RCPedia: Rtcs

Summary

Retrocopy Name	HSPE1P23	Plot displaying the genomic locations of a retrocopy (in chr4) and its respective parental gene (in chr2). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr4:74917839-74918256 UCSC
Coordinates (T2T)	chr4:78257979-78258396 UCSC
Coordinates (hg19)	chr4:75843049-75843466 UCSC
Strand	+
Parental Sequence	NM_002157.3
Parental seq. overlap	356 bp
Parental seq. overlap (%)	62.5%
Genomic Region	Intergenic
Retrocopy Summary	HSPE1P23, located on chr4:74917839-74918256, is a retrocopy of the parental gene HSPE1. 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	HSPE1
Full Name	heat shock protein family E (Hsp10) member 1
Also known as	CPN10\|EPF\|GROES\|HSP10
Coordinate	chr2:197500379-197503449
Strand	+
Gene summary	This gene encodes a major heat shock protein which functions as a chaperonin. Its structure consists of a heptameric ring which binds to another heat shock protein in order to form a symmetric, functional heterodimer which enhances protein folding in an ATP-dependent manner. This gene and its co-chaperonin, HSPD1, are arranged in a head-to-head orientation on chromosome 2. Naturally occurring read-through transcription occurs between this locus and the neighboring locus MOBKL3.[provided by RefSeq, Feb 2011]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	HSPE1P9
Bonobo	Pan paniscus	LOC100982477P9
Gorilla	Gorilla gorilla	LOC101151505P8
Orangutan	Pongo abelii	HSPE1P6
Gibbon	Nomascus leucogenys	LOC100605912P9
Green monkey	Chlorocebus sabaeus	LOC103217585P8
Crab-eating macaque	Macaca fascicularis	LOC102147033P6
Rhesus	Macaca mulatta	HSPE1P7
Baboon	Papio anubis	LOC101019904P3
Golden snub-nosed monkey	Rhinopithecus roxellana	LOC104676747P3
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

>HSPE1P23
TGAAAGTTTATTTCTCTCTTTGACCGAGTATTTGTTGAAAGAACTGCAGCTGAAACTGTAGCCAAAGGAGGCATGATGCTTCCAGAACAAATGTCAAAGAAAAGTATTACATGCATCAGTAGTAGCTGTTAGATTGGTCTCTAAAAGAAAGGGTGGAGAGATTCAACCAGTTAGCATCCAAGTTGGAGATAAAGTTATTTTCCCAGAATATGGAAGCACCAAAGTGCTTTAGACAAGGATTATTTCTTATTTAGAGATGGTTTAGAGATGGTGACTTTCTTGGAAAGTATGCAGACTGAAATAAATCACCATTGAAATGGCATAATAGTGAAGCTGCCCATTCCACTAAAGTTCTGAAATCTTTCATTATGTACATAAGTTCTACGTCTCTCTTTTGTAATAAACTAATAATAGCTAA

>NM_002157.3
GCGAGTCTCTTTGCGGCGCTACACTAGAGCAGAGTACGAGTCTGAGGCGGAGGGAGTAATGGCAGGACAAGCGTTTAGAAAGTTTCTTCCACTCTTTGACCGAGTATTGGTTGAAAGGAGTGCTGCTGAAACTGTAACCAAAGGAGGCATTATGCTTCCAGAAAAATCTCAAGGAAAAGTATTGCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTAAAGGAAAGGGTGGAGAGATTCAACCAGTTAGCGTGAAAGTTGGAGATAAAGTTCTTCTCCCAGAATATGGAGGCACCAAAGTAGTTCTAGATGACAAGGATTATTTCCTATTTAGAGATGGTGACATTCTTGGAAAGTACGTAGACTGAAATAAGTCACTATTGAAATGGCATCAACATGATGCTGCCCATTCCACTGAAGTTCTGAAATCTTTCGTCATGTAAATAATTTCCATATTTCTCTTTTATAATAAACTAATGATAACTAATGACATCCAGTGTCTCCAAAATTGTTTCCTTGTACTGATATAAACACTTCCAAATAAAAATATGTAAATGA

>NM_002157.3 

GCGAGTCTCTTTGCGGCGCTACACTAGAGCAGAGTACGAGTCTGAGGCGGAGGGAGTAATGGCAGGACAAGCGTTTAGAAAGTTTCTTCCACTCTTTGACCGAGTATTGGTTGAAAGGAGTGCTGCTGAAACTGTAACCAAAGGAGGCATTATGCTTCCAGAAAAATCTCAAGGAAAAGTATTGCAAGCAACAGTAGTCGCTGTTGGATCGGGTTCTAAAGGAAAGGGTGGAGAGATTCAACCAGTTAGCGTGAAAGTTGGAGATAAAGTTCTTCTCCCAGAATATGGAGGCACCAAAGTAGTTCTAGATGACAAGGATTATTTCCTATTTAGAGATGGTGACATTCTTGGAAAGTACGTAGACTGAAATAAGTCACTATTGAAATGGCATCAACATGATGCTGCCCATTCCACTGAAGTTCTGAAATCTTTCGTCATGTAAATAATTTCCATATTTCTCTTTTATAATAAACTAATGATAACTAATGACATCCAGTGTCTCCAAAATTGTTTCCTTGTACTGATATAAACACTTCCAAATAAAAATATGTAAATGA

Publications

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