RCPedia: Rtcs

Summary

Retrocopy Name	SSR1P1	Plot displaying the genomic locations of a retrocopy (in scaffold_m29_p_3) and its respective parental gene (in scaffold_m29_p_9). Each line represents a retrocopy.
Species	Rhinolophus ferrumequinum
Coordinates	scaffold_m29_p_3:79929076-79929240 UCSC
Strand	-
Parental Sequence	SSR1_x1
Parental seq. overlap	135 bp
Parental seq. overlap (%)	11.9%
Genomic Region	Intergenic
Retrocopy Summary	SSR1P1, located on scaffold_m29_p_3:79929076-79929240, is a retrocopy of the parental gene SSR1. 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	SSR1
Full Name	N/A
Also known as	NULL
Coordinate	scaffold_m29_p_9:87406561-87445112
Strand	+
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Gibbon	Nomascus leucogenys	SSR1P1
Green monkey	Chlorocebus sabaeus	SSR1P1
Crab-eating macaque	Macaca fascicularis	SSR1P1
Rhesus	Macaca mulatta	SSR1P1
Baboon	Papio anubis	SSR1P1
Horse	Equus caballus	SSR1P1
Velvety free-tailed bat	Molossus molossus	SSR1P1
Egyptian rousette	Rousettus aegyptiacus	SSR1P2
Sloth	Choloepus didactylus	SSR1P6
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
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
Pig	Sus scrofa	Without Homology
Cow	Bos taurus	Without Homology
Sheep	Ovis aries	Without Homology
Dolphin	Tursiops truncatus	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
Greater mouse-eared bat	Myotis myotis	Without Homology
Kuhl's pipistrelle	Pipistrellus kuhlii	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

>SSR1P1
CAAAGATTTGAATGGGAGTGTATTCCAAGATGCTATCTCCTATCGGTTACAATTAATGAAAGAGAGGATAGATTAGATGAAGAAGTGATCTTTATATATATGTTTCTTACTGGTTTTGAGCTACTAGTTGTCGTTGGATTTTATCAACTCCTAGAATATAGAAAT

>SSR1_x1
ATTCGCGGACGGGGACTGGACACCGGACGGGTCGCGCCATGAGACTCCTCCCCCGCCTGCTTGTGCTTCTCTTGCTCGTGTTCCCCGCCACCCTCTTGCTCCGAGGCAGCCCAGGAGGCTCAGTAGCAGTGGCTCAAGATCTTACagaagatgaagaaacagtagaagattcaataattgaagatgaagatgatgaagcagaggtggaagaagatgaaCCCACAGATTTGGCAGAAGATAAAGAGGAAGAAGATGTATCTGGTGAACCTGAAGCTTCACCAAGTGCAGACACGACTATCCTGTTTGTGAAAGGAGAAGATTTTCCAGCAAATAACATTGTGAAATTCCTGGTTGGCTTTACAAACAAGGGTACAGAAGATTTTATTGTTGAATCCCTAGATGCCTCATTCCGTTATCCTCAGGACTACCAGTTTTATATCCAGAATTTCACAGCTCTTCCTCTGAACACTGTAGTGCCACCCCAGAGACAGGCAACTTTTGAGTACTCCTTCATTCCTGCGGAGCCCATGGGTGGACGACCCTTTGGTCTAGTCATCAATCTGAACTACAAAGATTTGAACGGTAATGTATTCCAAGATGCTGTCTTCAATCAAACAGTCACAATTATTGAAAGAGAGGATGGGTTAGATGGAGAAACAATCTTTATGTATATGTTCCTTGCTGGTCTTGGGCTCTTGGTGGTTGTTGGCCTTCATCAACTCCTAGAATCTAGAAAGCGCAAGAGACCCATACAGAAAGTAGAGATGGGTACATCAAGTCAGAATGATGTTGACATGAGTTGGATTCCTCAGGAAACTTTGAATCAGATCAACAAAGCTTCACCAAGAAGGTTGCCCAGGAAACGGGCACAGAAGAGATCCGTGGGATCTGATGAGTAAATGTTCCTTTGTGCAACAATTCAGTCTTTACTTAACCTGCCCTAATGTTTTTCGGCCTGATGGGAATTAGTGCAGAGAAGCCATATCACCATAGAAGGCAACTACTACTTATGTGTGGACTGAGCAAGCAGAGTCTATGGCGATAATATTGCTGAAAATGCACTGCATTCATTTTTCTAAAGTAACACATTTGGGTTTTTTTAAAACCATTAAAATCTAtgtgtgtgcgtgtgt

>SSR1_x1 

ATTCGCGGACGGGGACTGGACACCGGACGGGTCGCGCCATGAGACTCCTCCCCCGCCTGCTTGTGCTTCTCTTGCTCGTGTTCCCCGCCACCCTCTTGCTCCGAGGCAGCCCAGGAGGCTCAGTAGCAGTGGCTCAAGATCTTACagaagatgaagaaacagtagaagattcaataattgaagatgaagatgatgaagcagaggtggaagaagatgaaCCCACAGATTTGGCAGAAGATAAAGAGGAAGAAGATGTATCTGGTGAACCTGAAGCTTCACCAAGTGCAGACACGACTATCCTGTTTGTGAAAGGAGAAGATTTTCCAGCAAATAACATTGTGAAATTCCTGGTTGGCTTTACAAACAAGGGTACAGAAGATTTTATTGTTGAATCCCTAGATGCCTCATTCCGTTATCCTCAGGACTACCAGTTTTATATCCAGAATTTCACAGCTCTTCCTCTGAACACTGTAGTGCCACCCCAGAGACAGGCAACTTTTGAGTACTCCTTCATTCCTGCGGAGCCCATGGGTGGACGACCCTTTGGTCTAGTCATCAATCTGAACTACAAAGATTTGAACGGTAATGTATTCCAAGATGCTGTCTTCAATCAAACAGTCACAATTATTGAAAGAGAGGATGGGTTAGATGGAGAAACAATCTTTATGTATATGTTCCTTGCTGGTCTTGGGCTCTTGGTGGTTGTTGGCCTTCATCAACTCCTAGAATCTAGAAAGCGCAAGAGACCCATACAGAAAGTAGAGATGGGTACATCAAGTCAGAATGATGTTGACATGAGTTGGATTCCTCAGGAAACTTTGAATCAGATCAACAAAGCTTCACCAAGAAGGTTGCCCAGGAAACGGGCACAGAAGAGATCCGTGGGATCTGATGAGTAAATGTTCCTTTGTGCAACAATTCAGTCTTTACTTAACCTGCCCTAATGTTTTTCGGCCTGATGGGAATTAGTGCAGAGAAGCCATATCACCATAGAAGGCAACTACTACTTATGTGTGGACTGAGCAAGCAGAGTCTATGGCGATAATATTGCTGAAAATGCACTGCATTCATTTTTCTAAAGTAACACATTTGGGTTTTTTTAAAACCATTAAAATCTAtgtgtgtgcgtgtgt

Publications

PMID - Link	Title