RCPedia: Rtcs

Summary

Retrocopy Name	STMP1P6	Plot displaying the genomic locations of a retrocopy (in chrX) and its respective parental gene (in chr7). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chrX:46893791-46894069 UCSC
Coordinates (T2T)	chrX:46300793-46301071 UCSC
Coordinates (hg19)	chrX:46753226-46753504 UCSC
Strand	-
Parental Sequence	NM_001130929.2
Parental seq. overlap	240 bp
Parental seq. overlap (%)	9.7%
Genomic Region	Intergenic
Retrocopy Summary	STMP1P6, located on chrX:46893791-46894069, is a retrocopy of the parental gene STMP1. 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	STMP1
Full Name	short transmembrane mitochondrial protein 1
Also known as	C7orf73\|Mm47\|PL-5283
Coordinate	chr7:135662514-135676416
Strand	+
Gene summary	Predicted to be involved in positive regulation of NLRP3 inflammasome complex assembly and positive regulation of interleukin-1 beta production. Predicted to be located in mitochondrial intermembrane space and mitochondrial outer membrane. Predicted to be active in mitochondrial respirasome. [provided by Alliance of Genome Resources, Apr 2022]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	STMP1P6
Bonobo	Pan paniscus	STMP1P6
Gorilla	Gorilla gorilla	STMP1P6
Orangutan	Pongo abelii	STMP1P5
Gibbon	Nomascus leucogenys	STMP1P3
Green monkey	Chlorocebus sabaeus	C21H7orf73P6
Crab-eating macaque	Macaca fascicularis	C3H7orf73P6
Baboon	Papio anubis	STMP1P6
Marmoset	Callithrix jacchus	STMP1P6
Rhesus	Macaca mulatta	Without Homology
Golden snub-nosed monkey	Rhinopithecus roxellana	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

>STMP1P6
CGACATCACGTTCCAGTTCCTGCTTGCACTTGCTTTTGGCAATGTGGTTGGAATGTATGTGGCTCAGAACTATGACATACCAAATCTAGCTAAAACATGTGAAGAAATTAAAAAGGAATTGGGTGCCAAGAAGACACCCCCTAGTTCATGAGGTTGACTCCAGCACTGCCTTCTGGATACACCGATTCCACTGCTCTTCAGGCCCTCCTTTACCATCTGAACCAAAAACTTTTGCTTTGTCTTCAGCCTCAGTGATTTTTCTTCTTTGCTAGACCCTGC

>NM_001130929.2
AGGCTCGGACCGGCCCGCGGAGCTGCTGCAGTCCTTCGCGCCCTCCTCGCCCTCCCCACCGACATCATGCTCCAGTTCCTGCTTGGATTTACACTGGGCAACGTGGTTGGAATGTATCTGGCTCAGAACTATGATATACCAAACCTGGCTAAAAAACTTGAAGAAATTAAAAAGGACTTGGATGCCAAGAAGAAACCCCCTAGTGCATGAGACTGCCTCCAGCACTGCCTTCAGGATATACTGATTCTACTGCTCTTGAGGGCCTCGTTTACTATCTGAACCAAAAGCTTTTGTTTTCGTCTCCAGCCTCAGCACTTCTCTTCTTTGCTAGACCCTGTGTTTTTTGCTTTAAAGCAAGCAAAATGGGGCCCCAATTTGAGAACTACCCGACATTTCCAACATACTCACCTCTTCCCATAATCCCTTTCCAACTGCATGGGAGGTTCTAAGACTGGAATTATGGTGCTAGATTAGTAAACATGACTTTTAATGAGTAGTGTCTTCTTTATCGTTTGCGATTTTTACTACCTTTTTTCAAAAGAAAAATTGATGAGTTTTGTATAGCTGGTCAGATACAAATAATAGTGACTTCACAGTTTAGTAATTATAATGGGTACTTGTTAAACATTTGGTACTAAATTATGTTGCTGCAAAGTAATTAAAATTAGTATCTAGAGCTAGTTTCTGGTGAATTATTCATTTATTTTGTACTGTTGTTAGGCAGCTCTGTAGTTGCTAATTTAACCAATAAGTCAATTTGCTATTCATGAAGAAACGATTCTGAGAATCCtgtcaggaattggggaatgaaaaaatacacaaaataatggtctttgtcccagtagagttcatagtctaTTTAGTGTGCATGTTTTTCCTTAATGATGTATTTGATCTGACTTTTTTCCTTCTCAAAAGAATCATACTTGGGATTACAGGTACATTTGATGTTATATGATGGATAAGTGAAAAGTTTTTAAAGGAGATTTTATACCTTTTCACATTAAAAAAGGTATTTATATTATTACTTTGTAGTGATTGTCTTAAGAAAAAATATAGCCCAAATGTATAGTAAAATCAGCAGCTCAAGAAGAATTTCTGCTTCTCTTTGTAGTTGATGCTTTGTTTTTTCCTGCAGTCAGAAATTCCTTGTATTTGTCAAATGTATAATCAGCTTGTATTGTTTTTAAATTAAAAAAAAATTTGAATAATTAACTTTTGCCATGGGACaagatacaaaagtaatttcatataaagggcctctcccacccctgttctctggctcctggctcctgtttgacaagttactgttaccacttcgccttatacttttgagaaagagtctgtgcctaaacaaacacgtgtaacacaaatagtaactatacatggaggtctagccctcgccttttttttttctttttttcttttttaatggagatcattctataccagcatgtaagtagcaaggaacctcattctttttttggctgcctaaaatttttttgaatagatataacataattgatttaatctgctactggtgaatgcttaggttgttcttttgctattacagtgataacttcaatcctaatgttattaagcatatcgattcagggtatagctataagatgaagtcctaaaagtataattTAGACTAAATACAAATACCCATTTCGCTAGCTGTTTTGTTTCAGAGGACTTGTTGAGCAGCTTCACTAATAATGCCATTTTTGAAGACATGGCAGGTTCAGAATCAATAAACTGGAAGAATTGTTCAGAGCATCTTTTTTCAGACAGTGATGACATTGATTCTGTATATGATAAAGTGATTCTGCTTCTCTTTGACAACTTGCATCTCTCCTACATGGAAGTAAGTTTTATTCCTGTCAATGTTGTCTTTGTGTGTgacagattaggattaaattatggtttgacttttcctagcagcgtgatcatgggcaagtGGCttttttttttttttttttttgagacagagtctcactctgctgcccaggctggagtgcagtggcacagtcttggctcactgcaactcctgcctcccggtccaagtgattctcgtgctgcagcttctcaagtagctggcatcaccaccacacctggctaatttttgtatttttagtaacgacgaggtttcaccatgttggcaaagctggtctcaaattcctggcctcaagtgatctgcccacttcagcctcccaaagtgttgggattacaggcgtgagccactgcgcccagcTTTTTTAAACTTTTAGATTCATTTAATAGGTAAATTGCATGTCACGGGTTTGTAGcttattctttcagaaactcttgcattatctgtagacgtggacgtaaatatccacctcatagggttttcataaaaaataattgagataatgtatgtaatgtttcacagtgctttgcagactatctaataaatagtagctattaGTACAAA

>NM_001130929.2 

AGGCTCGGACCGGCCCGCGGAGCTGCTGCAGTCCTTCGCGCCCTCCTCGCCCTCCCCACCGACATCATGCTCCAGTTCCTGCTTGGATTTACACTGGGCAACGTGGTTGGAATGTATCTGGCTCAGAACTATGATATACCAAACCTGGCTAAAAAACTTGAAGAAATTAAAAAGGACTTGGATGCCAAGAAGAAACCCCCTAGTGCATGAGACTGCCTCCAGCACTGCCTTCAGGATATACTGATTCTACTGCTCTTGAGGGCCTCGTTTACTATCTGAACCAAAAGCTTTTGTTTTCGTCTCCAGCCTCAGCACTTCTCTTCTTTGCTAGACCCTGTGTTTTTTGCTTTAAAGCAAGCAAAATGGGGCCCCAATTTGAGAACTACCCGACATTTCCAACATACTCACCTCTTCCCATAATCCCTTTCCAACTGCATGGGAGGTTCTAAGACTGGAATTATGGTGCTAGATTAGTAAACATGACTTTTAATGAGTAGTGTCTTCTTTATCGTTTGCGATTTTTACTACCTTTTTTCAAAAGAAAAATTGATGAGTTTTGTATAGCTGGTCAGATACAAATAATAGTGACTTCACAGTTTAGTAATTATAATGGGTACTTGTTAAACATTTGGTACTAAATTATGTTGCTGCAAAGTAATTAAAATTAGTATCTAGAGCTAGTTTCTGGTGAATTATTCATTTATTTTGTACTGTTGTTAGGCAGCTCTGTAGTTGCTAATTTAACCAATAAGTCAATTTGCTATTCATGAAGAAACGATTCTGAGAATCCtgtcaggaattggggaatgaaaaaatacacaaaataatggtctttgtcccagtagagttcatagtctaTTTAGTGTGCATGTTTTTCCTTAATGATGTATTTGATCTGACTTTTTTCCTTCTCAAAAGAATCATACTTGGGATTACAGGTACATTTGATGTTATATGATGGATAAGTGAAAAGTTTTTAAAGGAGATTTTATACCTTTTCACATTAAAAAAGGTATTTATATTATTACTTTGTAGTGATTGTCTTAAGAAAAAATATAGCCCAAATGTATAGTAAAATCAGCAGCTCAAGAAGAATTTCTGCTTCTCTTTGTAGTTGATGCTTTGTTTTTTCCTGCAGTCAGAAATTCCTTGTATTTGTCAAATGTATAATCAGCTTGTATTGTTTTTAAATTAAAAAAAAATTTGAATAATTAACTTTTGCCATGGGACaagatacaaaagtaatttcatataaagggcctctcccacccctgttctctggctcctggctcctgtttgacaagttactgttaccacttcgccttatacttttgagaaagagtctgtgcctaaacaaacacgtgtaacacaaatagtaactatacatggaggtctagccctcgccttttttttttctttttttcttttttaatggagatcattctataccagcatgtaagtagcaaggaacctcattctttttttggctgcctaaaatttttttgaatagatataacataattgatttaatctgctactggtgaatgcttaggttgttcttttgctattacagtgataacttcaatcctaatgttattaagcatatcgattcagggtatagctataagatgaagtcctaaaagtataattTAGACTAAATACAAATACCCATTTCGCTAGCTGTTTTGTTTCAGAGGACTTGTTGAGCAGCTTCACTAATAATGCCATTTTTGAAGACATGGCAGGTTCAGAATCAATAAACTGGAAGAATTGTTCAGAGCATCTTTTTTCAGACAGTGATGACATTGATTCTGTATATGATAAAGTGATTCTGCTTCTCTTTGACAACTTGCATCTCTCCTACATGGAAGTAAGTTTTATTCCTGTCAATGTTGTCTTTGTGTGTgacagattaggattaaattatggtttgacttttcctagcagcgtgatcatgggcaagtGGCttttttttttttttttttttgagacagagtctcactctgctgcccaggctggagtgcagtggcacagtcttggctcactgcaactcctgcctcccggtccaagtgattctcgtgctgcagcttctcaagtagctggcatcaccaccacacctggctaatttttgtatttttagtaacgacgaggtttcaccatgttggcaaagctggtctcaaattcctggcctcaagtgatctgcccacttcagcctcccaaagtgttgggattacaggcgtgagccactgcgcccagcTTTTTTAAACTTTTAGATTCATTTAATAGGTAAATTGCATGTCACGGGTTTGTAGcttattctttcagaaactcttgcattatctgtagacgtggacgtaaatatccacctcatagggttttcataaaaaataattgagataatgtatgtaatgtttcacagtgctttgcagactatctaataaatagtagctattaGTACAAA

Publications

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