RCPedia: Rtcs

Summary

Retrocopy Name	VIMP2	Plot displaying the genomic locations of a retrocopy (in scaffold_m16_p_8) and its respective parental gene (in scaffold_m16_p_1). Each line represents a retrocopy.
Species	Molossus molossus
Coordinates	scaffold_m16_p_8:80579658-80579907 UCSC
Strand	-
Parental Sequence	VIM_x2
Parental seq. overlap	205 bp
Parental seq. overlap (%)	13.1%
Genomic Region	Intergenic
Retrocopy Summary	VIMP2, located on scaffold_m16_p_8:80579658-80579907, is a retrocopy of the parental gene VIM. 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	VIM
Full Name	N/A
Also known as	NULL
Coordinate	scaffold_m16_p_1:111137432-111145688
Strand	-
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Human	Homo sapiens	VIMP1
Chimpanzee	Pan troglodytes	VIMP1
Bonobo	Pan paniscus	VIMP1
Gorilla	Gorilla gorilla	VIMP1
Orangutan	Pongo abelii	VIMP1
Gibbon	Nomascus leucogenys	VIMP1
Green monkey	Chlorocebus sabaeus	VIMP1
Crab-eating macaque	Macaca fascicularis	VIMP1
Rhesus	Macaca mulatta	VIMP1
Baboon	Papio anubis	VIMP1
Golden snub-nosed monkey	Rhinopithecus roxellana	VIMP1
Mouse lemur	Microcebus murinus	VIMP1
Horse	Equus caballus	VIMP1
Greater horseshoe bat	Rhinolophus ferrumequinum	VIMP2
Egyptian rousette	Rousettus aegyptiacus	VIMP1
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
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
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

>VIMP2
AGATTGGCACCTACAGAAAACTGCTGGGAGGTGGGGAACAGGATGTCTCTGCCCCTTCCAAACTTTTCTTTTCTGAACCTGAAGGAAACCGTTCTAGGTTCACTCCTTCGGGTTGGCAGCCACTCAAAACAAACCCTTCTGATTATGAGGATTGGAACTAGAGAGAGGTTATCATTAAAATTTCTCAGCATCATGATCATCTTGATGAAAATTGCACTCAGTGCAGCAATATATTTCCAGCAAGAATAAA

>VIM_x2
GTAGTCGGCTGCGGGGGATGGGGGCAGCAGGAGAACGGGGCTGTGGCTGCGGTGGCGTAGCCCCACCCAGAACCCTGCAGTTGCAGTCAGCGTTTCCCCTCTACCCCCACTCATTGCCTAAGAACTCCCGTTTCAAGTTACAGATTTTTTGAAACTACCACTTTGTAGTAGATGGCCCTTGCAAGCTGTGAGCGTGATATCTCCAAACTTTTTGAAAGTTTCCTAGCCCCATCTGGCGGGCTGCCAGCCCAGGCGCGGAGGAGGGAGGAAAGGATGGCCGTGTAGCCAGAGAGACAAAGGGTTGCCGAGGCTTCTCGGGGGGTGGGGTGGCGGCTTTCGCCTTGCAGGGCCGTGCGAAGGTTTGTCTACGCTGCGGCCCCAGTCCCGCTAAAAACTTGCAGGGAGTGGCGGTTCTGAAAGCCGCAATCGCTCTCCGGCTGTCTGCAGAGGTTGCAGGAGGAGATGCTTCAGAGAGAGGAAGCCGAGGGCACCCTCCAGTCATTCAGACAGGATGTTGACAATGCTTCTTTGGCACGTCTTGACCTTGAGCGTAAAGTGGAATCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTCCACGATGAGGAAATCCGTGAGCTGCAGGCCCAGATTCAGGAGCAGCACGTCCAAATCGATGTGGATGTTTCCAAGCCTGACCTCACGGCTGCCCTGCGTGACGTCCGTCAGCAGTATGAAAGTGTAGCTGCCAAGAACCTTCAGGAGGCTGAGGAATGGTACAAGTCCAAGTTTGCCGACCTCTCTGAGGCTGCTAACCGGAACAATGATGCCCTGCGCCAGGCGAAGCAGGAGTCAAATGAGTACCGGAGACAGGTGCAGTCCCTCACCTGCGAAGTGGATGCACTTAAAGGAACTAACGAGTCCCTGGAACGCCAGATGCGTGAAATGGAAGAGAACTTTGCTCTTGAAGCTGCTAACTACCAAGACACTATCGGCCGCCTGCAGGATGAGATTCAGAACATGAAGGAAGAAATGGCTCGTCACCTTCGTgaataccaggacctgctgaatgttaagatggctcttgacattgagattgccacctacaggaagctgctggaaggggaggagAGCAGGATTTCTCTGCCTCTTCCCAACTTTTCTTCCCTGAACCTCAGAGAAACCAATCTGGATTCACTCCCTCTGGTTGACACCCACTCAAAAAGGACACTTCTGATTAAGACTGTTGAAACTAGAGATGGACAGGTCATCAATGAGACTTCTCAGCATCATGATGATCTGGAATGAAAACTGCATGCACTCGGTGCAGCAATGTATTACCAGCAAGAATAACATGGAAATCCATATCTTACAGAAACAGCTTTCAAGTGCCTTTCTGCAGTTTTTTCCAGAGCGCAAGGTAGATTTGGAATAGGAATAAGCTCTAGTTCTTAAGAACCAACACTTCTAAGAGATTTAGAGAAAAAAAAAAGTTTACAACATAATCTAGTTTACGAAGAAGACTTGTGCTAGAATACTTTTTTAAAAGTATTTTTGAATACCATTAAAACTGCTTTTTTCC

>VIM_x2 

GTAGTCGGCTGCGGGGGATGGGGGCAGCAGGAGAACGGGGCTGTGGCTGCGGTGGCGTAGCCCCACCCAGAACCCTGCAGTTGCAGTCAGCGTTTCCCCTCTACCCCCACTCATTGCCTAAGAACTCCCGTTTCAAGTTACAGATTTTTTGAAACTACCACTTTGTAGTAGATGGCCCTTGCAAGCTGTGAGCGTGATATCTCCAAACTTTTTGAAAGTTTCCTAGCCCCATCTGGCGGGCTGCCAGCCCAGGCGCGGAGGAGGGAGGAAAGGATGGCCGTGTAGCCAGAGAGACAAAGGGTTGCCGAGGCTTCTCGGGGGGTGGGGTGGCGGCTTTCGCCTTGCAGGGCCGTGCGAAGGTTTGTCTACGCTGCGGCCCCAGTCCCGCTAAAAACTTGCAGGGAGTGGCGGTTCTGAAAGCCGCAATCGCTCTCCGGCTGTCTGCAGAGGTTGCAGGAGGAGATGCTTCAGAGAGAGGAAGCCGAGGGCACCCTCCAGTCATTCAGACAGGATGTTGACAATGCTTCTTTGGCACGTCTTGACCTTGAGCGTAAAGTGGAATCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTCCACGATGAGGAAATCCGTGAGCTGCAGGCCCAGATTCAGGAGCAGCACGTCCAAATCGATGTGGATGTTTCCAAGCCTGACCTCACGGCTGCCCTGCGTGACGTCCGTCAGCAGTATGAAAGTGTAGCTGCCAAGAACCTTCAGGAGGCTGAGGAATGGTACAAGTCCAAGTTTGCCGACCTCTCTGAGGCTGCTAACCGGAACAATGATGCCCTGCGCCAGGCGAAGCAGGAGTCAAATGAGTACCGGAGACAGGTGCAGTCCCTCACCTGCGAAGTGGATGCACTTAAAGGAACTAACGAGTCCCTGGAACGCCAGATGCGTGAAATGGAAGAGAACTTTGCTCTTGAAGCTGCTAACTACCAAGACACTATCGGCCGCCTGCAGGATGAGATTCAGAACATGAAGGAAGAAATGGCTCGTCACCTTCGTgaataccaggacctgctgaatgttaagatggctcttgacattgagattgccacctacaggaagctgctggaaggggaggagAGCAGGATTTCTCTGCCTCTTCCCAACTTTTCTTCCCTGAACCTCAGAGAAACCAATCTGGATTCACTCCCTCTGGTTGACACCCACTCAAAAAGGACACTTCTGATTAAGACTGTTGAAACTAGAGATGGACAGGTCATCAATGAGACTTCTCAGCATCATGATGATCTGGAATGAAAACTGCATGCACTCGGTGCAGCAATGTATTACCAGCAAGAATAACATGGAAATCCATATCTTACAGAAACAGCTTTCAAGTGCCTTTCTGCAGTTTTTTCCAGAGCGCAAGGTAGATTTGGAATAGGAATAAGCTCTAGTTCTTAAGAACCAACACTTCTAAGAGATTTAGAGAAAAAAAAAAGTTTACAACATAATCTAGTTTACGAAGAAGACTTGTGCTAGAATACTTTTTTAAAAGTATTTTTGAATACCATTAAAACTGCTTTTTTCC

Publications

PMID - Link	Title