RCPedia: Rtcs

Summary

Retrocopy Name	IDH1P1	Plot displaying the genomic locations of a retrocopy (in chr6) and its respective parental gene (in chr2). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr6:7515988-7518374 UCSC
Coordinates (hg19)	chr6:7516221-7518607 UCSC
Strand	-
Parental Sequence	NM_005896.4
Parental seq. overlap	1847 bp
Parental seq. overlap (%)	76.7%
Genomic Region	Intergenic
Retrocopy Summary	IDH1P1, located on chr6:7515988-7518374, is a retrocopy of the parental gene IDH1. 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	IDH1
Full Name	isocitrate dehydrogenase (NADP(+)) 1
Also known as	HEL-216\|HEL-S-26\|IDCD\|IDH\|IDP\|IDPC\|PICD
Coordinate	chr2:208236227-208255071
Strand	-
Gene summary	Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. Each NADP(+)-dependent isozyme is a homodimer. The protein encoded by this gene is the NADP(+)-dependent isocitrate dehydrogenase found in the cytoplasm and peroxisomes. It contains the PTS-1 peroxisomal targeting signal sequence. The presence of this enzyme in peroxisomes suggests roles in the regeneration of NADPH for intraperoxisomal reductions, such as the conversion of 2, 4-dienoyl-CoAs to 3-enoyl-CoAs, as well as in peroxisomal reactions that consume 2-oxoglutarate, namely the alpha-hydroxylation of phytanic acid. The cytoplasmic enzyme serves a significant role in cytoplasmic NADPH production. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	IDH1P1
Bonobo	Pan paniscus	IDH1P1
Gorilla	Gorilla gorilla	IDH1P1
Orangutan	Pongo abelii	IDH1P1
Gibbon	Nomascus leucogenys	IDH1P2
Green monkey	Chlorocebus sabaeus	IDH1P1
Rhesus	Macaca mulatta	IDH1P1
Golden snub-nosed monkey	Rhinopithecus roxellana	IDH1P1
Marmoset	Callithrix jacchus	IDH1P2
Crab-eating macaque	Macaca fascicularis	Without Homology
Baboon	Papio anubis	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)

Related Sequence

>IDH1P1
TTGATTCACTTTCAAGGTTTATTAAACTCAAAATGTCTAAAAAAATCAGTGGCGGTTCTGTGGTAGAGATGCAAGGAGATGAAATGACACAAATCATTTGGGAATTGAATAAAGAGAAACTCATTTTTCCCTATGTGGAACTGGATGTACATAGCTATGATTTAGGCATAGAGTACTGTGATGCCACCAACGACCAGGTCACCAAGGATGCTGCAGAAGCTATAAAGAAGTATAACGTTGGTGTCAAGTGTGCCACTATCACTGCTGATGAGAAAAGGGTTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCGCCAAATGGCACCATCCAAAATATTCTGGTTGGCACGGTCCTCAGAGAAGCCATTATCTGCAAAAATATCCCCCAGCTTGTGAGTGGATGGGTAAAATCCATCATCGTAGGTCGCATTGCTTATGGGGATCAATACAGAGCAGCTGATTTTGTTGTTCCTGGGCCTGGAAAAGTAGAGATAACCTACACACTAAGTGACAGAACCCAAAAGGTGACATACCTGGTACATAACTTGGAAGAGGGTGGTGGTGTTGCCATAGGGATGTATAATCAAGATAAGTCAATCGAAGATTTTGCACACAGTTCCTTCCAAATGGCTCTAAGGATTGGCCTTTGTAGCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGACGTTTTAAAGACATCTTTCAGGAGATATATGACAAGCAGTACAAGTCCCAGTTTGAAGCCCAAAAGATCTGGTATGAGCATAGGCTCGCTGATGACATGGTGGCCCAAGCTATGAAATCAGAAGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACATGCAGTCAGACTCTGTGGCCCAAGGGTATGGCTCTCTTGGCATGATGACCAGCATGCTAGTGTGTCCACATGGCAAGACAGTAGAAGCAGAGGCTGCCCACTGGACTGTAACCCGTCACTTCTGCATGTACCAGAAAGGCCAGGAGATATCCACCAATCCCATTGCTTCCATTTTTGCCTGGACCAGAGGGTTGGCCCTCCGAGCAAAGACTGATAACAATAAAGAGCTTGCCTTTTTTGCAAATGCTTTGGAAGAAGTCTGTATTGAGACAATTGAGGCTGGTTTCATGACCAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAGTGCGCAATGTTCTGACTACTTGAATACTTTTGAGTTCATGGACAAACTTGGAGAAAACTTGAAGATCAAACTGGCTCAGGCCAAACTTTACGTTCATACCTGGGCTGAGGAGGATAAGTGTCTTTTGATAACTAGGTCTACAGGTTTTCATTTTTCTGTGTCACACTCAAGGATAAAGGCAAAATCGATTGTGTAATTTGTTTAGAAGCTAGAGTTTATCTTTATTGTAAGTTTATAGACATATATATATATACAGTTATTGCCACCGTTGTGAATATGGGAAGGGACTTTAAATTTTATTTTCTGGTAGCAGCCTAGGAATTCGGTTAGTACTCATTTGTATTCACTGTCACTGTTTCTCATGTTCTAATATAAATGACCAAAATCAAGAGTGCTCAAAGGGTAAGTGATAGCCACAGTATTGTTCCCTAAAATATGCATAAAGTAGAAATTCACTCCCTTCTTCTCCTGTGCATGACCTTGGGCACGGGAAGGTTTTGTTGTTAAAGATGTCCCATTACGTGATGTAGAGTTGTACGTTAAACTCGCACGTGACTGGGGCAAACTATGAGTGCAACTCAAACGCGTTGAAGACACTGCAGTCATTTTTGTAAAGAGCTTGCTGAATGTTTCCAATAGACTAAATAGCTTTTAGGCCACAGGAAAGTTTGGAATCTGGGATAAATACTACCTGGAGGTTTGGGGGTTTCTGCAGAGGCTGTGTCAGAAGCCAAGGCAGCGGGAGTCCGGTTTTGGATTGCCAGCCTGTGTGTGTGAGTCTGAGCATGTGAGCAGCTGTAGCGCCCCAGCTCCCCATCAGCATATCATCCCGGCAGGAGATAAACTACGTTCAGTTAAGTCTGAAAGACTGGAAGGAATTGGGGTGATAAGAAATTGATGCACTGTTg

>NM_005896.4
GGGTTTCTGCAGAGTCTACTTCAGAAGCGGAGGCACTGGGAGTCCGGTTTGGGATTGCCAGGCTGTGGTTGTGAGTCTGAGCTTGTGAGCGGCTGTGGCGCCCCAACTCTTCGCCAGCATATCATCCCGGCAGGCGATAAACTACATTCAGTTGAGTCTGCAAGACTGGGAGGAACTGGGGTGATAAGAAATCTATTCACTGTCAAGGTTTATTGAAGTCAAAATGTCCAAAAAAATCAGTGGCGGTTCTGTGGTAGAGATGCAAGGAGATGAAATGACACGAATCATTTGGGAATTGATTAAAGAGAAACTCATTTTTCCCTACGTGGAATTGGATCTACATAGCTATGATTTAGGCATAGAGAATCGTGATGCCACCAACGACCAAGTCACCAAGGATGCTGCAGAAGCTATAAAGAAGCATAATGTTGGCGTCAAATGTGCCACTATCACTCCTGATGAGAAGAGGGTTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCACCAAATGGCACCATACGAAATATTCTGGGTGGCACGGTCTTCAGAGAAGCCATTATCTGCAAAAATATCCCCCGGCTTGTGAGTGGATGGGTAAAACCTATCATCATAGGTCGTCATGCTTATGGGGATCAATACAGAGCAACTGATTTTGTTGTTCCTGGGCCTGGAAAAGTAGAGATAACCTACACACCAAGTGACGGAACCCAAAAGGTGACATACCTGGTACATAACTTTGAAGAAGGTGGTGGTGTTGCCATGGGGATGTATAATCAAGATAAGTCAATTGAAGATTTTGCACACAGTTCCTTCCAAATGGCTCTGTCTAAGGGTTGGCCTTTGTATCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGGCGTTTTAAAGACATCTTTCAGGAGATATATGACAAGCAGTACAAGTCCCAGTTTGAAGCTCAAAAGATCTGGTATGAGCATAGGCTCATCGACGACATGGTGGCCCAAGCTATGAAATCAGAGGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACGTGCAGTCGGACTCTGTGGCCCAAGGGTATGGCTCTCTCGGCATGATGACCAGCGTGCTGGTTTGTCCAGATGGCAAGACAGTAGAAGCAGAGGCTGCCCACGGGACTGTAACCCGTCACTACCGCATGTACCAGAAAGGACAGGAGACGTCCACCAATCCCATTGCTTCCATTTTTGCCTGGACCAGAGGGTTAGCCCACAGAGCAAAGCTTGATAACAATAAAGAGCTTGCCTTCTTTGCAAATGCTTTGGAAGAAGTCTCTATTGAGACAATTGAGGCTGGCTTCATGACCAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAATGTGCAACGTTCTGACTACTTGAATACATTTGAGTTCATGGATAAACTTGGAGAAAACTTGAAGATCAAACTAGCTCAGGCCAAACTTTAAGTTCATACCTGAGCTAAGAAGGATAATTGTCTTTTGGTAACTAGGTCTACAGGTTTACATTTTTCTGTGTTACACTCAAGGATAAAGGCAAAATCAATTTTGTAATTTGTTTAGAAGCCAGAGTTTATCTTTTCTATAAGTTTACAGCCTTTTTCTTATATATACAGTTATTGCCACCTTTGTGAACATGGCAAGGGACTTTTTTACAATTTTTATTTTATTTTCTAGTACCAGCCTAGGAATTCGGTTAGTACTCATTTGTATTCACTGTCACTTTTTCTCATGTTCTAATTATAAATGACCAAAATCAAGATTGCTCAAAAGGGTAAATGATAGCCACAGTATTGCTCCCTAAAATATGCATAAAGTAGAAATTCACTGCCTTCCCCTCCTGTCCATGACCTTGGGCACAGGGAAGTTCTGGTGTCATAGATATCCCGTTTTGTGAGGTAGAGCTGTGCATTAAACTTGCACATGACTGGAACGAAGTAGGAGTGCAACTCAAATGTGTTGAAGATACTGCAGTCATTTTTGTAAAGACCTTGCTGAATGTTTCCAATAGACTAAATACTGTTTAGGCCGCAGGAGAGTTTGGAATCCGGAATAAATACTACCTGGAGGTTTGTCCTCTCCATTTTTCTCTTTCTCCTCCTGGCCTGGCCTGAATATTATACTACTCTAAATAGCATATTTCATCCAAGTGCAATAATGTAAGCTGAATCTTTTTTGGACTTCTGCTGGCCTGTTTTATTTCTTTTATATAAATGTGATTTCTCAGAAATTGATATTAAACACTATCTTATCTTCTCCTGAACTGTTGATTTTAATTAAAATTAAGTGCTAATTACCA

>NM_005896.4 

GGGTTTCTGCAGAGTCTACTTCAGAAGCGGAGGCACTGGGAGTCCGGTTTGGGATTGCCAGGCTGTGGTTGTGAGTCTGAGCTTGTGAGCGGCTGTGGCGCCCCAACTCTTCGCCAGCATATCATCCCGGCAGGCGATAAACTACATTCAGTTGAGTCTGCAAGACTGGGAGGAACTGGGGTGATAAGAAATCTATTCACTGTCAAGGTTTATTGAAGTCAAAATGTCCAAAAAAATCAGTGGCGGTTCTGTGGTAGAGATGCAAGGAGATGAAATGACACGAATCATTTGGGAATTGATTAAAGAGAAACTCATTTTTCCCTACGTGGAATTGGATCTACATAGCTATGATTTAGGCATAGAGAATCGTGATGCCACCAACGACCAAGTCACCAAGGATGCTGCAGAAGCTATAAAGAAGCATAATGTTGGCGTCAAATGTGCCACTATCACTCCTGATGAGAAGAGGGTTGAGGAGTTCAAGTTGAAACAAATGTGGAAATCACCAAATGGCACCATACGAAATATTCTGGGTGGCACGGTCTTCAGAGAAGCCATTATCTGCAAAAATATCCCCCGGCTTGTGAGTGGATGGGTAAAACCTATCATCATAGGTCGTCATGCTTATGGGGATCAATACAGAGCAACTGATTTTGTTGTTCCTGGGCCTGGAAAAGTAGAGATAACCTACACACCAAGTGACGGAACCCAAAAGGTGACATACCTGGTACATAACTTTGAAGAAGGTGGTGGTGTTGCCATGGGGATGTATAATCAAGATAAGTCAATTGAAGATTTTGCACACAGTTCCTTCCAAATGGCTCTGTCTAAGGGTTGGCCTTTGTATCTGAGCACCAAAAACACTATTCTGAAGAAATATGATGGGCGTTTTAAAGACATCTTTCAGGAGATATATGACAAGCAGTACAAGTCCCAGTTTGAAGCTCAAAAGATCTGGTATGAGCATAGGCTCATCGACGACATGGTGGCCCAAGCTATGAAATCAGAGGGAGGCTTCATCTGGGCCTGTAAAAACTATGATGGTGACGTGCAGTCGGACTCTGTGGCCCAAGGGTATGGCTCTCTCGGCATGATGACCAGCGTGCTGGTTTGTCCAGATGGCAAGACAGTAGAAGCAGAGGCTGCCCACGGGACTGTAACCCGTCACTACCGCATGTACCAGAAAGGACAGGAGACGTCCACCAATCCCATTGCTTCCATTTTTGCCTGGACCAGAGGGTTAGCCCACAGAGCAAAGCTTGATAACAATAAAGAGCTTGCCTTCTTTGCAAATGCTTTGGAAGAAGTCTCTATTGAGACAATTGAGGCTGGCTTCATGACCAAGGACTTGGCTGCTTGCATTAAAGGTTTACCCAATGTGCAACGTTCTGACTACTTGAATACATTTGAGTTCATGGATAAACTTGGAGAAAACTTGAAGATCAAACTAGCTCAGGCCAAACTTTAAGTTCATACCTGAGCTAAGAAGGATAATTGTCTTTTGGTAACTAGGTCTACAGGTTTACATTTTTCTGTGTTACACTCAAGGATAAAGGCAAAATCAATTTTGTAATTTGTTTAGAAGCCAGAGTTTATCTTTTCTATAAGTTTACAGCCTTTTTCTTATATATACAGTTATTGCCACCTTTGTGAACATGGCAAGGGACTTTTTTACAATTTTTATTTTATTTTCTAGTACCAGCCTAGGAATTCGGTTAGTACTCATTTGTATTCACTGTCACTTTTTCTCATGTTCTAATTATAAATGACCAAAATCAAGATTGCTCAAAAGGGTAAATGATAGCCACAGTATTGCTCCCTAAAATATGCATAAAGTAGAAATTCACTGCCTTCCCCTCCTGTCCATGACCTTGGGCACAGGGAAGTTCTGGTGTCATAGATATCCCGTTTTGTGAGGTAGAGCTGTGCATTAAACTTGCACATGACTGGAACGAAGTAGGAGTGCAACTCAAATGTGTTGAAGATACTGCAGTCATTTTTGTAAAGACCTTGCTGAATGTTTCCAATAGACTAAATACTGTTTAGGCCGCAGGAGAGTTTGGAATCCGGAATAAATACTACCTGGAGGTTTGTCCTCTCCATTTTTCTCTTTCTCCTCCTGGCCTGGCCTGAATATTATACTACTCTAAATAGCATATTTCATCCAAGTGCAATAATGTAAGCTGAATCTTTTTTGGACTTCTGCTGGCCTGTTTTATTTCTTTTATATAAATGTGATTTCTCAGAAATTGATATTAAACACTATCTTATCTTCTCCTGAACTGTTGATTTTAATTAAAATTAAGTGCTAATTACCA

Publications

PMID - Link	Title
No publications available for this retrocopy