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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name RPLP0P11
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Plot displaying the genomic locations of a retrocopy (in chr18) and its respective parental gene (in chr12). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr18:50457837-50458868  UCSC
Coordinates (T2T) chr18:50659589-50660620  UCSC
Coordinates (hg19) chr18:47984207-47985238  UCSC
Strand +
Parental Sequence NM_053275.4
Parental seq. overlap 833 bp
Parental seq. overlap (%) 71%
Genomic Region Intergenic
Retrocopy Summary RPLP0P11, located on chr18:50457837-50458868, is a retrocopy of the parental gene RPLP0. 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 RPLP0
Full Name ribosomal protein lateral stalk subunit P0
Also known as L10E|LP0|P0|PRLP0|RPP0
Coordinate chr12:120196699-120201111
Strand -
Gene summary Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein, which is the functional equivalent of the E. coli L10 ribosomal protein, belongs to the L10P family of ribosomal proteins. It is a neutral phosphoprotein with a C-terminal end that is nearly identical to the C-terminal ends of the acidic ribosomal phosphoproteins P1 and P2. The P0 protein can interact with P1 and P2 to form a pentameric complex consisting of P1 and P2 dimers, and a P0 monomer. The protein is located in the cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes RPLP0P7
Bonobo Pan paniscus RPLP0P8
Gorilla Gorilla gorilla RPLP0P9
Orangutan Pongo abelii RPLP0P11
Gibbon Nomascus leucogenys RPLP0P3
Green monkey Chlorocebus sabaeus RPLP0P4
Crab-eating macaque Macaca fascicularis RPLP0P9
Rhesus Macaca mulatta RPLP0P9
Baboon Papio anubis RPLP0P4
Golden snub-nosed monkey Rhinopithecus roxellana RPLP0P13
Marmoset Callithrix jacchus RPLP0P9
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)

Adipose SubcutaneousMuscle SkeletalArtery TibialArtery CoronaryHeart Atrial AppendageAdipose VisceralUterusVaginaBreast Mammary TissueSkin Not Sun ExposedMinor Salivary GlandBrain CortexAdrenal GlandThyroidLungSpleenPancreasEsophagus MuscularisEsophagus MucosaEsophagus Gastroesophageal JunctionStomachColon SigmoidSmall Intestine Terminal IleumColon TransverseProstateTestisNerve TibialSkin Sun ExposedHeart Left VentricleBrain CerebellumWhole BloodArtery AortaPituitaryBrain Frontal CortexBrain CaudateBrain Nucleus AccumbensBrain PutamenBrain HypothalamusBrain Spinal CordBrain HippocampusBrain Anterior Cingulate CortexOvaryBrain Cerebellar HemisphereLiverBrain Substantia NigraKidney CortexBrain AmygdalaCervix EctocervixFallopian TubeCervix EndocervixBladderKidney Medulla00.20.40.60.8
log10(TPM+1)

Related Sequence

>RPLP0P11
ATGACATCATCTTTAAAACTCTGCATGGCAATCCCTGACACACTACTGTGATGCCCAGGGAAGACAGGGCAACCTGGAAGTCCAACTACTTCCTTAAGGTCATCGAACATTTGGATGATTATCCAAAATGCTTCATTGTGGGAGTGAACAATGTGGGCTCCGAGCAGATGAAGCAGATCCAAATGTCCCTGCAAGGGAAGGCTGGTGGACAAGAGCACCATGATGCATGAGGCTATCCAAGGACATCTGGAAAACAACACAGCTCTGGAGAAACCATTGCCTCATTTCATTTCTGGGGGTATGTAGGTTTTGTGTTCACCAAGTAGGACCTCACTGAGATCAGGGACTTGCTGCCACTTATGCTGGTGCTATTGCCCCATGTGAAGTCACTATGCTCACCTGGAACCCTGGTCTGGGGCCCAAGAAGACCTTTCTTACAGGTTTTCGGCATCAGGAACTAAGATGTTCAGGGGCTCCGTTGAAATCCTGAGTGAGGTGCCACTGATTAAGACTGGAGACAAAGCGGGAGCCAGTGAAGCCACACTGGTGAACATGTGGAACATCTCCCCCTCCTCCTTTGAGCTGATCATCCAGCCGGTGTTTGACAACTGCAGCATCTACAACCCTGAAGTGCTTGACATGGCAGAGGAAACTGCATCCTTGCTTCCTGGAGGGTGTCTGTAATGTTCCCAGTGTCTGTCTGCAGATTGGTTACCCAACTGTTGCATCAGTTCCCTATCCTATCATCAGCAGGTACAAATGGGTGCTGGCTTTGTCTGTGGAGACTGATTACGCCTTCCTGCTTGCTGGAAAGGCCAAGGCCATCTTcCCCAAACAAAGTTGAAGCCAAGGAAGAGTCAGAGGAGGATATGGAATTTGGTCTCTTTGACTAATCACTGAAAAGCAACAAACTCAGCTAACTTTATTTGCAAAACAAGGAAATCAAGGCTTGCTTCTCTTAAAAAG
>NM_053275.4
CCTTCTCTCGCCAGGCGTCCTCGTGGAAGGCCCGGGACCGCGGGATGGGTGTCGGCGTGACCAGGCCTGAGCTCCCTGTCTCTCCTCAGTGACATCGTCTTTAAACCCTGCGTGGCAATCCCTGACGCACCGCCGTGATGCCCAGGGAAGACAGGGCGACCTGGAAGTCCAACTACTTCCTTAAGATCATCCAACTATTGGATGATTATCCGAAATGTTTCATTGTGGGAGCAGACAATGTGGGCTCCAAGCAGATGCAGCAGATCCGCATGTCCCTTCGCGGGAAGGCTGTGGTGCTGATGGGCAAGAACACCATGATGCGCAAGGCCATCCGAGGGCACCTGGAAAACAACCCAGCTCTGGAGAAACTGCTGCCTCATATCCGGGGGAATGTGGGCTTTGTGTTCACCAAGGAGGACCTCACTGAGATCAGGGACATGTTGCTGGCCAATAAGGTGCCAGCTGCTGCCCGTGCTGGTGCCATTGCCCCATGTGAAGTCACTGTGCCAGCCCAGAACACTGGTCTCGGGCCCGAGAAGACCTCCTTTTTCCAGGCTTTAGGTATCACCACTAAAATCTCCAGGGGCACCATTGAAATCCTGAGTGATGTGCAGCTGATCAAGACTGGAGACAAAGTGGGAGCCAGCGAAGCCACGCTGCTGAACATGCTCAACATCTCCCCCTTCTCCTTTGGGCTGGTCATCCAGCAGGTGTTCGACAATGGCAGCATCTACAACCCTGAAGTGCTTGATATCACAGAGGAAACTCTGCATTCTCGCTTCCTGGAGGGTGTCCGCAATGTTGCCAGTGTCTGTCTGCAGATTGGCTACCCAACTGTTGCATCAGTACCCCATTCTATCATCAACGGGTACAAACGAGTCCTGGCCTTGTCTGTGGAGACGGATTACACCTTCCCACTTGCTGAAAAGGTCAAGGCCTTCTTGGCTGATCCATCTGCCTTTGTGgctgctgcccctgtggctgctgccaccacagctgctcctgctgctgctgcagcCCCAGCTAAGGTTGAAGCCAAGGAAGAGTCGGAGGAGTCGGACGAGGATATGGGATTTGGTCTCTTTGACTAATCACCAAAAAGCAACCAACTTAGCCAGTTTTATTTGCAAAACAAGGAAATAAAGGCTTACTTCTTTAAAAAGTC

Publications

PMID - Link Title
26448942Long Noncoding RNA Expression Signatures of Metastatic Nasopharyngeal Carcinoma and Their Prognostic Value.
19123937Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.