RCPedia: Rtcs

Summary

Retrocopy Name	DNAJA1P5	Plot displaying the genomic locations of a retrocopy (in chr1) and its respective parental gene (in chr9). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr1:101893103-101894196 UCSC
Coordinates (T2T)	chr1:101742298-101743391 UCSC
Coordinates (hg19)	chr1:102358659-102359752 UCSC
Strand	+
Parental Sequence	NM_001539.4
Parental seq. overlap	923 bp
Parental seq. overlap (%)	39.1%
Genomic Region	Intragenic (OLFM3)
Retrocopy Summary	DNAJA1P5, located on chr1:101893103-101894196, is a retrocopy of the parental gene DNAJA1. 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	DNAJA1
Full Name	DnaJ heat shock protein family (Hsp40) member A1
Also known as	DJ-2\|DjA1\|HDJ2\|HSDJ\|HSJ-2\|HSJ2\|HSPF4\|NEDD7\|hDJ-2
Coordinate	chr9:33025273-33039907
Strand	+
Gene summary	This gene encodes a member of the DnaJ family of proteins, which act as heat shock protein 70 cochaperones. Heat shock proteins facilitate protein folding, trafficking, prevention of aggregation, and proteolytic degradation. Members of this family are characterized by a highly conserved N-terminal J domain, a glycine/phenylalanine-rich region, four CxxCxGxG zinc finger repeats, and a C-terminal substrate-binding domain. The J domain mediates the interaction with heat shock protein 70 to recruit substrates and regulate ATP hydrolysis activity. In humans, this gene has been implicated in positive regulation of virus replication through co-option by the influenza A virus. Several pseudogenes of this gene are found on other chromosomes. [provided by RefSeq, Sep 2015]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	DNAJA1P1
Bonobo	Pan paniscus	DNAJA1P1
Gorilla	Gorilla gorilla	DNAJA1P1
Orangutan	Pongo abelii	DNAJA1P1
Gibbon	Nomascus leucogenys	DNAJA1P5
Green monkey	Chlorocebus sabaeus	DNAJA1P5
Crab-eating macaque	Macaca fascicularis	DNAJA1P1
Rhesus	Macaca mulatta	DNAJA1P1
Baboon	Papio anubis	DNAJA1P1
Golden snub-nosed monkey	Rhinopithecus roxellana	DNAJA1P4
Marmoset	Callithrix jacchus	DNAJA1P11
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

>DNAJA1P5
AGAGGAGGAAGGATGCAGAGTAAAAGGAAATGTAAAAGTGTTGTACACCAGCTCTCAGTAACCTTAGAAGATTTATATGATGCTGCAACAAGAAAACAGGCTCTGCAAAATAATGTGCTTTGTGACAGGTGTGAAGACAGAGGTGGGGAAAAAAAAAAGGAACAGTACAGTGCTGTCATAATTGCCAAGGTATTGGAATGCAAATAAGAATTCATCAGATAGAACCCGGAATAGCTCAGCAAATTCAAGCTGTGTGCATGGAGACCCAGGGCCATGGGGAACAGATCAGTCCTCAAGATAGATGTAAAAGCTGCAACAGAAAGAAGATAGTTTTGGGAGAAGACGATTCTAGAAATTCATATTGACAAAAGCATGAAAGATGGCCAGAAAATAACATCTCATGATGAAAGAGACCAAAAACCAGGACTGGAGCCAGGAGATATTATCATTGCATTAGATCAGAAGGACCATGCTGTTTTTACTTGACAAAGAAAAGACCTTTTCATATGTATGGATATACAGCTGGTTGTAGTATTGCATGGCTTCTGAAAACCAATATCCACTCTTGACAACTGAACCATAGTCATCATCTCTCATCCAGGTCAAACTGTCAAGCATGGAGCCATCAAGCATGTGTTAAATGAAGGCAGGCCAATTTATTGTAGACCACATGAAGAGTCACTTAATCATTGAATTTAAGGTAAACTTTCTTGATAATGGCTTTCCCTTTTTTGACAAACTCCTTGCTGGAAAAACTCCTACAAAAGAGTAAAGAAGTAGAAGAGACTGATGAGATGAATCAAGTAGAATTTGTGGACTTTGATTCAAATCAGGAAAGATGATGCTGATGCCACTACAGTGCAGAAGCAAATGTGGGACCATTACAATGGAAAAGCATGAGGATGATAAACATCATTTCAGAGGTGTTCAGTGTCAAACATCTTAATGGGACCAGTGATAATACTCGCTGCTGGCATTTTATGGGCAGTAGTGAATGAGCAAAGGACTGTAATCCTAATATGCTCACTACTTGCTATTGTTTTGGTTTTACTATTCAACTAGAGTAGTGTTTTAAAAATTAAAGGAAGAATAAA

>NM_001539.4
GCGGAACTTTCCAGAACGCTCGGTGAGAGGCGGAGGAGCGGTAACTACCCCGGCTGCGCACAGCTCGGCGCTCCTTCCCGCTCCCTCACACACCGGCCTCAGCCCGCACCGGCAGTAGAAGATGGTGAAAGAAACAACTTACTACGATGTTTTGGGGGTCAAACCCAATGCTACTCAGGAAGAATTGAAAAAGGCTTATAGGAAACTGGCTTTGAAGTACCATCCTGATAAGAACCCAAATGAAGGAGAGAAGTTTAAACAGATTTCTCAAGCTTACGAAGTTCTCTCTGATGCAAAGAAAAGGGAATTATATGACAAAGGAGGAGAACAGGCAATTAAAGAGGGTGGAGCAGGTGGCGGTTTTGGCTCCCCCATGGACATCTTTGATATGTTTTTTGGAGGAGGAGGAAGGATGCAGAGAGAAAGGAGAGGTAAAAATGTTGTACATCAGCTCTCAGTAACCCTAGAAGACTTATATAATGGTGCAACAAGAAAACTGGCTCTGCAAAAGAATGTGATTTGTGACAAATGTGAAGGTAGAGGAGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAATTGCCGAGGTACTGGAATGCAAATAAGAATTCATCAGATAGGACCTGGAATGGTTCAGCAAATTCAGTCTGTGTGCATGGAGTGCCAGGGCCATGGGGAGCGGATCAGTCCTAAAGATAGATGTAAAAGCTGCAACGGAAGGAAGATAGTTCGAGAGAAGAAAATTTTAGAAGTTCATATTGACAAAGGCATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAGGAGACCAAGAACCAGGACTGGAGCCAGGCGATATTATCATTGTGTTAGATCAGAAGGACCATGCTGTTTTTACTCGACGAGGAGAAGACCTTTTCATGTGTATGGACATACAGCTCGTTGAAGCACTGTGTGGCTTCCAGAAGCCAATATCTACTCTTGACAACCGAACCATCGTCATCACCTCTCATCCAGGTCAGATTGTCAAGCATGGAGATATCAAGTGTGTACTAAATGAAGGCATGCCAATTTATCGTAGACCATATGAAAAGGGTCGCCTAATCATCGAATTTAAGGTAAACTTTCCTGAGAATGGCTTTCTCTCTCCTGATAAACTGTCTTTGCTGGAAAAACTCCTACCCGAGAGGAAGGAAGTGGAAGAGACTGATGAGATGGACCAAGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGACGGCGCCACTACAATGGAGAAGCATATGAGGATGATGAACATCATCCCAGAGGTGGTGTTCAGTGTCAGACCTCTTAATGGGCCAGTGAATAACACTCACTGCTGGCATTTAATGTGCAGTAGTGAATGAGTGAAGGACTGTAATCATAATATGCTCACTACTTGCTCTTGTTTTTGTTTTAATAAACTATAGTAGTGTTTTAAAAAGTTAAATGAAGAATAAACGCAAATATAAAAGCTCTGATTTTGCCCTGTATGTATGATGACTTCAGTGTGCAAGATGAAGTTTAATACCTGTAAAAACTACAAAGAAGTTCCCCTAGCATTTCTAGGCCAAACCTTGTAATTGACTTCAGCTATGTACGTGGACAAGCTTAGACTGAAATGCTAGGTATATGTATTGGCTTCAGTGTATGACCCTTCATTGTTAAGCTATGAAAGTAAAACTCTGTATTTAACTGGCAATGAGGAAAAAAAAATTTTGTAGAGAAGTGTTGGTCTGTATAGTTCTTTATATTAAGTGGGATTCATTGTAATGCCTCTGCATTTATTCTGTTGCCTCAGCTGTTACTTGAAGATGGCGTAATATATAATTTATCCTGTGGTATCAGTGATAAAAATGATACCTTTCTGTAGGAGGGGTTTATCATAATATGCTGCTTCTTGAAGGCTTGCACTTCCAGAATTGTGTTTCCTTCTGCTGTGCCATTCatatatatatacatatatatatataATCTTGACCAGTCCTGGTCATTTGCTCCCCTCCTTGTCTGTGGACCATGATAAGCCCAAGTAGTGACTTCAGAGCTGGGTAACAGAAATTAAAGTGAAAAGACCTTTACGTGGAGAATTTGCATGCGTAATATAGGAAGGTGTTCTTTAGGTATGTTACAGGATTACTTTAAACCATTTGACTTTCGCTCCAAAGTTATGTTGGTAGTATAGCAAATTATGATGAATAGCTTTAATTGTATGTTTAAAAGTCTCATATGTTCACATGCTTAAATCTGGGTATCAGAATTTAAGCAATTCTTGAAATGTATTGTCTCCTTAATATACTAATTACAAAGCATCTCCAA

>NM_001539.4 

GCGGAACTTTCCAGAACGCTCGGTGAGAGGCGGAGGAGCGGTAACTACCCCGGCTGCGCACAGCTCGGCGCTCCTTCCCGCTCCCTCACACACCGGCCTCAGCCCGCACCGGCAGTAGAAGATGGTGAAAGAAACAACTTACTACGATGTTTTGGGGGTCAAACCCAATGCTACTCAGGAAGAATTGAAAAAGGCTTATAGGAAACTGGCTTTGAAGTACCATCCTGATAAGAACCCAAATGAAGGAGAGAAGTTTAAACAGATTTCTCAAGCTTACGAAGTTCTCTCTGATGCAAAGAAAAGGGAATTATATGACAAAGGAGGAGAACAGGCAATTAAAGAGGGTGGAGCAGGTGGCGGTTTTGGCTCCCCCATGGACATCTTTGATATGTTTTTTGGAGGAGGAGGAAGGATGCAGAGAGAAAGGAGAGGTAAAAATGTTGTACATCAGCTCTCAGTAACCCTAGAAGACTTATATAATGGTGCAACAAGAAAACTGGCTCTGCAAAAGAATGTGATTTGTGACAAATGTGAAGGTAGAGGAGGTAAGAAAGGAGCAGTAGAGTGCTGTCCCAATTGCCGAGGTACTGGAATGCAAATAAGAATTCATCAGATAGGACCTGGAATGGTTCAGCAAATTCAGTCTGTGTGCATGGAGTGCCAGGGCCATGGGGAGCGGATCAGTCCTAAAGATAGATGTAAAAGCTGCAACGGAAGGAAGATAGTTCGAGAGAAGAAAATTTTAGAAGTTCATATTGACAAAGGCATGAAAGATGGCCAGAAGATAACATTCCATGGTGAAGGAGACCAAGAACCAGGACTGGAGCCAGGCGATATTATCATTGTGTTAGATCAGAAGGACCATGCTGTTTTTACTCGACGAGGAGAAGACCTTTTCATGTGTATGGACATACAGCTCGTTGAAGCACTGTGTGGCTTCCAGAAGCCAATATCTACTCTTGACAACCGAACCATCGTCATCACCTCTCATCCAGGTCAGATTGTCAAGCATGGAGATATCAAGTGTGTACTAAATGAAGGCATGCCAATTTATCGTAGACCATATGAAAAGGGTCGCCTAATCATCGAATTTAAGGTAAACTTTCCTGAGAATGGCTTTCTCTCTCCTGATAAACTGTCTTTGCTGGAAAAACTCCTACCCGAGAGGAAGGAAGTGGAAGAGACTGATGAGATGGACCAAGTAGAACTGGTGGACTTTGATCCAAATCAGGAAAGACGGCGCCACTACAATGGAGAAGCATATGAGGATGATGAACATCATCCCAGAGGTGGTGTTCAGTGTCAGACCTCTTAATGGGCCAGTGAATAACACTCACTGCTGGCATTTAATGTGCAGTAGTGAATGAGTGAAGGACTGTAATCATAATATGCTCACTACTTGCTCTTGTTTTTGTTTTAATAAACTATAGTAGTGTTTTAAAAAGTTAAATGAAGAATAAACGCAAATATAAAAGCTCTGATTTTGCCCTGTATGTATGATGACTTCAGTGTGCAAGATGAAGTTTAATACCTGTAAAAACTACAAAGAAGTTCCCCTAGCATTTCTAGGCCAAACCTTGTAATTGACTTCAGCTATGTACGTGGACAAGCTTAGACTGAAATGCTAGGTATATGTATTGGCTTCAGTGTATGACCCTTCATTGTTAAGCTATGAAAGTAAAACTCTGTATTTAACTGGCAATGAGGAAAAAAAAATTTTGTAGAGAAGTGTTGGTCTGTATAGTTCTTTATATTAAGTGGGATTCATTGTAATGCCTCTGCATTTATTCTGTTGCCTCAGCTGTTACTTGAAGATGGCGTAATATATAATTTATCCTGTGGTATCAGTGATAAAAATGATACCTTTCTGTAGGAGGGGTTTATCATAATATGCTGCTTCTTGAAGGCTTGCACTTCCAGAATTGTGTTTCCTTCTGCTGTGCCATTCatatatatatacatatatatatataATCTTGACCAGTCCTGGTCATTTGCTCCCCTCCTTGTCTGTGGACCATGATAAGCCCAAGTAGTGACTTCAGAGCTGGGTAACAGAAATTAAAGTGAAAAGACCTTTACGTGGAGAATTTGCATGCGTAATATAGGAAGGTGTTCTTTAGGTATGTTACAGGATTACTTTAAACCATTTGACTTTCGCTCCAAAGTTATGTTGGTAGTATAGCAAATTATGATGAATAGCTTTAATTGTATGTTTAAAAGTCTCATATGTTCACATGCTTAAATCTGGGTATCAGAATTTAAGCAATTCTTGAAATGTATTGTCTCCTTAATATACTAATTACAAAGCATCTCCAA

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