RCPedia: Rtcs

Summary

Retrocopy Name	SHLD1P1	Plot displaying the genomic locations of a retrocopy (in chr1) and its respective parental gene (in chr20). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr1:88923410-88924026 UCSC
Coordinates (T2T)	chr1:88766802-88767418 UCSC
Coordinates (hg19)	chr1:89389093-89389709 UCSC
Strand	+
Parental Sequence	NM_152504.4
Parental seq. overlap	526 bp
Parental seq. overlap (%)	32.1%
Genomic Region	Intergenic
Retrocopy Summary	SHLD1P1, located on chr1:88923410-88924026, is a retrocopy of the parental gene SHLD1. 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	SHLD1
Full Name	shieldin complex subunit 1
Also known as	C20orf196\|RINN3
Coordinate	chr20:5750286-5864395
Strand	+
Gene summary	Involved in negative regulation of double-strand break repair via homologous recombination; positive regulation of double-strand break repair via nonhomologous end joining; and positive regulation of isotype switching. Located in site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	C20H20orf196P1
Bonobo	Pan paniscus	SHLD1P1
Gorilla	Gorilla gorilla	SHLD1P1
Orangutan	Pongo abelii	C20H20orf196P1
Green monkey	Chlorocebus sabaeus	C2H20orf196P1
Crab-eating macaque	Macaca fascicularis	C10H20orf196P1
Rhesus	Macaca mulatta	SHLD1P1
Baboon	Papio anubis	SHLD1P1
Golden snub-nosed monkey	Rhinopithecus roxellana	SHLD1P1
Gibbon	Nomascus leucogenys	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
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

>SHLD1P1
ACAGCCTGTCAGAGGAGAGCAGTACTTTGGACCTGCCATAAGCCTGTATGTGAAGGATTATGTCCTGCAGAGATGCAGCCAAGAGGCCAACAGCAAGGCTTTTAGTTCTGTGAAATTCCATTCTTTTCCTTGCTTTTCTGATGTGGATCCAGACACCAGGAGCCTAAATACTAAACAAAATGACTCTGGGACCACTGAGAACTTTTGATTTCACCTTTCTGTGTAAGGCCAATCAGAGACCGTAGAAGAGGATAATGGACTTCAGAAATCTCTGGATAAATTCTATGAAATGTTTGGATATCCAAAGCTAGCCTCTGGGAATCCATTCTCTGCATCTGTCTGCCAGTGCCTGTCTCAGAAAATCCCTCAACTAAGAGTCCAGGAGAGCCAAAAGTATGCCCTCTATAGTTTTCAAATGTCCCAGGTCATCTTTAACTGCGATGGCTGCTCAGTCTTGCAGAGGGACATCCACTTCTACTCACTGGAGGAAGGAAGTACATCTGTAGATGATGAAAAACCAACCCAGAACTTTCAAAAGATATTAATTTTCTCTTATGGCAGAATTCAACGAAAGACCCAAAACTGGTGCCTGGCGGTGAGCAGGGAGTATTGGAGGT

>NM_152504.4
GTTCCGGTTGCGGATGGTGAGTGTGTCGGGGGGCTTGGCGGCTTTTCTCCTCAGTTTTCTGGAGTGCTTTGGAGGAGAGGACTATGGCAGCCAGGGACGCCACTTCAGGCAGCCTGTCAGAGGAGAGCAGTGCTTTGGACCTGCCATCAGCGTGTGACATAAGAGATTACGTCCTGCAGGGACCCAGCCAAGAAGCCAACAGCGAGGCTTTCAGTTCTTTGGAATTCCATTCTTTTCCTTATTCTTCTGATGTGGATCCAGACACCAGTAACTTAAATATAGAACAAAATAACTCCTGGACCGCTGAGAACTTCTGGCTTGACCCTGCTGTGAAAGGCCAGTCAGAGAAGGAAGAGGATGATGGCCTTCGGAAATCCCTGGATAGATTCTATGAAATGTTTGGTCATCCACAGCCAGGCTCTGCAAACTCACTCTCTGCATCTGTCTGCAAGTGCCTGTCTCAGAAAATCACTCAACTAAGAGGCCAGGAGAGCCAAAAGTATGCCCTCCGCAGTTTTCAAATGGCCCGGGTGATCTTCAACCGGGACGGCTGCTCCGTCTTACAGAGGCATTCCAGGGACACCCACTTCTACCCACTGGAGGAAGGAAGTACATCTTTGGATGATGAAAAGCCAAACCCAGGACTGTCAAAGGATATTACTCATTTCCTCTTGCAGCAGAATGTAATGAAAGACCTGTAACTGGTGCCGGGCAGTGTGCAGGGTAGTAATGGAGGTGCTGTGCCATGACCagcagtgttggtggccacccagatcccctagggtctctggccagctctgtgtgcccaatcccaattaagtgctttgaggttaaaggctggcacctgtgacctggtattggagccagtcagcccatatggagagccagcagggtctgggagttctccgtcctcttggccaaggccgctgactgactgggctacgagtcaaaagcccagctcccttgcctcaaggaaggacattctctgaggagtaatttatgctctagcactccctttcctctagatcggcctgaggctgggacattacatgaaatcacacccttgctgggcttaatccctttccctaccctcccatttatttactggtgtctctgggagcctttccttaataaacctcttatatctgaatccttgactcagagtctacttctgggagaattcaccctgagaGAACATGCTTCTGTGAGATGAGGTTTTAGAAGGATACAAAGCTCTACACCGAATCAGGTATAAGGAATTATATCAAGTTGTAAAACTGAGACCATGTCATTGAGAATACATGTCCTAAAATAATATAAAGATTGAAATACAGTTGAGAAAAGTATATCACATCTTGATCACACCCTTGCCTCCTCTCCAAAGCTAGAAATCCATGTTTTATCATACTAACTGGGTGTGGAAGGAACATTTGGACAATCTAAAATAACAGCGAAAATTCACAATTCTTTTTAAAATCTCTTGTCTTTTATCAGATTGCAAACGTGAAAGGTGAGAAGGTAACAAATGTGCACCACCCACCACAGTATATGTAAGCACAATTATGCTACGCTAGGCTGATGCCACGTGGCCTTGTCAAGTTGTGTTTGAAGAGAATAAATAATCCTTTGCCCA

>NM_152504.4 

GTTCCGGTTGCGGATGGTGAGTGTGTCGGGGGGCTTGGCGGCTTTTCTCCTCAGTTTTCTGGAGTGCTTTGGAGGAGAGGACTATGGCAGCCAGGGACGCCACTTCAGGCAGCCTGTCAGAGGAGAGCAGTGCTTTGGACCTGCCATCAGCGTGTGACATAAGAGATTACGTCCTGCAGGGACCCAGCCAAGAAGCCAACAGCGAGGCTTTCAGTTCTTTGGAATTCCATTCTTTTCCTTATTCTTCTGATGTGGATCCAGACACCAGTAACTTAAATATAGAACAAAATAACTCCTGGACCGCTGAGAACTTCTGGCTTGACCCTGCTGTGAAAGGCCAGTCAGAGAAGGAAGAGGATGATGGCCTTCGGAAATCCCTGGATAGATTCTATGAAATGTTTGGTCATCCACAGCCAGGCTCTGCAAACTCACTCTCTGCATCTGTCTGCAAGTGCCTGTCTCAGAAAATCACTCAACTAAGAGGCCAGGAGAGCCAAAAGTATGCCCTCCGCAGTTTTCAAATGGCCCGGGTGATCTTCAACCGGGACGGCTGCTCCGTCTTACAGAGGCATTCCAGGGACACCCACTTCTACCCACTGGAGGAAGGAAGTACATCTTTGGATGATGAAAAGCCAAACCCAGGACTGTCAAAGGATATTACTCATTTCCTCTTGCAGCAGAATGTAATGAAAGACCTGTAACTGGTGCCGGGCAGTGTGCAGGGTAGTAATGGAGGTGCTGTGCCATGACCagcagtgttggtggccacccagatcccctagggtctctggccagctctgtgtgcccaatcccaattaagtgctttgaggttaaaggctggcacctgtgacctggtattggagccagtcagcccatatggagagccagcagggtctgggagttctccgtcctcttggccaaggccgctgactgactgggctacgagtcaaaagcccagctcccttgcctcaaggaaggacattctctgaggagtaatttatgctctagcactccctttcctctagatcggcctgaggctgggacattacatgaaatcacacccttgctgggcttaatccctttccctaccctcccatttatttactggtgtctctgggagcctttccttaataaacctcttatatctgaatccttgactcagagtctacttctgggagaattcaccctgagaGAACATGCTTCTGTGAGATGAGGTTTTAGAAGGATACAAAGCTCTACACCGAATCAGGTATAAGGAATTATATCAAGTTGTAAAACTGAGACCATGTCATTGAGAATACATGTCCTAAAATAATATAAAGATTGAAATACAGTTGAGAAAAGTATATCACATCTTGATCACACCCTTGCCTCCTCTCCAAAGCTAGAAATCCATGTTTTATCATACTAACTGGGTGTGGAAGGAACATTTGGACAATCTAAAATAACAGCGAAAATTCACAATTCTTTTTAAAATCTCTTGTCTTTTATCAGATTGCAAACGTGAAAGGTGAGAAGGTAACAAATGTGCACCACCCACCACAGTATATGTAAGCACAATTATGCTACGCTAGGCTGATGCCACGTGGCCTTGTCAAGTTGTGTTTGAAGAGAATAAATAATCCTTTGCCCA

Publications

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