RCPedia: Rtcs

Summary

Retrocopy Name	ADH5P4	Plot displaying the genomic locations of a retrocopy (in chr6) and its respective parental gene (in chr4). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr6:65835476-65838056 UCSC
Coordinates (T2T)	chr6:66987810-66990390 UCSC
Coordinates (hg19)	chr6:66545369-66547949 UCSC
Strand	-
Parental Sequence	NM_000671.4
Parental seq. overlap	1592 bp
Parental seq. overlap (%)	58%
Genomic Region	Intergenic
Retrocopy Summary	ADH5P4, located on chr6:65835476-65838056, is a retrocopy of the parental gene ADH5. 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	ADH5
Full Name	alcohol dehydrogenase 5 (class III), chi polypeptide
Also known as	ADH-3\|ADHX\|AMEDS\|BMFS7\|FALDH\|FDH\|GSH-FDH\|GSNOR\|HEL-S-60p
Coordinate	chr4:99070978-99088788
Strand	-
Gene summary	This gene encodes a member of the alcohol dehydrogenase family. Members of this family metabolize a wide variety of substrates, including ethanol, retinol, other aliphatic alcohols, hydroxysteroids, and lipid peroxidation products. The encoded protein forms a homodimer. It has virtually no activity for ethanol oxidation, but exhibits high activity for oxidation of long-chain primary alcohols and for oxidation of S-hydroxymethyl-glutathione, a spontaneous adduct between formaldehyde and glutathione. This enzyme is an important component of cellular metabolism for the elimination of formaldehyde, a potent irritant and sensitizing agent that causes lacrymation, rhinitis, pharyngitis, and contact dermatitis. The human genome contains several non-transcribed pseudogenes related to this gene. [provided by RefSeq, Oct 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	ADH5P4
Bonobo	Pan paniscus	ADH5P4
Orangutan	Pongo abelii	ADH5P4
Gorilla	Gorilla gorilla	Without Homology
Gibbon	Nomascus leucogenys	Without Homology
Green monkey	Chlorocebus sabaeus	Without Homology
Crab-eating macaque	Macaca fascicularis	Without Homology
Rhesus	Macaca mulatta	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)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

Related Sequence

>ADH5P4
TGGGCTCACTACATTAGTTACTTAAGATGTGTATCACAGAATAAACACATTTAGCCTTATAGACATTGCCAAATTTATCTTCAAAGTAAATGTGACAGCATTCTGGACTTAAATAGGTGTATGTGTGTGTTGGTTGTGGCTGTACTATTTCTACATTGCGAACCAGGTTATGAAGTGCAAGGCTGCAGTTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGTGGCACCCCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCGGTTTGCCACACCGACGCCTATACCCTGAGGGGAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCCGGAATTGAGGAAAGTGTTGGCGAGGGAGTTACTAAGCTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTATATCCTAAAACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAGGAAAGACAATTTTGCGTTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTAGCTGATATCTCTGTTGCTAAAATAGATCCTTTAGCACCTTTGGATAAACTCTGCCTTCTAGGTTGTGGCATTTCAGCTGGTGATGGTGCTGCTGTGAACACTGCCAAGGTGGAACCTGGCTCTGTTTGTGCCGTCTTTGGTCTGGGAGGAGTTGGATTGGCAGTTATCAAGGGCTGTAAAGTGGCTGGTGCATCCCGGATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAGTTTGGAGCCACTGAATGTATTAACCCTCAGGGTTTTAGTAAACCCATCCAGGAAGGGCTCATTGAGACGACTGATGGAGGAGTGGACTATTCCTTTGAATGTATTGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCTTATCACAAGGGCTGGGGAGTCAGCGTGGTGGTTGGAGTAGCTGCTTCAGGTGAAGAAATTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGAACTGCCTTTGGAGGATGGAAGAGTGTAGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAAATAAAAGTTGATGAATTTGTGACTCACAATCTGTCTTTTGGTGAAATTAACAAAGCCTTTCAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTAAAGATTTAATTCAAAAGAGAAAAATAATGTCCAACCTGTCGTGATGTGATGGGAGCAGCTTAACAGGCAGGGAGAAGCGCCTCCAAACTCACAGCCTCGTAGAGCTTCGCAGCTACCCCAGAGAATAGTGTTATGAGTGTAATTCATGAATCTCTATAATCAACGACAAGGATAATTCAGTCATGGACCTGTTTTCTGGACGCTCCTCCACATAAATAATTGCTAGCTTATTAAGGAATATTTTAACATAATAAAAGTAATTTCTACATTTGTGTAGAAATTGTCTTTGTTTTATGCTGTAATCATTGTCATGGTTTGTCTGCCCATTATCTTCATTCTGTAAGGGAAATGTAAAGGAAGCAGGGCAGTGGTGGGTGTCTGAAACCTCAGAAACATTCGTTGAAGTTTTAAGGGTCTCAGTCCCGTTGATTGAAGAACAGATCCTAGCCATCAGTGACAAAGTTAATCAGGAGCCAAGTCTGCTTc

>NM_000671.4
CTCGCTAGGCGCTCGCCACGCCCATGCCTCCGTCGCTGCGCGGCCCACCCCGGATGTCAGCCCCCCGCGCCGACCAGAATCCGTGAACATGGCGAACGAGGTTATCAAGTGCAAGGCTGCAGTTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGTGGCACCCCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCGGTTTGCCACACCGATGCCTATACCCTGAGTGGAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGAAAGTGTTGGTGAGGGAGTTACTAAGCTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAAAACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAGGAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGATATCTCTGTTGCTAAAATAGATCCTTTAGCACCTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAACCGGTTATGGTGCTGCTGTGAACACTGCCAAGTTGGAGCCTGGCTCTGTTTGTGCCGTCTTTGGTCTGGGAGGAGTCGGATTGGCAGTTATCATGGGCTGTAAAGTGGCTGGTGCTTCCCGGATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAGTTTGGAGCCACTGAATGTATTAACCCTCAGGATTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGATGACCGATGGAGGAGTGGACTATTCCTTTGAATGTATTGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCATGTCACAAGGGCTGGGGCGTCAGCGTCGTGGTTGGAGTAGCTGCTTCAGGTGAAGAAATTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGGAGGATGGAAGAGTGTAGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATAAAAGTTGATGAATTTGTGACTCACAATCTGTCTTTTGATGAAATCAACAAAGCCTTTGAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTAAAGATTTAATTCAAAAGAGAAAAATAATGTCCATCCTGTCGTGATGTGATAGGAGCAGCTTAACAGGCAGGGAGAAGCGCCTCCAACCTCACAGCCTCGTAGAGCTTCACAGCTACTCCAGAAAATAGGGTTATGTGTGTCATTCATGAATCTCTATAATCAAGGACAAGGATAATTCAGTCATGAACCTGTTTTCTGGATGCTCCTCCACATAAATAATTGCTAGTTTATTAAGGAATATTTTAACATAATAAAAGTAATTTCTACATTTGTGTGGAAATTGTCTTGTTTTATGCTGTCATCATTGTCACGGTTTGTCTGCCCATTATCTTCATTCTGCAAGGGAAAGGGAAAGGAAGCAGGGCAGTGGTGGGTGTCTGAAACCTCAGAAACATAACGTTGAACTTTTAAGGGTCTCAGTCCCCGTTGATTAAAGAACAGATCCTAGCCATCAGTGACAAAGTTAATCAGGACCCAAGTCTGCTTctgtgatattatcttgaagggaggtactgtgccttgttcatacctgtaccccaaattcctaggatggcatctgcccttcagggggcactaaaatgtattattgaaACAGCATTCTGGGCTTAAATAGGTGTATGTATGTGTTGGTTGTGACTGTACTATTTCTagtatagtgaactacatactgaatatccaagttctcagcacctacttttgtcaaatcttaacattttgccacttcgagatcacattgccattcctcccctccagaggtaacaattatccacaatttgatgtttatcattcctgtgttgttgtactttcactgtgtataacctaaaccatctactctttagtactgttttatatatttttaagcctcatacttgctcattctacagcttttttcactcattattgtataattatatctgaagctctcgttcattaattttagtcctgtgtagcagaattcaattacgggaactaccataatttatctgttctccagttgaaggcatgaagttgttgccagtttctgtattataacactgtagtggaacattcttctgcatTGGGCTCACTGCGTGTTACCTAAGACGTAtcacagaataaacacatttagccttatagacattgccaaattgctcttcaaagtaaatgtgagtttttgtgaattacatgagtatggaatggtgttttattatgactttagtttgcattttcctcaattctcgttaaatccttcattctaatggacattttattgtgaagaacctgttcatatcctgtgctcaactttgtattgaattatttttctctgaataatttttaggagttcttttattctagacatcaatcatttgtcagttttatatgttgcaaatatcttctagtctatcttgtgacttttctttttactttatggtattttgttgaataaagttttaatgtagtcacatAAA

>NM_000671.4 

CTCGCTAGGCGCTCGCCACGCCCATGCCTCCGTCGCTGCGCGGCCCACCCCGGATGTCAGCCCCCCGCGCCGACCAGAATCCGTGAACATGGCGAACGAGGTTATCAAGTGCAAGGCTGCAGTTGCTTGGGAGGCTGGAAAGCCTCTCTCCATAGAGGAGATAGAGGTGGCACCCCCAAAGGCTCATGAAGTTCGAATCAAGATCATTGCCACTGCGGTTTGCCACACCGATGCCTATACCCTGAGTGGAGCTGATCCTGAGGGTTGTTTTCCAGTGATCTTGGGACATGAAGGTGCTGGAATTGTGGAAAGTGTTGGTGAGGGAGTTACTAAGCTGAAGGCGGGTGACACTGTCATCCCACTTTACATCCCACAGTGTGGAGAATGCAAATTTTGTCTAAATCCTAAAACTAACCTTTGCCAGAAGATAAGAGTCACTCAAGGGAAAGGATTAATGCCAGATGGTACCAGCAGATTTACTTGCAAAGGAAAGACAATTTTGCATTACATGGGAACCAGCACATTTTCTGAATACACAGTTGTGGCTGATATCTCTGTTGCTAAAATAGATCCTTTAGCACCTTTGGATAAAGTCTGCCTTCTAGGTTGTGGCATTTCAACCGGTTATGGTGCTGCTGTGAACACTGCCAAGTTGGAGCCTGGCTCTGTTTGTGCCGTCTTTGGTCTGGGAGGAGTCGGATTGGCAGTTATCATGGGCTGTAAAGTGGCTGGTGCTTCCCGGATCATTGGTGTGGACATCAATAAAGATAAATTTGCAAGGGCCAAAGAGTTTGGAGCCACTGAATGTATTAACCCTCAGGATTTTAGTAAACCCATCCAGGAAGTGCTCATTGAGATGACCGATGGAGGAGTGGACTATTCCTTTGAATGTATTGGTAATGTGAAGGTCATGAGAGCAGCACTTGAGGCATGTCACAAGGGCTGGGGCGTCAGCGTCGTGGTTGGAGTAGCTGCTTCAGGTGAAGAAATTGCCACTCGTCCATTCCAGCTGGTAACAGGTCGCACATGGAAAGGCACTGCCTTTGGAGGATGGAAGAGTGTAGAAAGTGTCCCAAAGTTGGTGTCTGAATATATGTCCAAAAAGATAAAAGTTGATGAATTTGTGACTCACAATCTGTCTTTTGATGAAATCAACAAAGCCTTTGAACTGATGCATTCTGGAAAGAGCATTCGAACTGTTGTAAAGATTTAATTCAAAAGAGAAAAATAATGTCCATCCTGTCGTGATGTGATAGGAGCAGCTTAACAGGCAGGGAGAAGCGCCTCCAACCTCACAGCCTCGTAGAGCTTCACAGCTACTCCAGAAAATAGGGTTATGTGTGTCATTCATGAATCTCTATAATCAAGGACAAGGATAATTCAGTCATGAACCTGTTTTCTGGATGCTCCTCCACATAAATAATTGCTAGTTTATTAAGGAATATTTTAACATAATAAAAGTAATTTCTACATTTGTGTGGAAATTGTCTTGTTTTATGCTGTCATCATTGTCACGGTTTGTCTGCCCATTATCTTCATTCTGCAAGGGAAAGGGAAAGGAAGCAGGGCAGTGGTGGGTGTCTGAAACCTCAGAAACATAACGTTGAACTTTTAAGGGTCTCAGTCCCCGTTGATTAAAGAACAGATCCTAGCCATCAGTGACAAAGTTAATCAGGACCCAAGTCTGCTTctgtgatattatcttgaagggaggtactgtgccttgttcatacctgtaccccaaattcctaggatggcatctgcccttcagggggcactaaaatgtattattgaaACAGCATTCTGGGCTTAAATAGGTGTATGTATGTGTTGGTTGTGACTGTACTATTTCTagtatagtgaactacatactgaatatccaagttctcagcacctacttttgtcaaatcttaacattttgccacttcgagatcacattgccattcctcccctccagaggtaacaattatccacaatttgatgtttatcattcctgtgttgttgtactttcactgtgtataacctaaaccatctactctttagtactgttttatatatttttaagcctcatacttgctcattctacagcttttttcactcattattgtataattatatctgaagctctcgttcattaattttagtcctgtgtagcagaattcaattacgggaactaccataatttatctgttctccagttgaaggcatgaagttgttgccagtttctgtattataacactgtagtggaacattcttctgcatTGGGCTCACTGCGTGTTACCTAAGACGTAtcacagaataaacacatttagccttatagacattgccaaattgctcttcaaagtaaatgtgagtttttgtgaattacatgagtatggaatggtgttttattatgactttagtttgcattttcctcaattctcgttaaatccttcattctaatggacattttattgtgaagaacctgttcatatcctgtgctcaactttgtattgaattatttttctctgaataatttttaggagttcttttattctagacatcaatcatttgtcagttttatatgttgcaaatatcttctagtctatcttgtgacttttctttttactttatggtattttgttgaataaagttttaatgtagtcacatAAA

Publications

PMID - Link	Title
No publications available for this retrocopy

Summary

Parental Gene

Homology

Expression

The Genotype-Tissue Expression project - (GTEx)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

log10(TPM+1) <=> TPM

Related Sequence

Publications