RCPedia: Rtcs

Summary

Retrocopy Name	YBX1P11	Plot displaying the genomic locations of a retrocopy (in scaffold_m29_p_11) and its respective parental gene (in scaffold_m29_p_9). Each line represents a retrocopy.
Species	Rhinolophus ferrumequinum
Coordinates	scaffold_m29_p_11:27373129-27373900 UCSC
Strand	+
Parental Sequence	YBX1_x1
Parental seq. overlap	620 bp
Parental seq. overlap (%)	62.4%
Genomic Region	Intergenic
Retrocopy Summary	YBX1P11, located on scaffold_m29_p_11:27373129-27373900, is a retrocopy of the parental gene YBX1. 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	YBX1
Full Name	N/A
Also known as	NULL
Coordinate	scaffold_m29_p_9:29966323-29985745
Strand	+
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Bonobo	Pan paniscus	YBX1P3
Orangutan	Pongo abelii	YBX1P5
Green monkey	Chlorocebus sabaeus	YBX1P4
Crab-eating macaque	Macaca fascicularis	YBX1P9
Rhesus	Macaca mulatta	YBX1P10
Baboon	Papio anubis	YBX1P8
Marmoset	Callithrix jacchus	YBX1P6
Human	Homo sapiens	Without Homology
Chimpanzee	Pan troglodytes	Without Homology
Gorilla	Gorilla gorilla	Without Homology
Gibbon	Nomascus leucogenys	Without Homology
Golden snub-nosed monkey	Rhinopithecus roxellana	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
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
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

>YBX1P11
CAAGGTCATTGCAAAGAAGAGGTGGATTTGTACACCAGACTGCCATAAAGAAGAATAACCCCAGGAAGCACCTTCGCAGTGCAGGAGATGGAGAGACTGTGGAGTTTGATGATGTTGAAGGAGAAAAGGGTGCAGAGGCAGCACATGTTACAGGCCCTGGTGGAGTTCCAGTGCGAGGCAGCAAATATGCAGCAGACGGTAACCATGATAGACGCTATCCAAGTCACAGGGTCTCTACGGCAATTACCAGCAGAATTACCAGAACAGGGAAAGTAGGGAAAAGAATGAGAGATGGGAGAGCTCCCATCAGCACTCCAGGCCCAACAGAACCGGCCCTACTGCAGGCGATGGTTGCTACCTTATTTATTACGTGTGGAGACCCTATGGGCGTCGACCACAGTATTCCAACCCTCCTGTGCAGGGACAGAGAGAGGGAGGGTGCTGACAACCAGGGTGCAGGAGAACAAGGTAGACCAGTGAGACAGAACATGTATCAGGGCTATAGACCACGATTCCGCAGTGGCCCTCCTCGCCAAAGACAGCCTAGATAGGACAGAATGAAAGTAGATAAGGAAAATGAAGGAGATGAGACACAAGGTCAGCAGCCACCTAAACCTTGGTACCACAGTAAGAGCGTTCAATTATGGACGCACACTCCCAGAAAACCCTAAACCATAAGATGGCAAAGAGGCAAAAGCAGC

>YBX1_x1
ATGAGCAGCGAGGCCGAGACCCAgcagccgcccgccgccccccccgccgcccccgccctcagcgctgccgACACCAAGCCCGGCACCACGGGCAGCGGCGCAGGGAGCGGCGGCCCGGGCGGCCTTACATCGGCGGCGCCCGCCGGCGGGGACAAGAAGGTCATCGcaacgaaggttttgggaacagtaaaatggttcaatgtaagaaacggatatggtttcatcaACAGGAATGACACCAAGGAAGACGTATTTGTACACCAGACTGCCATAAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGAGATGGAGAGACTGTGGAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCAAATGTTACAGGCCCTGGTGGAGTTCCTGTGCAAGGCAGTAAATATGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCGCAGGGGTCCTCCACGCAATTACCAGCAGAATTACCAGAACAGTGAGAGTGGGGAAAAGAATGAGGGATCGGAGAGCGCTCCCGAAGGCCAGGCCCAACAGCGCCGGCCCTACCGCAGGCGACGGTTCCCACCTTACTACATGCGGAGACCCTACGGGCGTCGACCACAGTATTCCAACCCTCCAGTGCAGGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTGCAGGAGAACAAGGTAGACCAGTGAGACAGAATATGTATCGAGGCTATAGACCACGATTCCGCAGGGGCCCTCCTCGCCAAAGACAGCCTAGAGAGGACGGCAATGAAGAAGATAAAGAAAATCAAGGAGATGAGACCCAAGGTCAGCAGCCACCTCAACGTCGGTACCGCCGTAACTTTAATTACCGACGCAGACGCCCAGAAAACCCTAAACCACAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATTCGTCCGCTCCCGAGGCTGAGCAGGGCGGGGCTGAGTAA

>YBX1_x1 

ATGAGCAGCGAGGCCGAGACCCAgcagccgcccgccgccccccccgccgcccccgccctcagcgctgccgACACCAAGCCCGGCACCACGGGCAGCGGCGCAGGGAGCGGCGGCCCGGGCGGCCTTACATCGGCGGCGCCCGCCGGCGGGGACAAGAAGGTCATCGcaacgaaggttttgggaacagtaaaatggttcaatgtaagaaacggatatggtttcatcaACAGGAATGACACCAAGGAAGACGTATTTGTACACCAGACTGCCATAAAGAAGAATAACCCCAGGAAGTACCTTCGCAGTGTAGGAGATGGAGAGACTGTGGAGTTTGATGTTGTTGAAGGAGAAAAGGGTGCGGAGGCAGCAAATGTTACAGGCCCTGGTGGAGTTCCTGTGCAAGGCAGTAAATATGCAGCAGACCGTAACCATTATAGACGCTATCCACGTCGCAGGGGTCCTCCACGCAATTACCAGCAGAATTACCAGAACAGTGAGAGTGGGGAAAAGAATGAGGGATCGGAGAGCGCTCCCGAAGGCCAGGCCCAACAGCGCCGGCCCTACCGCAGGCGACGGTTCCCACCTTACTACATGCGGAGACCCTACGGGCGTCGACCACAGTATTCCAACCCTCCAGTGCAGGGAGAAGTGATGGAGGGTGCTGACAACCAGGGTGCAGGAGAACAAGGTAGACCAGTGAGACAGAATATGTATCGAGGCTATAGACCACGATTCCGCAGGGGCCCTCCTCGCCAAAGACAGCCTAGAGAGGACGGCAATGAAGAAGATAAAGAAAATCAAGGAGATGAGACCCAAGGTCAGCAGCCACCTCAACGTCGGTACCGCCGTAACTTTAATTACCGACGCAGACGCCCAGAAAACCCTAAACCACAAGATGGCAAAGAGACAAAAGCAGCCGATCCACCAGCTGAGAATTCGTCCGCTCCCGAGGCTGAGCAGGGCGGGGCTGAGTAA

Publications

PMID - Link	Title