RCPedia: Rtcs

Summary

Retrocopy Name	TUBA4AP1	Plot displaying the genomic locations of a retrocopy (in scaffold_m19_p_3) and its respective parental gene (in scaffold_m19_p_8). Each line represents a retrocopy.
Species	Myotis myotis
Coordinates	scaffold_m19_p_3:164608211-164609146 UCSC
Strand	-
Parental Sequence	TUBA4A_x11
Parental seq. overlap	337 bp
Parental seq. overlap (%)	30%
Genomic Region	Intergenic
Retrocopy Summary	TUBA4AP1, located on scaffold_m19_p_3:164608211-164609146, is a retrocopy of the parental gene TUBA4A. 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	TUBA4A
Full Name	N/A
Also known as	NULL
Coordinate	scaffold_m19_p_8:22577515-22582181
Strand	-
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	TUBA8P1
Bonobo	Pan paniscus	TUBA8P1
Baboon	Papio anubis	TUBA8P2
Golden snub-nosed monkey	Rhinopithecus roxellana	TUBA8P1
Mouse lemur	Microcebus murinus	TUBA8P1
Cow	Bos taurus	LOC100295712P2
Sheep	Ovis aries	LOC101108295P2
Dolphin	Tursiops truncatus	TUBA8P3
Dog	Canis familiaris	LOC100855995P2
Egyptian rousette	Rousettus aegyptiacus	TUBA8P2
Sloth	Choloepus didactylus	LOC119526134P6
Human	Homo sapiens	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
Marmoset	Callithrix jacchus	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
Horse	Equus caballus	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
Kuhl's pipistrelle	Pipistrellus kuhlii	Without Homology
Greater horseshoe bat	Rhinolophus ferrumequinum	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

>TUBA4AP1
CTGACCAGTGCACAGGCCTTCAGGGCTTCTTGGTTTTCCACAGCTTTGGTGGGGGAACTGGTTCTGGGTTCACCTCCCTGCTGATGGAACGTCTCTCCGTCGATTATGGCAAGAAGTCCAAGCTGGAGTTCTCCATTTACCCGGCCCTGGCTTCAAAGTTGGCATTAACTACCAGCCTCCCACTGTGGTCCCTGGTGGAGACCTGGCCAAAGTACAGCGAGCTGTGTGTGTGCATGCTGAGCAACACCACAGCTATTGCTGAGGCCTGGGCTCGCCTGGACCACAAGTTTGACCTGATGTATGCCAAGCGTGCCTTTGTCCACTGGTACGTGGGTGAGGGCATGGAGGAAGGAGAGTTTTCTGAGGCCCGTGAGGACATGGCTGCCCTTGAGAa

>TUBA4A_x11
ACTGCAGCTAGCGCACTTCTCACTGAGACCCGTCGCCCGGACTCTACGTGAGACCCACCGCCCGGACTCAACATGCGTGAATGTATCTCAGTCCATGTGGGGCAAGCAGGTGTCCAGATGGGCAATGCCTGCTGGGAACTCTACTGTCTGGAACATGGGATTCAGCCTGATGGGCAGATGCCCAGTGACAAGACCATTGGTGGAGGAGACGACTCCTTCACCACCTTCTTCTGTGAAACCGGAGCTGGAAAGCACGTGCCCCGGGCAGTTTTTGTGGATTTGGAGCCCACTGTAATAGATGAGATCCGAAATGGCCCATACCGGCAGCTCTTCCATCCAGAGCAGCTCATCACCGGGAAAGAGGATGCTGCGAACAACTACGCCCGGGGCCACTACACCATTGGCAAGGAGATCATTGACCCAGTACTGGACCGGATCCGCAAGCTGTCTGACCAGTGCACAGGActtcagggcttcctggtcttccacagctttggcgggggcaccggctccggcttcacctcactcttgatggagaggctctctgttgattatggcaagaaatccaagctggagttctccatctacccagccccccaggtgtccacagctgtggtcgagccctacaactccatcctgaccacccacaccaccctggagcactcagactgcgccttcatggatgtcaacgctgccatcgctgccatcaagaccaagcgcagtattcagttcgtggactggtgccccacaggcttcaaggttggcatcaactaccagccacccactgtggtgcccggcggtgacctggccaaggtgcagcgtgccgtgtgcatgctgagtaacacgaccgccatcgccgaggcctgggcccgtctggaccacaagttcgacctgatgtatgccaagagggcatttgtgcactggtatgtgggcgagggcatggaggagggtgagttctctgaggcccgggaggatatggctgccctggAGAAGGATTATGAGGAAGTTGGCATCGACTCCTATGAGGACGAGGATGAGGGAGAAGAATAGACCAGCTGCCTGGAGCCCACTCACTATGTTCATTGCAAAATCCTTTCGAAATAAACAGTCTCCTTGCACG

>TUBA4A_x11 

ACTGCAGCTAGCGCACTTCTCACTGAGACCCGTCGCCCGGACTCTACGTGAGACCCACCGCCCGGACTCAACATGCGTGAATGTATCTCAGTCCATGTGGGGCAAGCAGGTGTCCAGATGGGCAATGCCTGCTGGGAACTCTACTGTCTGGAACATGGGATTCAGCCTGATGGGCAGATGCCCAGTGACAAGACCATTGGTGGAGGAGACGACTCCTTCACCACCTTCTTCTGTGAAACCGGAGCTGGAAAGCACGTGCCCCGGGCAGTTTTTGTGGATTTGGAGCCCACTGTAATAGATGAGATCCGAAATGGCCCATACCGGCAGCTCTTCCATCCAGAGCAGCTCATCACCGGGAAAGAGGATGCTGCGAACAACTACGCCCGGGGCCACTACACCATTGGCAAGGAGATCATTGACCCAGTACTGGACCGGATCCGCAAGCTGTCTGACCAGTGCACAGGActtcagggcttcctggtcttccacagctttggcgggggcaccggctccggcttcacctcactcttgatggagaggctctctgttgattatggcaagaaatccaagctggagttctccatctacccagccccccaggtgtccacagctgtggtcgagccctacaactccatcctgaccacccacaccaccctggagcactcagactgcgccttcatggatgtcaacgctgccatcgctgccatcaagaccaagcgcagtattcagttcgtggactggtgccccacaggcttcaaggttggcatcaactaccagccacccactgtggtgcccggcggtgacctggccaaggtgcagcgtgccgtgtgcatgctgagtaacacgaccgccatcgccgaggcctgggcccgtctggaccacaagttcgacctgatgtatgccaagagggcatttgtgcactggtatgtgggcgagggcatggaggagggtgagttctctgaggcccgggaggatatggctgccctggAGAAGGATTATGAGGAAGTTGGCATCGACTCCTATGAGGACGAGGATGAGGGAGAAGAATAGACCAGCTGCCTGGAGCCCACTCACTATGTTCATTGCAAAATCCTTTCGAAATAAACAGTCTCCTTGCACG

Publications

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