RCPedia: Rtcs

Summary

Retrocopy Name	SQSTM1P1	Plot displaying the genomic locations of a retrocopy (in chr13) and its respective parental gene (in chr5). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr13:62406070-62406263 UCSC
Coordinates (T2T)	chr13:61627072-61627265 UCSC
Coordinates (hg19)	chr13:62980203-62980396 UCSC
Strand	-
Parental Sequence	NM_003900.5_2
Parental seq. overlap	158 bp
Parental seq. overlap (%)	5.6%
Genomic Region	Intergenic
Retrocopy Summary	SQSTM1P1, located on chr13:62406070-62406263, is a retrocopy of the parental gene SQSTM1. 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	SQSTM1
Full Name	sequestosome 1
Also known as	A170\|DMRV\|FTDALS3\|NADGP\|OSIL\|PDB3\|ZIP3\|p60\|p62\|p62B
Coordinate	chr5:179806393-179838078
Strand	+
Gene summary	This gene encodes a multifunctional protein that binds ubiquitin and regulates activation of the nuclear factor kappa-B (NF-kB) signaling pathway. The protein functions as a scaffolding/adaptor protein in concert with TNF receptor-associated factor 6 to mediate activation of NF-kB in response to upstream signals. Alternatively spliced transcript variants encoding either the same or different isoforms have been identified for this gene. Mutations in this gene result in sporadic and familial Paget disease of bone. [provided by RefSeq, Mar 2009]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	SQSTM1P1
Bonobo	Pan paniscus	SQSTM1P1
Gorilla	Gorilla gorilla	SQSTM1P1
Crab-eating macaque	Macaca fascicularis	SQSTM1P1
Rhesus	Macaca mulatta	SQSTM1P1
Orangutan	Pongo abelii	Without Homology
Gibbon	Nomascus leucogenys	Without Homology
Green monkey	Chlorocebus sabaeus	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
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

The Genotype-Tissue Expression project - (GTEx)

Related Sequence

>SQSTM1P1
GACCCACAGGACTGAAGGAGGCTGCCTTGTTCCCACATATTCCTTCAGGAACTGACTCCTGGCTGCTTCAGCCCCTCTCCCAGATGCAGTCCATGGGACTCTCCGATGAAGGTGGCTGCCTCATCAGGCTCCTAGACACCAGGAATTACCACATCAGAGCTGCCCTGGACATCATCCAGTATTCAAAGAATCCA

>NM_003900.5_2
ACGGCCCGTTTTCCGCCAGCTCGCCGCTCGCTATGGCGTCGCTCACCGTGAAGGCCTACCTTCTGGGCAAGGAGGACGCGGCGCGCGAGATTCGCCGCTTCAGCTTCTGCTGCAGCCCCGAGCCTGAGGCGGAAGCCGAGGCTGCGGCGGGTCCGGGACCCTGCGAGCGGCTGCTGAGCCGGGTGGCCGCCCTGTTCCCCGCGCTGCGGCCTGGCGGCTTCCAGGCGCACTACCGCGATGAGGACGGGGACTTGGTTGCCTTTTCCAGTGACGAGGAATTGACAATGGCCATGTCCTACGTGAAGGATGACATCTTCCGAATCTACATTAAAGAGAAAAAAGAGTGCCGGCGGGACCACCGCCCACCGTGTGCTCAGGAGGCGCCCCGCAACATGGTGCACCCCAATGTGATCTGCGATGGCTGCAATGGGCCTGTGGTAGGAACCCGCTACAAGTGCAGCGTCTGCCCAGACTACGACTTGTGTAGCGTCTGCGAGGGAAAGGGCTTGCACCGGGGGCACACCAAGCTCGCATTCCCCAGCCCCTTCGGGCACCTGTCTGAGGGCTTCTCGCACAGCCGCTGGCTCCGGAAGGTGAAACACGGACACTTCGGGTGGCCAGGATGGGAAATGGGTCCACCAGGAAACTGGAGCCCACGTCCTCCTCGTGCAGGGGAGGCCCGCCCTGGCCCCACGGCAGAATCAGCTTCTGGTCCATCGGAGGATCCGAGTGTGAATTTCCTGAAGAACGTTGGGGAGAGTGTGGCAGCTGCCCTTAGCCCTCTGGGCATTGAAGTTGATATCGATGTGGAGCACGGAGGGAAAAGAAGCCGCCTGACCCCCGTCTCTCCAGAGAGTTCCAGCACAGAGGAGAAGAGCAGCTCACAGCCAAGCAGCTGCTGCTCTGACCCCAGCAAGCCGGGTGGGAATGTTGAGGGCGCCACGCAGTCTCTGGCGGAGCAGATGAGGAAGATCGCCTTGGAGTCCGAGGGGCGCCCTGAGGAACAGATGGAGTCGGATAACTGTTCAGGAGGAGATGATGACTGGACCCATCTGTCTTCAAAAGAAGTGGACCCGTCTACAGGTGAACTCCAGTCCCTACAGATGCCAGAATCCGAAGGGCCAAGCTCTCTGGACCCCTCCCAGGAGGGACCCACAGGGCTGAAGGAAGCTGCCTTGTACCCACATCTCCCGCCAGAGGCTGACCCGCGGCTGATTGAGTCCCTCTCCCAGATGCTGTCCATGGGCTTCTCTGATGAAGGCGGCTGGCTCACCAGGCTCCTGCAGACCAAGAACTATGACATCGGAGCGGCTCTGGACACCATCCAGTATTCAAAGCATCCCCCGCCGTTGTGACCACTTTTGCCCACCTCTTCTGCGTGCCCCTCTTCTGTCTCATAGTTGTGTTAAGCTTGCGTAGAATTGCAGGTCTCTGTACGGGCCAGTTTCTCTGCCTTCTTCCAGGATCAGGGGTTAGGGTGCAAGAAGCCATTTAGGGCAGCAAAACAAGTGACATGAAGGGAGGGTCCCTGTGTGTGTGTGTGCTGATGTTTCCTGGGTGCCCTGGCTCCTTGCAGCAGGGCTGGGCCTGCGAGACCCAAGGCTCACTGCAGCGCGCTCCTGACCCCTCCCTGCAGGGGCTACGTTAGCAGCCCAGCACATAGCTTGCCTAATGGCTTTCACTTTCTCTTTTGTTTTAAATGACTCATAGGTCCCTGACATTTAGTTGATTATTTTCTGCTACAGACCTGGTACACTCTGATTTTAGATAAAGTAAGCCTAGGTGTTGTCAGCAGGCAGGCTGGGGAGGCCAGTGTTGTGGGCTTCCTGCTGGGACTGAGAAGGCTCACGAAGGGCATCCGCAATGTTGGTTTCACTGAGAGCTGCCTCCTGGTCTCTTCACCACTGTAGTTCTCTCATTTCCAAACCATCAGCTGCTTTTAAAATAAGATCTCTTTGTAGCCATCCTGTTAAATTTGTAAACAATCTAATTAAATGGCATCAGCACTTTAACCAATGACGTTTGCATAGAGAGAAATGATTGACAGTAAGTTTATTGTTAATGGTTCTTACAGAGTATCTTTAAAAGTGCCTTAGGGGAACCCTGTCCCTCCTAACAAGTGTATCTCGATTAATAACCTGCCAGTCCCAGATCACACATCATCATCGAAGTCTTCCCCAGTTATAAAGAGGTCACATAGTCGTGTGGGTCGAGGATTCTGTGCCTCCAGGACCAGGGGCCCACCCTCTGCCCAGGGAGTCCTTGCGTCCCATGAGGTCTTCCCGCAAGGCCTCTCAGACCCAGATGTGACGGGGTGTGTGGCCCGAGGAAGCTGGACAGCGGCAGTGGGCCTGCTGAGGCCTTCTCTTGAGGCCTGTGCTCTGGGGGTCCCTTGCTTAGCCTGTGCTGGACCAGCTGGCCTGGGGTCCCTCTGAAGAGACCTTGGCTGCTCACTGTCCACATGTGAACTTTTTCTAGGTGGCAGGACAAATTGCGCCCATTTAGAGGATGTGGCTGTAACCTGCTGGATGGGACTCCATAGCTCCTTCCCAGGACCCCTCAGCTCCCCGGCACTGCAGTCTGCAGAGTTCTCCTGGAGGCAGGGGCTGCTGCCTTGTTTCACCTTCCATGTCAGGCCAGCCTGTCCCTGAAAGAGAAGATGGCCATGCCCTCCATGTGTAAGAACAATGCCAGGGCCCAGGAGGACCGCCTGCCCTGCCTGGGCCTTGGCTGGGCCTCTGGTTCTGACACTTTCTGCTGGAAGCTGTCAGGCTGGGACAGGCTTTGATTTTGAGGGTTAGCAAGACAAAGCAAATAAATGCCTTCCACCTCACCGCAAA

>NM_003900.5_2 

ACGGCCCGTTTTCCGCCAGCTCGCCGCTCGCTATGGCGTCGCTCACCGTGAAGGCCTACCTTCTGGGCAAGGAGGACGCGGCGCGCGAGATTCGCCGCTTCAGCTTCTGCTGCAGCCCCGAGCCTGAGGCGGAAGCCGAGGCTGCGGCGGGTCCGGGACCCTGCGAGCGGCTGCTGAGCCGGGTGGCCGCCCTGTTCCCCGCGCTGCGGCCTGGCGGCTTCCAGGCGCACTACCGCGATGAGGACGGGGACTTGGTTGCCTTTTCCAGTGACGAGGAATTGACAATGGCCATGTCCTACGTGAAGGATGACATCTTCCGAATCTACATTAAAGAGAAAAAAGAGTGCCGGCGGGACCACCGCCCACCGTGTGCTCAGGAGGCGCCCCGCAACATGGTGCACCCCAATGTGATCTGCGATGGCTGCAATGGGCCTGTGGTAGGAACCCGCTACAAGTGCAGCGTCTGCCCAGACTACGACTTGTGTAGCGTCTGCGAGGGAAAGGGCTTGCACCGGGGGCACACCAAGCTCGCATTCCCCAGCCCCTTCGGGCACCTGTCTGAGGGCTTCTCGCACAGCCGCTGGCTCCGGAAGGTGAAACACGGACACTTCGGGTGGCCAGGATGGGAAATGGGTCCACCAGGAAACTGGAGCCCACGTCCTCCTCGTGCAGGGGAGGCCCGCCCTGGCCCCACGGCAGAATCAGCTTCTGGTCCATCGGAGGATCCGAGTGTGAATTTCCTGAAGAACGTTGGGGAGAGTGTGGCAGCTGCCCTTAGCCCTCTGGGCATTGAAGTTGATATCGATGTGGAGCACGGAGGGAAAAGAAGCCGCCTGACCCCCGTCTCTCCAGAGAGTTCCAGCACAGAGGAGAAGAGCAGCTCACAGCCAAGCAGCTGCTGCTCTGACCCCAGCAAGCCGGGTGGGAATGTTGAGGGCGCCACGCAGTCTCTGGCGGAGCAGATGAGGAAGATCGCCTTGGAGTCCGAGGGGCGCCCTGAGGAACAGATGGAGTCGGATAACTGTTCAGGAGGAGATGATGACTGGACCCATCTGTCTTCAAAAGAAGTGGACCCGTCTACAGGTGAACTCCAGTCCCTACAGATGCCAGAATCCGAAGGGCCAAGCTCTCTGGACCCCTCCCAGGAGGGACCCACAGGGCTGAAGGAAGCTGCCTTGTACCCACATCTCCCGCCAGAGGCTGACCCGCGGCTGATTGAGTCCCTCTCCCAGATGCTGTCCATGGGCTTCTCTGATGAAGGCGGCTGGCTCACCAGGCTCCTGCAGACCAAGAACTATGACATCGGAGCGGCTCTGGACACCATCCAGTATTCAAAGCATCCCCCGCCGTTGTGACCACTTTTGCCCACCTCTTCTGCGTGCCCCTCTTCTGTCTCATAGTTGTGTTAAGCTTGCGTAGAATTGCAGGTCTCTGTACGGGCCAGTTTCTCTGCCTTCTTCCAGGATCAGGGGTTAGGGTGCAAGAAGCCATTTAGGGCAGCAAAACAAGTGACATGAAGGGAGGGTCCCTGTGTGTGTGTGTGCTGATGTTTCCTGGGTGCCCTGGCTCCTTGCAGCAGGGCTGGGCCTGCGAGACCCAAGGCTCACTGCAGCGCGCTCCTGACCCCTCCCTGCAGGGGCTACGTTAGCAGCCCAGCACATAGCTTGCCTAATGGCTTTCACTTTCTCTTTTGTTTTAAATGACTCATAGGTCCCTGACATTTAGTTGATTATTTTCTGCTACAGACCTGGTACACTCTGATTTTAGATAAAGTAAGCCTAGGTGTTGTCAGCAGGCAGGCTGGGGAGGCCAGTGTTGTGGGCTTCCTGCTGGGACTGAGAAGGCTCACGAAGGGCATCCGCAATGTTGGTTTCACTGAGAGCTGCCTCCTGGTCTCTTCACCACTGTAGTTCTCTCATTTCCAAACCATCAGCTGCTTTTAAAATAAGATCTCTTTGTAGCCATCCTGTTAAATTTGTAAACAATCTAATTAAATGGCATCAGCACTTTAACCAATGACGTTTGCATAGAGAGAAATGATTGACAGTAAGTTTATTGTTAATGGTTCTTACAGAGTATCTTTAAAAGTGCCTTAGGGGAACCCTGTCCCTCCTAACAAGTGTATCTCGATTAATAACCTGCCAGTCCCAGATCACACATCATCATCGAAGTCTTCCCCAGTTATAAAGAGGTCACATAGTCGTGTGGGTCGAGGATTCTGTGCCTCCAGGACCAGGGGCCCACCCTCTGCCCAGGGAGTCCTTGCGTCCCATGAGGTCTTCCCGCAAGGCCTCTCAGACCCAGATGTGACGGGGTGTGTGGCCCGAGGAAGCTGGACAGCGGCAGTGGGCCTGCTGAGGCCTTCTCTTGAGGCCTGTGCTCTGGGGGTCCCTTGCTTAGCCTGTGCTGGACCAGCTGGCCTGGGGTCCCTCTGAAGAGACCTTGGCTGCTCACTGTCCACATGTGAACTTTTTCTAGGTGGCAGGACAAATTGCGCCCATTTAGAGGATGTGGCTGTAACCTGCTGGATGGGACTCCATAGCTCCTTCCCAGGACCCCTCAGCTCCCCGGCACTGCAGTCTGCAGAGTTCTCCTGGAGGCAGGGGCTGCTGCCTTGTTTCACCTTCCATGTCAGGCCAGCCTGTCCCTGAAAGAGAAGATGGCCATGCCCTCCATGTGTAAGAACAATGCCAGGGCCCAGGAGGACCGCCTGCCCTGCCTGGGCCTTGGCTGGGCCTCTGGTTCTGACACTTTCTGCTGGAAGCTGTCAGGCTGGGACAGGCTTTGATTTTGAGGGTTAGCAAGACAAAGCAAATAAATGCCTTCCACCTCACCGCAAA

Publications

PMID - Link	Title
No publications available for this retrocopy