCTGTTAACTGAATACCACTCTGTAATTGCAAAAAAAAATTGCAGCTGTTTTGTTGACATTCTGAATGCTTCTAAGTAAATACAATTTTTTTTATTAGTATTGTTGTCCTTTTCATAGGTCTGGAATTTTTCTTCTTGAGGGGAAGCTAGTCTTTTGCTTTTTCCCATTTTGGATCACATGACTTATTACAGTGTTTAGCTTTTCATGTAGTTAGTTGACTGATAAAAAGCTTTTGTCCACACGCCCTGCATACTCACGATGAGGGTAATCAGAGTTAGATGGAGACAGTTTTCATCCATAGCCGAAACTCGAAAATCTCGATCAGTTGATATCAAATTTCACACAGCCCAGTTACATTTACGAAGTGAAGAGTAACCAGTCTGCTCACAGCATGGGATTATTAGAATCAAACGTTTTGAAAGTCTGTCCTTGAAGGACTAAATAGAAAAATACGTTCTAGTCTTTGCAATGAGGACTCCACGTTCTTTAACTCCCATTACCATGTAATGGCAGTTATATTTGCAGTTCCCACGTGAAAGACCTGAGGATATAGCCCCAAAAGCGTGACCTTAAAATACAAGACTGCCACGTTACGTTTTTTGTTGACGTTAGTCTAGGCAAAGGCTCTTTAAAAAGTGCTGGCTGTAAATGTCTTCTATTTACCTAAATTTGGATTGTTTAGGAAACGAGACTCCATTAAAGGTATTTCTAATTAATTAGGCCAACTTTTAAGATCGTGTACAACATTTAAAATCAACTATATTTTCCTATATTATGCTTTGTTCCTTTATAAGTCAAATACTTGAGGGAAGAAGACAATTTAAACTTTTGTGTCTCAGTATGAATTGTCCAATTTATTTGAACTTGATTTTTCTTTACAAAACAAACTCATTCATTAGGATCATATGTTTATCTGCTTAGCTGTTTAGGGAACAATTTGGCAATTTTGTGGTTTTTGAGATGATCGTTCTCTTAAAGTGCCAGTGTTTTAAAATAGCGTTCTTGTAATTTTACACGCTTTTGTGATGGAGTGCTGTTTTGTTATATAATTTTGACTTGGATTCTTTCCATTTGCATTTGTTTATGTAATTTCAGGAGGAATAACTGAACATCTGAGTCCTGGATGATACTAATAAACTAATAATTGCAGAGGTTTTAAATATT

>HMGB1_x5 

GTTACAGAGCGGAGAGAGTGAGGAGGCTGCGTCTGGCTCCCGCTCTCACAGCCATTGCAGTACATTGAGCTCCATAGAGACAGCGCCGGGGCAAGTGCGAGCCGGACGGGCACTGGGCGACTCTGTGCTCGCGGAGGAAAAATAAGTCAACATGGGCAAAGGAGATCCTAAGAAGCCCAGAGGCAAAATGTCATCATATGCATTCTTTGTGCAAACTTGCCGGGAGGAGCACAAGAAGAAGCACCCAGATGCTTCAGTCAACTTCTCAGAGTTTTCTAAGAAGTGCTCAGAGAGGTGGAAGACCATGTCTGCTAAAGAGAAGGGAAAATTCGAAGACATGGCAAAGGCGGACAAGGCCCGCTACGAAAGAGAAATGAAAACTTATATCCCCCCCAAAGGGGAAACAAAAAAGAAGTTCAAGGACCCCAATGCACCCAAGAGGCCTCCTTCGGCCTTTTTCTTGTTTTGTTCTGAGTATCGCCCCAAAATCAAAGGAGAGCACCCCGGCCTGTCCATTGGCGACGTCGCAAAGAAGCTGGGGGAGATGTGGAATAACACCGCCGCGGACGACAAGCAGCCTTACGAGAAGAAGGCCGCCAAGCTGAAGGAGAAaggaggaggaggaggatgaagacgaggaggatgaggacgaggacgaggaggaggacgacgaATGAGTCGCTGGCGCAGTTTTCTTGTCTATAAAGCATTTAACCCCCCTGTACACAACTCACTCCTTTTAAAGAAAAAAAAATTGAAATGTAAGGCTGTGTAAGATTTGTTTTTAAACTGTACAGTGTCTTTTTTTGTATAGTTAACACACTACCGAATGTGTCTTTAGGTAGCCCTGTCCTGGTGGTATTTCAGTAGCCACTGACCTTGCCTGGTACAGTATGGGGGTTGTAAATTGGCATGGAAACTTAAAGCAGGTTCTTGTTGGTGCACAGCACAAATTAGTTATATATGGGGATGGTAGTTTTTCATCTTCAGTTGTCTCTGATGCAGCTTATACGAAATAATTGTCGTTCTGTTAACTGAATACCACTCTGTAATTGCAAAAAAAAATTGCAGCTGTTTTGTTGACATTCTGAATGCTTCTAAGTAAATACAATTTTTTTTATTAGTATTGTTGTCCTTTTCATAGGTCTGGAATTTTTCTTCTTGAGGGGAAGCTAGTCTTTTGCTTTTTCCCATTTTGGATCACATGACTTATTACAGTGTTTAGCTTTTCATGTAGTTAGTTGACTGATAAAAAGCTTTTGTCCACACGCCCTGCATACTCACGATGAGGGTAATCAGAGTTAGATGGAGACAGTTTTCATCCATAGCCGAAACTCGAAAATCTCGATCAGTTGATATCAAATTTCACACAGCCCAGTTACATTTACGAAGTGAAGAGTAACCAGTCTGCTCACAGCATGGGATTATTAGAATCAAACGTTTTGAAAGTCTGTCCTTGAAGGACTAAATAGAAAAATACGTTCTAGTCTTTGCAATGAGGACTCCACGTTCTTTAACTCCCATTACCATGTAATGGCAGTTATATTTGCAGTTCCCACGTGAAAGACCTGAGGATATAGCCCCAAAAGCGTGACCTTAAAATACAAGACTGCCACGTTACGTTTTTTGTTGACGTTAGTCTAGGCAAAGGCTCTTTAAAAAGTGCTGGCTGTAAATGTCTTCTATTTACCTAAATTTGGATTGTTTAGGAAACGAGACTCCATTAAAGGTATTTCTAATTAATTAGGCCAACTTTTAAGATCGTGTACAACATTTAAAATCAACTATATTTTCCTATATTATGCTTTGTTCCTTTATAAGTCAAATACTTGAGGGAAGAAGACAATTTAAACTTTTGTGTCTCAGTATGAATTGTCCAATTTATTTGAACTTGATTTTTCTTTACAAAACAAACTCATTCATTAGGATCATATGTTTATCTGCTTAGCTGTTTAGGGAACAATTTGGCAATTTTGTGGTTTTTGAGATGATCGTTCTCTTAAAGTGCCAGTGTTTTAAAATAGCGTTCTTGTAATTTTACACGCTTTTGTGATGGAGTGCTGTTTTGTTATATAATTTTGACTTGGATTCTTTCCATTTGCATTTGTTTATGTAATTTCAGGAGGAATAACTGAACATCTGAGTCCTGGATGATACTAATAAACTAATAATTGCAGAGGTTTTAAATATT

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