RCPedia: Rtcs

Summary

Retrocopy Name	DPPA4P5	Plot displaying the genomic locations of a retrocopy (in chr13) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr13:31223765-31223925 UCSC
Coordinates (T2T)	chr13:30446775-30446935 UCSC
Coordinates (hg19)	chr13:31797902-31798062 UCSC
Strand	+
Parental Sequence	NM_001348928.2
Parental seq. overlap	138 bp
Parental seq. overlap (%)	5.1%
Genomic Region	Intragenic (B3GLCT)
Retrocopy Summary	DPPA4P5, located on chr13:31223765-31223925, is a retrocopy of the parental gene DPPA4. 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	DPPA4
Full Name	developmental pluripotency associated 4
Also known as	2410091M23Rik
Coordinate	chr3:109326141-109339635
Strand	-
Gene summary	This gene encodes a nuclear factor that is involved in the maintenance of pluripotency in stem cells and essential for embryogenesis. The encoded protein has a scaffold-attachment factor A/B, acinus and PIAS (SAP) domain that binds DNA and is thought to modify chromatin. Mice with a homozygous knockout of the orthologous gene die during late embryonic development or within hours after birth. Knockout embryos are normal in size at embryonic day 18.5 but exhibit skeletal and lung tissue abnormalities. This gene, when mutated, is highly expressed in embryonal carcinomas, pluripotent germ cell tumors, and other cancers and is thought to play an important role in tumor progression. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

Homology

Species	Scientific Name	Retrocopy
Orangutan	Pongo abelii	DPPA4P5
Crab-eating macaque	Macaca fascicularis	DPPA4P7
Rhesus	Macaca mulatta	DPPA4P6
Golden snub-nosed monkey	Rhinopithecus roxellana	DPPA4P10
Chimpanzee	Pan troglodytes	Without Homology
Bonobo	Pan paniscus	Without Homology
Gorilla	Gorilla gorilla	Without Homology
Gibbon	Nomascus leucogenys	Without Homology
Green monkey	Chlorocebus sabaeus	Without Homology
Baboon	Papio anubis	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

>DPPA4P5
ATCAGCCAGGACCTGGACACCAGTAGCAGTGGAACCTCACAGGAAGCCTATGGTGTCAGGGGGTATGCGGTCCATGGGAGAAGTCTCCCTTCAGACACAGGGGGTTGGCTCACCTCCAGTTTCATGATGGATAAGCCTGGGTTCCAGGAAACAAGAAGGGA

>NM_001348928.2
ATGTTGCGAGGCTCCGCTTCTTCTACAAGTATGGAGAAGGCAAAAGGCAAGGAGGAACATCAGCAAAGAGAACCAAAGAAAAAATGTCTATCAAAGGCAGTAAAGTGCTCTGCCCTAAGAAAAAGGCAGAGCACACTGACAACCCCAGACCTCAGAAGAAGATACCAATCCCTCCATTACCTTCTAAACTGCCACCTGTTAATCTGATTCACCGGGACATTCTGCGGGCCTGGTGCCAACAATTGAAGCTGAGCTCCAAAGGCCAGAAATTGGATGCATATAAGCGCCTGTGTGCCTTTGCCTACCCAAATCAAAAGGATTTTCCTAGCACAGCAAAAGAGGCCAAAATCCGGAAATCATTGCAAAAAAAATTAAAGGTGGAAAAGGGGGAAACGTCCCTGCAAAGTTCTGAGACACATCCTCCTGAAGTGGCTCTTCCTCCTGTGGGGGAGCCGCCTGCCCTGGAAAATTCCACTGCTCTCCTTGAGGGAGTTAATACAGTTGTGGTGACAACTTCTGCCCCAGAGGCTTTGCTGGCCTCCTGGGCGAGAATTTCAGCCAGGGCGAGGACACCAGAGGCAGTGGAATCTCCACAAGAGGCCTCTGGTGTCAGGTGGTGTGTGGTCCATGGGAAAAGTCTCCCTGCAGACACAGATGGTTGGGTTCACCTGCAGTTTCATGCTGGTCAAGCCTGGGTTCCAGAAAAGCAAGAAGGGAGAGTGAGTGCACTCTTCTTGCTTCCTGCCTCCAATTTTCCACCCCCGCACCTTGAAGACAATATGTTGTGCCCCAAATGTGTTCACAGGAACAAGGTCTTAATAAAAAGCCTCCAATGGGAATAGAATATCAGGAAAAAGGCCACATCTATGGTAATTAATGGCAGAAAAGCTGGAGAGTTGGATTCTGCGGTGCTGCTGACAGGTGAACTCTGGTCCTCTGCACCTGTTTATGGGCCATGCAGACTGGTGGGGTGGCAGATGTTAGCCTAAGACCCCTAGCAGTGCCTGTTGCTTTGTGAGTGGAGATAGAGACTCTTACATTTAAAAATGGAAAAACATTTCACAAATTACCATAAATTGTAGTTAATATGTAGAAAAACTCATTCATACTACTTTTCTAAAATAGACATGACTTCAGCAGCAGCttttttttgttgtattttgagacagtgtctcactgttgcccaggctggagtgcagtggtgcaatctcagttcagtgcaatctccgcctcctgggttcaaatgattctcctgcctcagcctcctgagtagctaggtacaggcacctgccaccacacccagctaattttttgtatttttagtagagatggggtttcaccatgttggccaggttggtctcaaactcctggactcaagtgatcaccctcctcagcctcccaaaatgctgggactatgggcatgagcccctgcgcctgaccTTCAACAGCTCTTTTAAGTGAGTTCTTCAGCTAAGCATTGTGATGGACTTGAGTAAAATGGTAGTTGGCTCTTGTGCTCAATTTTCTCTTCCTCTGAACACTGACTACTTTAGGAGCTGCTTCATTCCAATTGCAATTTCATAAAACGTAAAGTATTTTAAGGCAAAGAAAGGCTGTTAATTCCCTCCCTCCCCCAAACACATGATTTTTAATATTCTAAACAATATTTTTCAAAGTTCTCTTAATAACCTGAGATTTCTATGGTTTGACTCCAGGATCAAAACACAAGGGACTTTGTATTATTTCACTTATAATTGTTTTGTATATTTCTGGAGTTTAAAATGTTTAAGGTTGCTTCCCGCTCATAAATACATAATATATTGAATTTAAAATGTGTTTATTAACCGATTCTCCATAAATAAAAATAAGATGTGTATGTAAAATAATTCATCTGTTGTATTTAGAGAACCATATTCATTGCATGCAAATTTTATTGTTAGTGTTCTTAACTCAAGTAGGAGTAAACCAAAAAGTGTGATTTTTCTTTTGTATGACTCGTTTGTTCTTTATTAGTTGGTGGTATGGGTTGGATCATTTGtttttaaaactacttaggtatgattcacatacaaaaagctgcacatatttaatgtatcctattGTGTAATTAATTTTTAATTTTTTTGTGTACTTCCTAAACTTATAGTCCTGCGAGTCTGGGAACAGATCTGTTTTTCACTTATCCTGATTTAATGACAGTTTCCAACATTGTTTTGTTATTACAAGTAGGGGATCTTTTTTTTTGCCCGTTTAATGAAGATACTAAAAATAATGCACtggaaggagtggaagagttggaaaatttgtaaccatcataatacaggtgtaataggtttgggaaagaatcctcaaaaatgttaaagcaagggaggaaagtttgttgagaagcaagatgttCTTCTCTCCTGCCCGCCCCCGCCGTTGGTTGTTGGTGGTCAGAATTATTGTGTAATAAATAATAGAcattttttcttatactatgtgtattgttccttttgtttcctttttaaacttctcccctgctttatttggatgggtcaagtttctgttctgtttccttcctttctattaatttggaaatgtccttggctttacgattctgcttgtagatacttcccctgcttctaacacatttcaataaacttaaatttctctatatacaaaataaattaataattggagtcta

>NM_001348928.2 

ATGTTGCGAGGCTCCGCTTCTTCTACAAGTATGGAGAAGGCAAAAGGCAAGGAGGAACATCAGCAAAGAGAACCAAAGAAAAAATGTCTATCAAAGGCAGTAAAGTGCTCTGCCCTAAGAAAAAGGCAGAGCACACTGACAACCCCAGACCTCAGAAGAAGATACCAATCCCTCCATTACCTTCTAAACTGCCACCTGTTAATCTGATTCACCGGGACATTCTGCGGGCCTGGTGCCAACAATTGAAGCTGAGCTCCAAAGGCCAGAAATTGGATGCATATAAGCGCCTGTGTGCCTTTGCCTACCCAAATCAAAAGGATTTTCCTAGCACAGCAAAAGAGGCCAAAATCCGGAAATCATTGCAAAAAAAATTAAAGGTGGAAAAGGGGGAAACGTCCCTGCAAAGTTCTGAGACACATCCTCCTGAAGTGGCTCTTCCTCCTGTGGGGGAGCCGCCTGCCCTGGAAAATTCCACTGCTCTCCTTGAGGGAGTTAATACAGTTGTGGTGACAACTTCTGCCCCAGAGGCTTTGCTGGCCTCCTGGGCGAGAATTTCAGCCAGGGCGAGGACACCAGAGGCAGTGGAATCTCCACAAGAGGCCTCTGGTGTCAGGTGGTGTGTGGTCCATGGGAAAAGTCTCCCTGCAGACACAGATGGTTGGGTTCACCTGCAGTTTCATGCTGGTCAAGCCTGGGTTCCAGAAAAGCAAGAAGGGAGAGTGAGTGCACTCTTCTTGCTTCCTGCCTCCAATTTTCCACCCCCGCACCTTGAAGACAATATGTTGTGCCCCAAATGTGTTCACAGGAACAAGGTCTTAATAAAAAGCCTCCAATGGGAATAGAATATCAGGAAAAAGGCCACATCTATGGTAATTAATGGCAGAAAAGCTGGAGAGTTGGATTCTGCGGTGCTGCTGACAGGTGAACTCTGGTCCTCTGCACCTGTTTATGGGCCATGCAGACTGGTGGGGTGGCAGATGTTAGCCTAAGACCCCTAGCAGTGCCTGTTGCTTTGTGAGTGGAGATAGAGACTCTTACATTTAAAAATGGAAAAACATTTCACAAATTACCATAAATTGTAGTTAATATGTAGAAAAACTCATTCATACTACTTTTCTAAAATAGACATGACTTCAGCAGCAGCttttttttgttgtattttgagacagtgtctcactgttgcccaggctggagtgcagtggtgcaatctcagttcagtgcaatctccgcctcctgggttcaaatgattctcctgcctcagcctcctgagtagctaggtacaggcacctgccaccacacccagctaattttttgtatttttagtagagatggggtttcaccatgttggccaggttggtctcaaactcctggactcaagtgatcaccctcctcagcctcccaaaatgctgggactatgggcatgagcccctgcgcctgaccTTCAACAGCTCTTTTAAGTGAGTTCTTCAGCTAAGCATTGTGATGGACTTGAGTAAAATGGTAGTTGGCTCTTGTGCTCAATTTTCTCTTCCTCTGAACACTGACTACTTTAGGAGCTGCTTCATTCCAATTGCAATTTCATAAAACGTAAAGTATTTTAAGGCAAAGAAAGGCTGTTAATTCCCTCCCTCCCCCAAACACATGATTTTTAATATTCTAAACAATATTTTTCAAAGTTCTCTTAATAACCTGAGATTTCTATGGTTTGACTCCAGGATCAAAACACAAGGGACTTTGTATTATTTCACTTATAATTGTTTTGTATATTTCTGGAGTTTAAAATGTTTAAGGTTGCTTCCCGCTCATAAATACATAATATATTGAATTTAAAATGTGTTTATTAACCGATTCTCCATAAATAAAAATAAGATGTGTATGTAAAATAATTCATCTGTTGTATTTAGAGAACCATATTCATTGCATGCAAATTTTATTGTTAGTGTTCTTAACTCAAGTAGGAGTAAACCAAAAAGTGTGATTTTTCTTTTGTATGACTCGTTTGTTCTTTATTAGTTGGTGGTATGGGTTGGATCATTTGtttttaaaactacttaggtatgattcacatacaaaaagctgcacatatttaatgtatcctattGTGTAATTAATTTTTAATTTTTTTGTGTACTTCCTAAACTTATAGTCCTGCGAGTCTGGGAACAGATCTGTTTTTCACTTATCCTGATTTAATGACAGTTTCCAACATTGTTTTGTTATTACAAGTAGGGGATCTTTTTTTTTGCCCGTTTAATGAAGATACTAAAAATAATGCACtggaaggagtggaagagttggaaaatttgtaaccatcataatacaggtgtaataggtttgggaaagaatcctcaaaaatgttaaagcaagggaggaaagtttgttgagaagcaagatgttCTTCTCTCCTGCCCGCCCCCGCCGTTGGTTGTTGGTGGTCAGAATTATTGTGTAATAAATAATAGAcattttttcttatactatgtgtattgttccttttgtttcctttttaaacttctcccctgctttatttggatgggtcaagtttctgttctgtttccttcctttctattaatttggaaatgtccttggctttacgattctgcttgtagatacttcccctgcttctaacacatttcaataaacttaaatttctctatatacaaaataaattaataattggagtcta

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