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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name RPL9P16
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Plot displaying the genomic locations of a retrocopy (in chr4) and its respective parental gene (in chr4). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr4:168755797-168756481  UCSC
Coordinates (T2T) chr4:172114819-172115503  UCSC
Coordinates (hg19) chr4:169676948-169677632  UCSC
Strand +
Parental Sequence NM_000661.5
Parental seq. overlap 592 bp
Parental seq. overlap (%) 81.3%
Genomic Region Intragenic (PALLD)
Retrocopy Summary RPL9P16, located on chr4:168755797-168756481, is a retrocopy of the parental gene RPL9. 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 RPL9
Full Name ribosomal protein L9
Also known as L9|NPC-A-16
Coordinate chr4:39454124-39458922
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 L6P family of ribosomal proteins. It is located in the cytoplasm. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes RPL9P8
Bonobo Pan paniscus RPL9P8
Gorilla Gorilla gorilla RPL9P6
Orangutan Pongo abelii RPL9P9
Gibbon Nomascus leucogenys RPL9P12
Green monkey Chlorocebus sabaeus RPL9P5
Crab-eating macaque Macaca fascicularis RPL9P7
Rhesus Macaca mulatta RPL9P7
Baboon Papio anubis RPL9P7
Golden snub-nosed monkey Rhinopithecus roxellana RPL9P5
Marmoset Callithrix jacchus RPL9P7
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

>RPL9P16
aGCTGCATCTGCTGCAAGAATGAAGGCTGTTCTCAGTAATCAGACTGTCCACATTCCAGAAAATGTCGACATCACTCTGAAGGGGCACAGTTCTTGTGAAAGGCCCTAGAGGACCCTGCAGAGGGACTTCAGTCACGTCAGTATAGAACTCGGGCTCCTTGGAAAGAAAAAGCAGAGGCTCCAGATTGACAAATGCTGAGAAGATGGGAATTGGCTGCCATGCGTGCTATCTGTAGTCATGCACAGAAGATGATCAAGGGCGTTATACTGGGCTTCTGTGACAAGATGAGGTCTCTGTGTTCTCACTTCCCCATCAATGTCATTATGCAGGAGAATAGCTCTATTGTAGAAGTCAGAACTTTCTTGAGCGAAAAATATATCTGCAGGGTTCGGGTGAGCCCAGGTGTTGCTTGTTCAATATCCCAAGCCCAGAAAGATGAGTTCATCCTTAAAGGAAATGACATTGAACTTGTTTCAAATTCAGCTGCTTTGACTCAGCAAACCACAACAGCTAAAAACCAGGATATCAGAACATTTTGGATGGTATCTATGTCTCTGAAAAAGGGACAGTTCAGCAGGCTGATGAGTAAAATCTAAGAGTTGTACAGCTACAGAAACAAGATGTCAGATAATTCCTAAGACCTATTTGTGATATTTTAATAATGCAATAAAAGACAGCTATTGA
>NM_000661.5
AGACGTTCTTTCTTTGCTGCGTCTACTGCGAGAATGAAGACTATTCTCAGCAATCAGACTGTCGACATTCCAGAAAATGTCGACATTACTCTGAAGGGACGCACAGTTATCGTGAAGGGCCCCAGAGGAACCCTGCGGAGGGACTTCAATCACATCAATGTAGAACTCAGCCTTCTTGGAAAGAAAAAAAAGAGGCTCCGGGTTGACAAATGGTGGGGTAACAGAAAGGAACTGGCTACCGTTCGGACTATTTGTAGTCATGTACAGAACATGATCAAGGGTGTTACACTGGGCTTCCGTTACAAGATGAGGTCTGTGTATGCTCACTTCCCCATCAACGTTGTTATCCAGGAGAATGGGTCTCTTGTTGAAATCCGAAATTTCTTGGGTGAAAAATATATCCGCAGGGTTCGGATGAGACCAGGTGTTGCTTGTTCAGTATCTCAAGCCCAGAAAGATGAATTAATCCTTGAAGGAAATGACATTGAGCTTGTTTCAAATTCAGCGGCTTTGATTCAGCAAGCCACAACAGTTAAAAACAAGGATATCAGGAAATTTTTGGATGGTATCTATGTCTCTGAAAAAGGAACTGTTCAGCAGGCTGATGAATAAGATCTAAGAGTTACCTGGCTACAGAAAGAAGATGCCAGATGACACTTAAGACCTACTTGTGATATTTAAATGATGCAATAAAAGACCTATTGATTTGGACCTTCTTCTTAAA

Publications

PMID - Link Title
19123937Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.