RCPedia: Rtcs

Summary

Retrocopy Name	SPPL2AP1	Plot displaying the genomic locations of a retrocopy (in chr13) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species	Microcebus murinus
Coordinates	chr13:20151661-20151816 UCSC
Strand	-
Parental Sequence	XM_012763489.1
Parental seq. overlap	137 bp
Parental seq. overlap (%)	6.7%
Genomic Region	Intergenic
Retrocopy Summary	SPPL2AP1, located on chr13:20151661-20151816, is a retrocopy of the parental gene SPPL2A. 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	SPPL2A
Full Name	N/A
Also known as	-
Coordinate	chr3:81626586-81666017
Strand	+
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Human	Homo sapiens	SPPL2AP1
Chimpanzee	Pan troglodytes	SPPL2AP1
Bonobo	Pan paniscus	SPPL2AP1
Gorilla	Gorilla gorilla	SPPL2AP1
Orangutan	Pongo abelii	SPPL2AP1
Gibbon	Nomascus leucogenys	SPPL2AP1
Green monkey	Chlorocebus sabaeus	SPPL2AP1
Crab-eating macaque	Macaca fascicularis	SPPL2AP2
Rhesus	Macaca mulatta	SPPL2AP2
Baboon	Papio anubis	LOC100999214P2
Golden snub-nosed monkey	Rhinopithecus roxellana	SPPL2AP2
Marmoset	Callithrix jacchus	SPPL2AP1
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
Greater horseshoe bat	Rhinolophus ferrumequinum	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

>SPPL2AP1
aaatgaaaaattgtggAAAGGTAGCAGCTTTCAGATGATGGACCATCTGGACTATgcaatgaatgaagaaaatccTGTAACTGCTGGTGAACAGATGGTCCAACAATAATATTATGTGGTCCTGTAATAATGTGTCATTCATTTTCTacaaatagt

>XM_012763489.1
GCCGTGGCGGCCCCGGCGGCACAGCTGTCCCGGCCCAGCACGCCCGCCCGCCCTAGTAACGCCAGGCCACGGAGGCAGCCGGCGACAGCACCCGGAGCCTCCCCCCGagccgcgccgccccgcgccgcAGCGCCCGGCACCCGCCAGCCCGATGGGACCGCAGCGGCGGCTGCTCCCCGCCGCGGCCGCCCTGCTCTGGGGCTTCCTGCTCCCGCTGACAGCTGCTCAGGAAGCAGTCCTGCATGCATCTGGAAATGGCACACCTTTACCATCTAAGGACTACTGCATGTTGTATAACCCTCATTGGACAACTCTTCCAAGTACACTAGAAAATGCAacTTCCGTTAGTTTGATGAATCTGACTTCCACACCGCTATGCAACCTTTCTGATATTCCTCCTGATGGTATAAATAACAAAGCAGTTGTGGTACACTGGGGAACCTGCCATTTTCTTGAAAAAGCCAGAATTGCACAGAAAGGAGGTGCTGAAGCATTGCTGGTTGTCAATAACAGTGTCCTAtttcctcCCTCAGGGAACAGATCTGAATTTCATGATGTGAAAATACTGATTGCATTTGTAAGCCAAAAAGACTTTAAAGATATGAATCAGaCTCTTGGAAATAACATTACCGTGAAAATGTATTCCCCATCGTCACCTAGCTTTGATTATACCATGGTGGTCATTTTTGTAATTGCCGTGTCCACTGTGGCATTAGGTGGATACTGGAGTGGACAAATTGAATTGGAAAACTTGAAGGCAGTAACAAATACTGAagacagagaaatgaagaaaaagaaggaagaatatttaACTTTTAGTCCTCTTACAGTTATAATATTTGTGGTCATCTGCTGTGTTATGATGGTCTTACTTTATTTCTTCTACAAATGGTTGGtttatgttaTGATAGCAATTTTCTGCATAGCGTCAGCAATGAGTCTGTACAACTGTCTTGCTGCACTAATTCATAAGATACCATGTGGACAATGCACgATTGCGTGTCGTGGAAAAAGCATTGAAGTGAGACTAATTTTTCTCTCTGGACTATGCATAGCCACAGCTGCTGTTTGGGCTGTATTTCGAAATGAAGATAGGTGGGCGTGGATTTTACAGGATATTTTGGGGATTGCTTTCTGtctaaatttaattaaaacactgAAGTTACCCAACTTCAAGTCGTGTGTGATACTTCTAGGTCTTCTCCTCCTCTatgatgtgttttttgttttcataacacCATTCATCACAAAGAATGGTGAGAGTATCATGGTTGAACTTGCAGCTGGACCTTTTGGAAATAACGAAAAGAATGATGGAAACTTGGTGGAAGCCACTGCTCAACCCTCAGCTCCCCATGAGAAATTGCCAGTAGTCATCAGAGTACCAAAGCTGATCTATTTCTCAGTAATGAGTGTGTGCCTCATGCCTGTTTCCATATTGGGTTTTGGAGACATTATTGTACCAGgcCTGTTGATTGCATACTGTAGAAGATTTGATGTTCAGACTGGCTCTTCTTCTATATACTATGTTTCCTCCACAAttgCCTATGCTGTTGGCATGATACTTACATTTGTTGTTCTGGTGCTGATGAAAAAGGGGCAACCTGCTCTCCTCTATTTAGTACCTTGCACACTTATTACTGCCTCAATTGTTGCTTGGAGACGTAGggaaatgaaaaagttttggaaaggTAACAGCTATCAGATGATGGACCATCTGGACTATGCAACAAATGAAGAAAACCCTGTGATTGCTGGTGAACAGATTGTCCCGCAATAATAGTATGTGAACCTGCAATCATGTGCCAATTGATTTTCTACAAATAGAGTTTGACTTGTAAAATCGACCTTTGAATTGACAATCTGGAAGAATCTTCAGTGACATGCTTGcaagcatatatttttatgagCTGGTACTGACAATTACatcacaaataattaaaatgcatttgcTTTTAATCATGTTAAAGTTGTGCCTTCAcattaaataaaagcatatggtCTGTGTAATTACTAAGAAGtattatatacagtatatttttc

>XM_012763489.1 

GCCGTGGCGGCCCCGGCGGCACAGCTGTCCCGGCCCAGCACGCCCGCCCGCCCTAGTAACGCCAGGCCACGGAGGCAGCCGGCGACAGCACCCGGAGCCTCCCCCCGagccgcgccgccccgcgccgcAGCGCCCGGCACCCGCCAGCCCGATGGGACCGCAGCGGCGGCTGCTCCCCGCCGCGGCCGCCCTGCTCTGGGGCTTCCTGCTCCCGCTGACAGCTGCTCAGGAAGCAGTCCTGCATGCATCTGGAAATGGCACACCTTTACCATCTAAGGACTACTGCATGTTGTATAACCCTCATTGGACAACTCTTCCAAGTACACTAGAAAATGCAacTTCCGTTAGTTTGATGAATCTGACTTCCACACCGCTATGCAACCTTTCTGATATTCCTCCTGATGGTATAAATAACAAAGCAGTTGTGGTACACTGGGGAACCTGCCATTTTCTTGAAAAAGCCAGAATTGCACAGAAAGGAGGTGCTGAAGCATTGCTGGTTGTCAATAACAGTGTCCTAtttcctcCCTCAGGGAACAGATCTGAATTTCATGATGTGAAAATACTGATTGCATTTGTAAGCCAAAAAGACTTTAAAGATATGAATCAGaCTCTTGGAAATAACATTACCGTGAAAATGTATTCCCCATCGTCACCTAGCTTTGATTATACCATGGTGGTCATTTTTGTAATTGCCGTGTCCACTGTGGCATTAGGTGGATACTGGAGTGGACAAATTGAATTGGAAAACTTGAAGGCAGTAACAAATACTGAagacagagaaatgaagaaaaagaaggaagaatatttaACTTTTAGTCCTCTTACAGTTATAATATTTGTGGTCATCTGCTGTGTTATGATGGTCTTACTTTATTTCTTCTACAAATGGTTGGtttatgttaTGATAGCAATTTTCTGCATAGCGTCAGCAATGAGTCTGTACAACTGTCTTGCTGCACTAATTCATAAGATACCATGTGGACAATGCACgATTGCGTGTCGTGGAAAAAGCATTGAAGTGAGACTAATTTTTCTCTCTGGACTATGCATAGCCACAGCTGCTGTTTGGGCTGTATTTCGAAATGAAGATAGGTGGGCGTGGATTTTACAGGATATTTTGGGGATTGCTTTCTGtctaaatttaattaaaacactgAAGTTACCCAACTTCAAGTCGTGTGTGATACTTCTAGGTCTTCTCCTCCTCTatgatgtgttttttgttttcataacacCATTCATCACAAAGAATGGTGAGAGTATCATGGTTGAACTTGCAGCTGGACCTTTTGGAAATAACGAAAAGAATGATGGAAACTTGGTGGAAGCCACTGCTCAACCCTCAGCTCCCCATGAGAAATTGCCAGTAGTCATCAGAGTACCAAAGCTGATCTATTTCTCAGTAATGAGTGTGTGCCTCATGCCTGTTTCCATATTGGGTTTTGGAGACATTATTGTACCAGgcCTGTTGATTGCATACTGTAGAAGATTTGATGTTCAGACTGGCTCTTCTTCTATATACTATGTTTCCTCCACAAttgCCTATGCTGTTGGCATGATACTTACATTTGTTGTTCTGGTGCTGATGAAAAAGGGGCAACCTGCTCTCCTCTATTTAGTACCTTGCACACTTATTACTGCCTCAATTGTTGCTTGGAGACGTAGggaaatgaaaaagttttggaaaggTAACAGCTATCAGATGATGGACCATCTGGACTATGCAACAAATGAAGAAAACCCTGTGATTGCTGGTGAACAGATTGTCCCGCAATAATAGTATGTGAACCTGCAATCATGTGCCAATTGATTTTCTACAAATAGAGTTTGACTTGTAAAATCGACCTTTGAATTGACAATCTGGAAGAATCTTCAGTGACATGCTTGcaagcatatatttttatgagCTGGTACTGACAATTACatcacaaataattaaaatgcatttgcTTTTAATCATGTTAAAGTTGTGCCTTCAcattaaataaaagcatatggtCTGTGTAATTACTAAGAAGtattatatacagtatatttttc

Publications

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