RCPedia: Rtcs

Summary

Retrocopy Name	HDAC1P1	Plot displaying the genomic locations of a retrocopy (in chr10) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr10:94138295-94139540 UCSC
Coordinates (T2T)	chr10:95017410-95018655 UCSC
Coordinates (hg19)	chr10:95898052-95899297 UCSC
Strand	+
Parental Sequence	NM_004964.3
Parental seq. overlap	809 bp
Parental seq. overlap (%)	38%
Genomic Region	Intragenic (PLCE1)
Retrocopy Summary	HDAC1P1, located on chr10:94138295-94139540, is a retrocopy of the parental gene HDAC1. 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	HDAC1
Full Name	histone deacetylase 1
Also known as	GON-10\|HD1\|KDAC1\|RPD3\|RPD3L1
Coordinate	chr1:32292083-32333628
Strand	+
Gene summary	Histone acetylation and deacetylation, catalyzed by multisubunit complexes, play a key role in the regulation of eukaryotic gene expression. The protein encoded by this gene belongs to the histone deacetylase/acuc/apha family and is a component of the histone deacetylase complex. It also interacts with retinoblastoma tumor-suppressor protein and this complex is a key element in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2, it deacetylates p53 and modulates its effect on cell growth and apoptosis. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	HDAC1P3
Bonobo	Pan paniscus	HDAC1P3
Gorilla	Gorilla gorilla	HDAC1P3
Orangutan	Pongo abelii	HDAC1P3
Gibbon	Nomascus leucogenys	HDAC1P1
Green monkey	Chlorocebus sabaeus	LOC103239354P2
Crab-eating macaque	Macaca fascicularis	HDAC1P2
Rhesus	Macaca mulatta	HDAC1P2
Baboon	Papio anubis	HDAC1P4
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)

Related Sequence

>HDAC1P1
CGGTGATGGCATGGAAGAGGCCTTCTATGCCACAGACTGGGTCATGACTGTGTCCTTTCATAAATGAGGAGAGTACTTCCCAGGAACTGGGGACCTATGGGATATTGGGGCTGGAAAAGGCAAGTATTATGCTATTAACCACCCACTCTGAGATGGGATTGATAATGAATCCTGTGAGGCCATTTTCAAGCCAGATATGTCCGTAGTAATGGAGATGTTCCAGCCTAGTGCTGTGGTCATACAGTGTGACTCAGACTCCATCTGGGGATCAGTTAGGTTGCTTCAATCTGAACATCAAAGGGCATGTCAAGTGTGTGGAATTTGTTATGAGCTTCATCTTGCTGATGCTGATGCTAGGAGGAGGTGTTACATCATTCGCAATGTCACCTGCTGCTGGACATAGGAAACAGCTGTGGCCCTGGACACAGAGATCCATAATGAGCTCCCATATAATGACTACTTCAAATACTTTGGACCAGATTTCAAGCTTCATATCAGTCTTTCCAATATAACTAACCAGATCACTAATGATGCCTGGAAAAGATCAAACAGCAACTGTCTGGGAACCTGAGAATGCTGCCCCACACACCTAGGGCCCAAATGTGGGCTCTTGCTGAGGATGTAACCTAGAGGAGAGTGACAACAAGGACGAAGACCCTGACAAGTGCATCTCCATCTGTTCCTCTGACAAACAAACTGCCTGTGAaTTGCCTGTGAGGATGAATTCTCCGACTCTGATGAAGAGGGAAAGGGTGGCTGCAAGAATTCTTCCAACTTCAAAAAAGCCAAGTGGGTCTAAACAGGATGAAAGAGAGAAAGACCCAGAAGAGAAGAAGTCACAGCAGAGAAGACCAAGGAGAAGCCAGAGGCCAAAGGGGTCCAGAAGGAGGTCAAGTTGGCTGAGCAGGCCTTTCCAGCTCTGGCTTCTTGCTGGGTCCC

>NM_004964.3
CCCCTCCCCCCTGGGTCGGACGCTGAGCGGAGCCGCGGGCGGGAGGGCGGACGGACCGACTGACGGTAGGGACGGGAGGCGAGCAAGATGGCGCAGACGCAGGGCACCCGGAGGAAAGTCTGTTACTACTACGACGGGGATGTTGGAAATTACTATTATGGACAAGGCCACCCAATGAAGCCTCACCGAATCCGCATGACTCATAATTTGCTGCTCAACTATGGTCTCTACCGAAAAATGGAAATCTATCGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCCATCCGTCCAGATAACATGTCGGAGTACAGCAAGCAGATGCAGAGATTCAACGTTGGTGAGGACTGTCCAGTATTCGATGGCCTGTTTGAGTTCTGTCAGTTGTCTACTGGTGGTTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGACGGACATCGCTGTGAATTGGGCTGGGGGCCTGCACCATGCAAAGAAGTCCGAGGCATCTGGCTTCTGTTACGTCAATGATATCGTCTTGGCCATCCTGGAACTGCTAAAGTATCACCAGAGGGTGCTGTACATTGACATTGATATTCACCATGGTGACGGCGTGGAAGAGGCCTTCTACACCACGGACCGGGTCATGACTGTGTCCTTTCATAAGTATGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGATATCGGGGCTGGCAAAGGCAAGTATTATGCTGTTAACTACCCGCTCCGAGACGGGATTGATGACGAGTCCTATGAGGCCATTTTCAAGCCGGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGTGCGGTGGTCTTACAGTGTGGCTCAGACTCCCTATCTGGGGATCGGTTAGGTTGCTTCAATCTAACTATCAAAGGACACGCCAAGTGTGTGGAATTTGTCAAGAGCTTTAACCTGCCTATGCTGATGCTGGGAGGCGGTGGTTACACCATTCGTAACGTTGCCCGGTGCTGGACATATGAGACAGCTGTGGCCCTGGATACGGAGATCCCTAATGAGCTTCCATACAATGACTACTTTGAATACTTTGGACCAGATTTCAAGCTCCACATCAGTCCTTCCAATATGACTAACCAGAACACGAATGAGTACCTGGAGAAGATCAAACAGCGACTGTTTGAGAACCTTAGAATGCTGCCGCACGCACCTGGGGTCCAAATGCAGGCGATTCCTGAGGACGCCATCCCTGAGGAGAGTGGCGATGAGGACGAAGACGACCCTGACAAGCGCATCTCGATCTGCTCCTCTGACAAACGAATTGCCTGTGAGGAAGAGTTCTCCGATTCTGAAGAGGAGGGAGAGGGGGGCCGCAAGAACTCTTCCAACTTCAAAAAAGCCAAGAGAGTCAAAACAGAGGATGAAAAAGAGAAAGACCCAGAGGAGAAGAAAGAAGTCACCGAAGAGGAGAAAACCAAGGAGGAGAAGCCAGAAGCCAAAGGGGTCAAGGAGGAGGTCAAGTTGGCCTGAATGGACCTCTCCAGCTCTGGCTTCCTGCTGAGTCCCTCACGTTTCTTCCCCAACCCCTCAGATtttatattttctatttctctgtgtatttatataaaaatttattaaatataaatatCCCCAGGGACAGAAACCAAGGCCCCGAGCTCAGGGCAGCTGTGCTGGGTGAGCTCTTCCAGGAGCCACCTTGCCACCCATTCTTCCCGTTCTTAACTTTGAACCATAAAGGGTGCCAGGTCTGGGTGAAAGGGATACTTTTATGCAACCATAAGACAAACTCCTGAAATGCCAAGTGCCTGCTTAGTAGCTTTGGAAAGGTGCCCTTATTGAACATTCTAGAAGGGGTGGCTGGGTCTTCAAGGATCTCCTGTTTTTTTCAGGCTCCTAAAGTAACATCAGCCATTTTTAGATTGGTTCTGTTTTCGTACCTTCCCACTGGCCTCAAGTGAGCCAAGAAACACTGCCTGCCCTCTGTCTGTCTTCTCCTAATTCTGCAGGTGGAGGTTGCTAGTCTAGTTTCCTTTTTGAGATACTATTTTCATTTTTGTGAGCCTCTTTGTAATAAAATGGTACATTTCTATA

>NM_004964.3 

CCCCTCCCCCCTGGGTCGGACGCTGAGCGGAGCCGCGGGCGGGAGGGCGGACGGACCGACTGACGGTAGGGACGGGAGGCGAGCAAGATGGCGCAGACGCAGGGCACCCGGAGGAAAGTCTGTTACTACTACGACGGGGATGTTGGAAATTACTATTATGGACAAGGCCACCCAATGAAGCCTCACCGAATCCGCATGACTCATAATTTGCTGCTCAACTATGGTCTCTACCGAAAAATGGAAATCTATCGCCCTCACAAAGCCAATGCTGAGGAGATGACCAAGTACCACAGCGATGACTACATTAAATTCTTGCGCTCCATCCGTCCAGATAACATGTCGGAGTACAGCAAGCAGATGCAGAGATTCAACGTTGGTGAGGACTGTCCAGTATTCGATGGCCTGTTTGAGTTCTGTCAGTTGTCTACTGGTGGTTCTGTGGCAAGTGCTGTGAAACTTAATAAGCAGCAGACGGACATCGCTGTGAATTGGGCTGGGGGCCTGCACCATGCAAAGAAGTCCGAGGCATCTGGCTTCTGTTACGTCAATGATATCGTCTTGGCCATCCTGGAACTGCTAAAGTATCACCAGAGGGTGCTGTACATTGACATTGATATTCACCATGGTGACGGCGTGGAAGAGGCCTTCTACACCACGGACCGGGTCATGACTGTGTCCTTTCATAAGTATGGAGAGTACTTCCCAGGAACTGGGGACCTACGGGATATCGGGGCTGGCAAAGGCAAGTATTATGCTGTTAACTACCCGCTCCGAGACGGGATTGATGACGAGTCCTATGAGGCCATTTTCAAGCCGGTCATGTCCAAAGTAATGGAGATGTTCCAGCCTAGTGCGGTGGTCTTACAGTGTGGCTCAGACTCCCTATCTGGGGATCGGTTAGGTTGCTTCAATCTAACTATCAAAGGACACGCCAAGTGTGTGGAATTTGTCAAGAGCTTTAACCTGCCTATGCTGATGCTGGGAGGCGGTGGTTACACCATTCGTAACGTTGCCCGGTGCTGGACATATGAGACAGCTGTGGCCCTGGATACGGAGATCCCTAATGAGCTTCCATACAATGACTACTTTGAATACTTTGGACCAGATTTCAAGCTCCACATCAGTCCTTCCAATATGACTAACCAGAACACGAATGAGTACCTGGAGAAGATCAAACAGCGACTGTTTGAGAACCTTAGAATGCTGCCGCACGCACCTGGGGTCCAAATGCAGGCGATTCCTGAGGACGCCATCCCTGAGGAGAGTGGCGATGAGGACGAAGACGACCCTGACAAGCGCATCTCGATCTGCTCCTCTGACAAACGAATTGCCTGTGAGGAAGAGTTCTCCGATTCTGAAGAGGAGGGAGAGGGGGGCCGCAAGAACTCTTCCAACTTCAAAAAAGCCAAGAGAGTCAAAACAGAGGATGAAAAAGAGAAAGACCCAGAGGAGAAGAAAGAAGTCACCGAAGAGGAGAAAACCAAGGAGGAGAAGCCAGAAGCCAAAGGGGTCAAGGAGGAGGTCAAGTTGGCCTGAATGGACCTCTCCAGCTCTGGCTTCCTGCTGAGTCCCTCACGTTTCTTCCCCAACCCCTCAGATtttatattttctatttctctgtgtatttatataaaaatttattaaatataaatatCCCCAGGGACAGAAACCAAGGCCCCGAGCTCAGGGCAGCTGTGCTGGGTGAGCTCTTCCAGGAGCCACCTTGCCACCCATTCTTCCCGTTCTTAACTTTGAACCATAAAGGGTGCCAGGTCTGGGTGAAAGGGATACTTTTATGCAACCATAAGACAAACTCCTGAAATGCCAAGTGCCTGCTTAGTAGCTTTGGAAAGGTGCCCTTATTGAACATTCTAGAAGGGGTGGCTGGGTCTTCAAGGATCTCCTGTTTTTTTCAGGCTCCTAAAGTAACATCAGCCATTTTTAGATTGGTTCTGTTTTCGTACCTTCCCACTGGCCTCAAGTGAGCCAAGAAACACTGCCTGCCCTCTGTCTGTCTTCTCCTAATTCTGCAGGTGGAGGTTGCTAGTCTAGTTTCCTTTTTGAGATACTATTTTCATTTTTGTGAGCCTCTTTGTAATAAAATGGTACATTTCTATA

Publications

PMID - Link	Title
No publications available for this retrocopy