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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name RPL31P45
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Plot displaying the genomic locations of a retrocopy (in chr10) and its respective parental gene (in chr2). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr10:22266965-22267343  UCSC
Coordinates (T2T) chr10:22285998-22286376  UCSC
Coordinates (hg19) chr10:22555894-22556272  UCSC
Strand +
Parental Sequence NM_000993.5
Parental seq. overlap 329 bp
Parental seq. overlap (%) 25.5%
Genomic Region Intergenic
Retrocopy Summary RPL31P45, located on chr10:22266965-22267343, is a retrocopy of the parental gene RPL31. 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 RPL31
Full Name ribosomal protein L31
Also known as L31
Coordinate chr2:101002289-101019724
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 belongs to the L31E family of ribosomal proteins. It is located in the cytoplasm. Higher levels of expression of this gene in familial adenomatous polyps compared to matched normal tissues have been observed. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes RPL31P33
Bonobo Pan paniscus RPL31P33
Gorilla Gorilla gorilla RPL31P36
Orangutan Pongo abelii RPL31P35
Gibbon Nomascus leucogenys RPL31P24
Green monkey Chlorocebus sabaeus RPL31P20
Crab-eating macaque Macaca fascicularis RPL31P39
Rhesus Macaca mulatta RPL31P39
Baboon Papio anubis RPL31P49
Golden snub-nosed monkey Rhinopithecus roxellana RPL31P44
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)

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 Medulla00.20.4
log10(TPM+1)

Related Sequence

>RPL31P45
CTCCTTTCCAACTTGGGCCTGGCACAATGGCTGCTGCAAAGAAGGGTGGAAAGAAGAAAGGCTGTTCTGCCATCAGCAAGGTGGTGGCCCAAGAATACACCATCAACATTCAGAAATGCATCCATGGAGTAGGCTTCAAGAAGTGTGTCCCTTGGGCATTCAAAGAGATCTGGAAATTTGCTGTGAAGGAGGTGGGAACTCCAGATGTGCGTGTTGATACCAGGCTTGACAAAGCTGTCTAGGCTGAAGGAATAAGGGTGTCCCATACCCACCCATGTGTGGTTATCCAGAAAACGTGATGAGGATGAAGATTCACCAAATAAGTTCTATACTTTGGTTACCTATGCACCTGTTACCACTTTCAAAAATCTACAGACA
>NM_000993.5
CTTCCTTTCCAACTTGGACGCTGCAGAATGGCTCCCGCAAAGAAGGGTGGCGAGAAGAAAAAGGGCCGTTCTGCCATCAACGAAGTGGTAACCCGAGAATACACCATCAACATTCACAAGCGCATCCATGGAGTGGGCTTCAAGAAGCGTGCACCTCGGGCACTCAAAGAGATTCGGAAATTTGCCATGAAGGAGATGGGAACTCCAGATGTGCGCATTGACACCAGGCTCAACAAAGCTGTCTGGGCCAAAGGAATAAGGAATGTGCCATACCGAATCCGTGTGCGGCTGTCCAGAAAACGTAATGAGGATGAAGATTCACCAAATAAGCTATATACTTTGGTTACCTATGTACCTGTTACCACTTTCAAAAATCTACAGACAGTCAATGTGGATGAGAACTAATCGCTGATCGTCAGATCAAATAAAGTTATAAAATTGCCTTCATGTTTTTGTTCTTTTTAGTTGCAACATAATGTACTTGTATACCCTATCCTAATTATGGGATCATTTGAAGAGCTTTTCCCAAATTGATGGCCTGTGCTGCCTTCTCCCCATCCCCTGGGGTTTTAaagtgatttcaaactgcaacctagttttagaaccactgTTCTGGGTAGTTGGGATACTGAAGGCATATTGTTAATTATTCTACTTGTATGTTTTGCTAATTCTAAGATAAGCATTTTTCCAGAAACCAGGATGTAGAATCCAGTTGCCATTGACATCTTAACATTTTAGGAAACAACTTTAAAATGAtatactatctatctatctatctGTAGCATCTTAAAGGTAATGAAATTAATGTGGCAGTAGGTCTTTTAAGCTTCTGCCTACATCCATATTGAGTATAGTTGTTGTCTTCTAAAATAATTAATTGATTTTTGGTGAGATAACCAGATTCATATTTTAAGCCTTTTGTAATGGCCCCGTGGTACCTGGAGTCAAGGTTCAGAAGTAAAAAGTTCCTTAAGGTATCAATAACAAAAATTTGTATTAATAGTTCAGTCCTAAAGCAGTGTTGCTGAGATTATGTTTCACCAGCATTTACAAGCTGTATGTTAAATGCTGCCATAAAGAGGTCTCTGAAGCCGTAGGGCACACCCAAGGCAGGGCTGAGAAGTACCTAGTAGTGTTGCACCACCCAAAAACCATGGATGGGCAGCAGCAACATCTCCAGCTTACCCATTCACTGCCACAGTCTACAGCTTAAGACACTTAACTACAAGGTAAAAGAAAAGGACCAAGTAAATACAAAAAGTTTCTTATTAAAAAACTTGGAAGCCAA

Publications

PMID - Link Title
No publications available for this retrocopy