RCPedia: Rtcs

Summary

Retrocopy Name	Sub1P2	Plot displaying the genomic locations of a retrocopy (in chr5) and its respective parental gene (in chr15). Each line represents a retrocopy.
Species	Mus musculus
Coordinates	chr5:80441887-80442247 UCSC
Strand	+
Parental Sequence	NM_011294.3
Parental seq. overlap	286 bp
Parental seq. overlap (%)	8.6%
Genomic Region	Intergenic
Retrocopy Summary	Sub1P2, located on chr5:80441887-80442247, is a retrocopy of the parental gene Sub1. 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	Sub1
Full Name	SUB1 homolog, transcriptional regulator
Also known as	P15\|P9\|Pc4\|Rpo2tc1
Coordinate	chr15:11981422-11996124
Strand	-
Gene summary	Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within SMAD protein signal transduction. Predicted to be located in nucleolus and nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Is expressed in several structures, including branchial arch; central nervous system; genitourinary system; limb; and sensory organ. Orthologous to human SUB1 (SUB1 regulator of transcription). [provided by Alliance of Genome Resources, Apr 2022]

Homology

Species	Scientific Name	Retrocopy
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
Gibbon	Nomascus leucogenys	Without Homology
Green monkey	Chlorocebus sabaeus	Without Homology
Crab-eating macaque	Macaca fascicularis	Without Homology
Rhesus	Macaca mulatta	Without Homology
Baboon	Papio anubis	Without Homology
Golden snub-nosed monkey	Rhinopithecus roxellana	Without Homology
Marmoset	Callithrix jacchus	Without Homology
Mouse lemur	Microcebus murinus	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

>Sub1P2
AGATGGACTCAGAAAGTGATATGAAAGCAGGAAGAAAGGGTACTTCTTTAAATATGGGGCAGTCAAGCCAGATGAAGGCATTTCTGACACAGATGATGCAGCAAGGAAGCTCTAAAATCTGAGCCATCTCAATCCTCTACTGTTGCTGCTTTAGTCTGTTTTCTTACACTGCATTCTGCTCTCTAAATATTGTTTTCCAAGGTATTGAATATTTCgactacagagcaatttctaacatgaatactttttaaaatatacattgttAAAATATTCTGAGTAGAGCTAATTGCCAAatttattaaggagaatttttttGTGCTCCAAAATAGTGTAAAATAAAGTCGTATCATTACCATCTTAA

>NM_011294.3
TCAGTCCGGAGTAGGCGAGCGAGCGAGGCAGAGGTTTTTGGTCGGCCGGAGCGGAGCAATGCCTAAATCAAAGGAACTTGTTTCTTCAAGCTCTTCAGGCAGTGATTCGGACAGCGAAGTTGAAAAAAAGTTAAAGAGGAAAAAGCAAGCGGTTCCAGAGAAGCCCGTGAAGAAGCAGAAGCCTGGTGAGACTTCTAGAGCACTGGCATCCTCCaagcagagcagcagcagcagagatgaCAACATGTTCCAGATTGGAAAGATGAGATATGTCAGTGTTCGGGACTTCAAAGGAAAAATTCTAATTGATATTAGAGAATATTGGATGGATTCAGAAGGTGAAATGAAACCAGGAAGAAAAGGTATTTCTTTAAACATGGAACAATGGAGCCAGCTGAAGGAACAGATCTCTGATATAGATGACGCAGTAAGAAAGCTGTAAAATCTGAGCCATATCAAACCTGTACTGTTGTagttgtctttttacattggcttttgttttctaaatgttgTTTTCCAAGCTGTTGTATATTTGGATTGCAGAACAATTTGTAagacaaatacttttttttaatgtgcattatTAAAATGTTCTAAGTGAAGCTAATTGTCAAGTTTATTAAAGAGGATTGCTTTGTGCCCCCTACCTAGTGTGTAAAATAAAGTCAGATCATTACAATCTTAACTGTGGTACCCTTTTTTGATCAAAAAAACCTAGTTACTGTTTAAGGCCAAAAGAACAACTAGGCACACTGTTGAGTCAGCTTACATTCAGAAGGATTTGTATTACATTGAGTTTCTTAGATTGCTTTGTGAAATGTATACTCAGCCTTTTTCTTTCCAACCAGATTTACTGCGTTTTCCTCTCCAGGACTTCTCCCTACCACAATAACTTATCTTTTCTTCAGTTCTCTTAGTGCTCAAGTTTAAATCACTCTTTACTCAGATAGATTACGCTTATTTAGAAAGTCAAACTGTCAGTTTTGTTGCCTCCTAAGTCTACTGTGCTAATTACTAGTATCTGTTTGGCAACATGACTTATATGAGAACTCCAAGCAAGTGTATGTCATTATTCATAGTGCTCTGTGTAGATGTTGCTTAGTTTACAGAACATAGTGACTTTGATGTCTGATGAGCTGTCACTCAGTAAACATTTGTGCTAGGGTGATGGTTATAAAGTCAGATATTAAACTAGATTAGACTTGTAAAAAGTGTGAAACTTACTGGCCTACTGTTATATTCTAATAATGTGTGGATTCTATGTAGTCAGATGTGGCACTGAGCTCAACTGTGGTAGGTTCTGTGGGCAGTTTTAGAGTTGACTGTTCTACAGTTAATCTGGACAAGTGACTTCCAGACTTGATGTTAACTAGGTTTGATAGACATTTCCATTGGTTTTCATTTCAATTGTGATGATTAAGCAAGCAGACAGGCACATGTTTTAGGGACATTGCTCCAATGAAAAGGGCATAGTGTTCTGAGGGAAAATGTTTGCAAAGGAAAGTCACCACACTGAAGGGAGCTAGCCTGTGATGAGAAAGGAACTTTCTTGAAACTAAATGTTGTGCACATGATATGTTGGTGATAACATTAAGATGGGTCTTCGTAGAATAATAGCTAACAAGGACAATTTATAGATGTGAAAAAATGCTGCCACTAAGGGCTGCCATATCAGAATTGCACTGTCATACTGAGTCCCACCGTCTAAGCATTTTATAGAACTGTTAaggattaaatttaaaaaacagtctGCCAGGCCTCATGTGGTTAACTGTCCTCCCCACAGATACTCTTTAGGTAACTTTTTAGTGTGTTACTCCAAATTGATACATATATATCAAAGGGTTTAAGATATATACCATAGCTCATTCTTGAGGGATGATCCTCTTATAATGTGTTGCATTTCATTGATTTTATAAAGTATTCCTTATTTGTCATGTAAAGAAAGGATAGTTAGAACATAAGACTGGTTTGGTGCAGATGAGGGGAGAATAACAGGTAAATTCCTGAGGCCATGTGTTATATGTACATTTCAGCTGTCCGATTGCAGAGATCTGCCGTCTGCTACCTAGGCATTGCTAGCTGCTTAGCATAAAATTCCATGTGGAAAGCTTTCTCGGGCATAATTTGTTAGGTTGATAGCTAAATACATTCACTAATGTTATACCAgagttgttgttatttttctttgtgtgttgaaaaggaaaattgagttaaaagaagaggaaggacttttcagatggaaaagaaaGGGTACAGTCCTTCTATTTTGCGTTCAGATGCCTTTCTCCTcagtgtcttagtttcttttctgttgctgtggtgaaGTGCCCTGACAGAAGCAGccaagggagaaagggtttatcctGACTCACAGTTCCATGTTCCAGTCCGTTGTCGCATTGTCACAGTGGCAGGaactccagacatctggccacatGGCTCCATagccaggaagctgagagctgtgATTGCATGCTCAGTTCCTTTTTGTCTCATTAACCTgagcccaggagctggagttggcCACAGCAGGCAAGATGATTCTCCAGACATCATGCCTAGAGGCCTATCTTTTGGGTAGTTCTAGATTCTGTTGAACTAATAACCATCATAGTAAGTTTTCTCCCAGGAAGAAGGCTTGACATTTTAAGGCataatatcttattttgtaacaCTAAAATAATTAGATCTGCTGCCAGGTTTTGCCCTTTAATATGCTCCATAGTAAGGCTTCCaaatgggttttcctcttagggtAAAAAGCCTTTGGCCAATTTCCACaatcactgaaaaagaaaaactcagattttcttttgtttgcttcacAAATGCCTAAAATCTTGAGAAATACTACCTCCTTACCTAGTCAAGACGCTGTGATAACCAGTCTGTGCTGCGTAGTGTTGGAGTCAGCAGCGTGGGGAAAACCGTGGGGAAAGAGCATCCTGGTCTGGCTGCAAAGGGAGGAAGGGATTGAACAGTTATGTAAGCGTTCCTGACAGGAACGCTAGCACAGAGCTTGCCATAGAGCCTGTGAACGTCTTCAGAACCGTTGAGTTATATTTAGGTAtcttttctgaatttctttgtGGTTCACTTTTTATAGAAATTAATGTAGTGAAAcactaaagatttttttcttaagaaaggTATTTTTTTCCAGATAAACTATAATGTAAACATGCATCTAGTGAGAAGTATGTGACTCTGTAATTGTGGAATGACTGTATGCTTTGTTTAGTACATCTTCCGTGGAGGTGTCAATGAACCTATTATTCCACCtgtgaatattttaaatgttgaataaaaacaagaaac

>NM_011294.3 

TCAGTCCGGAGTAGGCGAGCGAGCGAGGCAGAGGTTTTTGGTCGGCCGGAGCGGAGCAATGCCTAAATCAAAGGAACTTGTTTCTTCAAGCTCTTCAGGCAGTGATTCGGACAGCGAAGTTGAAAAAAAGTTAAAGAGGAAAAAGCAAGCGGTTCCAGAGAAGCCCGTGAAGAAGCAGAAGCCTGGTGAGACTTCTAGAGCACTGGCATCCTCCaagcagagcagcagcagcagagatgaCAACATGTTCCAGATTGGAAAGATGAGATATGTCAGTGTTCGGGACTTCAAAGGAAAAATTCTAATTGATATTAGAGAATATTGGATGGATTCAGAAGGTGAAATGAAACCAGGAAGAAAAGGTATTTCTTTAAACATGGAACAATGGAGCCAGCTGAAGGAACAGATCTCTGATATAGATGACGCAGTAAGAAAGCTGTAAAATCTGAGCCATATCAAACCTGTACTGTTGTagttgtctttttacattggcttttgttttctaaatgttgTTTTCCAAGCTGTTGTATATTTGGATTGCAGAACAATTTGTAagacaaatacttttttttaatgtgcattatTAAAATGTTCTAAGTGAAGCTAATTGTCAAGTTTATTAAAGAGGATTGCTTTGTGCCCCCTACCTAGTGTGTAAAATAAAGTCAGATCATTACAATCTTAACTGTGGTACCCTTTTTTGATCAAAAAAACCTAGTTACTGTTTAAGGCCAAAAGAACAACTAGGCACACTGTTGAGTCAGCTTACATTCAGAAGGATTTGTATTACATTGAGTTTCTTAGATTGCTTTGTGAAATGTATACTCAGCCTTTTTCTTTCCAACCAGATTTACTGCGTTTTCCTCTCCAGGACTTCTCCCTACCACAATAACTTATCTTTTCTTCAGTTCTCTTAGTGCTCAAGTTTAAATCACTCTTTACTCAGATAGATTACGCTTATTTAGAAAGTCAAACTGTCAGTTTTGTTGCCTCCTAAGTCTACTGTGCTAATTACTAGTATCTGTTTGGCAACATGACTTATATGAGAACTCCAAGCAAGTGTATGTCATTATTCATAGTGCTCTGTGTAGATGTTGCTTAGTTTACAGAACATAGTGACTTTGATGTCTGATGAGCTGTCACTCAGTAAACATTTGTGCTAGGGTGATGGTTATAAAGTCAGATATTAAACTAGATTAGACTTGTAAAAAGTGTGAAACTTACTGGCCTACTGTTATATTCTAATAATGTGTGGATTCTATGTAGTCAGATGTGGCACTGAGCTCAACTGTGGTAGGTTCTGTGGGCAGTTTTAGAGTTGACTGTTCTACAGTTAATCTGGACAAGTGACTTCCAGACTTGATGTTAACTAGGTTTGATAGACATTTCCATTGGTTTTCATTTCAATTGTGATGATTAAGCAAGCAGACAGGCACATGTTTTAGGGACATTGCTCCAATGAAAAGGGCATAGTGTTCTGAGGGAAAATGTTTGCAAAGGAAAGTCACCACACTGAAGGGAGCTAGCCTGTGATGAGAAAGGAACTTTCTTGAAACTAAATGTTGTGCACATGATATGTTGGTGATAACATTAAGATGGGTCTTCGTAGAATAATAGCTAACAAGGACAATTTATAGATGTGAAAAAATGCTGCCACTAAGGGCTGCCATATCAGAATTGCACTGTCATACTGAGTCCCACCGTCTAAGCATTTTATAGAACTGTTAaggattaaatttaaaaaacagtctGCCAGGCCTCATGTGGTTAACTGTCCTCCCCACAGATACTCTTTAGGTAACTTTTTAGTGTGTTACTCCAAATTGATACATATATATCAAAGGGTTTAAGATATATACCATAGCTCATTCTTGAGGGATGATCCTCTTATAATGTGTTGCATTTCATTGATTTTATAAAGTATTCCTTATTTGTCATGTAAAGAAAGGATAGTTAGAACATAAGACTGGTTTGGTGCAGATGAGGGGAGAATAACAGGTAAATTCCTGAGGCCATGTGTTATATGTACATTTCAGCTGTCCGATTGCAGAGATCTGCCGTCTGCTACCTAGGCATTGCTAGCTGCTTAGCATAAAATTCCATGTGGAAAGCTTTCTCGGGCATAATTTGTTAGGTTGATAGCTAAATACATTCACTAATGTTATACCAgagttgttgttatttttctttgtgtgttgaaaaggaaaattgagttaaaagaagaggaaggacttttcagatggaaaagaaaGGGTACAGTCCTTCTATTTTGCGTTCAGATGCCTTTCTCCTcagtgtcttagtttcttttctgttgctgtggtgaaGTGCCCTGACAGAAGCAGccaagggagaaagggtttatcctGACTCACAGTTCCATGTTCCAGTCCGTTGTCGCATTGTCACAGTGGCAGGaactccagacatctggccacatGGCTCCATagccaggaagctgagagctgtgATTGCATGCTCAGTTCCTTTTTGTCTCATTAACCTgagcccaggagctggagttggcCACAGCAGGCAAGATGATTCTCCAGACATCATGCCTAGAGGCCTATCTTTTGGGTAGTTCTAGATTCTGTTGAACTAATAACCATCATAGTAAGTTTTCTCCCAGGAAGAAGGCTTGACATTTTAAGGCataatatcttattttgtaacaCTAAAATAATTAGATCTGCTGCCAGGTTTTGCCCTTTAATATGCTCCATAGTAAGGCTTCCaaatgggttttcctcttagggtAAAAAGCCTTTGGCCAATTTCCACaatcactgaaaaagaaaaactcagattttcttttgtttgcttcacAAATGCCTAAAATCTTGAGAAATACTACCTCCTTACCTAGTCAAGACGCTGTGATAACCAGTCTGTGCTGCGTAGTGTTGGAGTCAGCAGCGTGGGGAAAACCGTGGGGAAAGAGCATCCTGGTCTGGCTGCAAAGGGAGGAAGGGATTGAACAGTTATGTAAGCGTTCCTGACAGGAACGCTAGCACAGAGCTTGCCATAGAGCCTGTGAACGTCTTCAGAACCGTTGAGTTATATTTAGGTAtcttttctgaatttctttgtGGTTCACTTTTTATAGAAATTAATGTAGTGAAAcactaaagatttttttcttaagaaaggTATTTTTTTCCAGATAAACTATAATGTAAACATGCATCTAGTGAGAAGTATGTGACTCTGTAATTGTGGAATGACTGTATGCTTTGTTTAGTACATCTTCCGTGGAGGTGTCAATGAACCTATTATTCCACCtgtgaatattttaaatgttgaataaaaacaagaaac

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