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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name RPSAP40
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Plot displaying the genomic locations of a retrocopy (in chr6) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr6:148647630-148648652  UCSC
Coordinates (T2T) chr6:149843989-149845011  UCSC
Coordinates (hg19) chr6:148968766-148969788  UCSC
Strand -
Parental Sequence NM_001304288.2
Parental seq. overlap 826 bp
Parental seq. overlap (%) 69.4%
Genomic Region Intergenic
Retrocopy Summary RPSAP40, located on chr6:148647630-148648652, is a retrocopy of the parental gene RPSA. 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 RPSA
Full Name ribosomal protein SA
Also known as 37LRP|67LR|ICAS|LAMBR|LAMR1|LBP|LBP/p40|LRP|LRP/LR|NEM/1CHD4|SA|lamR|p40
Coordinate chr3:39406720-39412542
Strand +
Gene summary Laminins, a family of extracellular matrix glycoproteins, are the major noncollagenous constituent of basement membranes. They have been implicated in a wide variety of biological processes including cell adhesion, differentiation, migration, signaling, neurite outgrowth and metastasis. Many of the effects of laminin are mediated through interactions with cell surface receptors. These receptors include members of the integrin family, as well as non-integrin laminin-binding proteins. This gene encodes a high-affinity, non-integrin family, laminin receptor 1. This receptor has been variously called 67 kD laminin receptor, 37 kD laminin receptor precursor (37LRP) and p40 ribosome-associated protein. The amino acid sequence of laminin receptor 1 is highly conserved through evolution, suggesting a key biological function. It has been observed that the level of the laminin receptor transcript is higher in colon carcinoma tissue and lung cancer cell line than their normal counterparts. Also, there is a correlation between the upregulation of this polypeptide in cancer cells and their invasive and metastatic phenotype. Multiple copies of this gene exist, however, most of them are pseudogenes thought to have arisen from retropositional events. Two alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes RPSAP29
Bonobo Pan paniscus RPSAP30
Gorilla Gorilla gorilla RPSAP28
Orangutan Pongo abelii RPSAP32
Gibbon Nomascus leucogenys RPSAP8
Green monkey Chlorocebus sabaeus RPSAP24
Crab-eating macaque Macaca fascicularis RPSAP21
Rhesus Macaca mulatta RPSAP22
Baboon Papio anubis RPSAP19
Golden snub-nosed monkey Rhinopithecus roxellana RPSAP15
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 Medulla00.050.1
log10(TPM+1)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

AdiposeBone MarrowBreast Mammary TissueBrain CerebellumColonColon Colonic MucosaEsophagusHeartHeart VentricleKidneyLiverBrain MidbrainOvaryPancreasBrain PonsKidney CortexEye RetinaMuscle SkeletalSkinSmall IntestineBrain Spinal CordSpleenTestisThymusTracheaHeart ValveMuscle Smooth012
log10(TPM+1)

Related Sequence

>RPSAP40
GAGGATGTCCTCAAGTTTCTTGCAGCAGGGACCCAATTAGGTGGCATCAACCTCGACTTCCAAATGGAACAGTACACCTATAAAAGGAAAAGTGAAAGCATCTGCTTCCTAAATCTGAACAGGACCTGGGAGAAGCTTCTTCTGGCAGCTGGCGCCATTGTTGCCATTGAAAACTGTGCTGATGTCAGTGTCACGCCCTCCAGAATACTGGCCAGTGGGCTGTGCTGAAGTTTGCTGCTGCCACTGGAGTCACTCCTATTGCTGGCTGTTTCATTGTTTCACTCTTGAAACTTTCACTAACCAGACCCAGGCAGCCTTCTGGGAGCCATGGCTCTTGGCAATTACTGATCCCAGAGCTGACCACCAGCCTCTCACAGAGGTGTCTTATGCTAACCTGCCTACCATTGCTTTGGGTCACACAGATTCTCGTCTGCGCTGTGGACATTGCCATCCCCTGCAACAACAAGGGCACTCACTCAGTGGGTCTGATGTGGAAGATGCCAGCCTGGAAGTTCTGCATATGCATGGCACCATCTCCTGTGAACACCCATAGGAGGTCGTGCCTGATCTCTATGTCTACAGAGATCCCAAGGAGATTAGAAAGAAAGAGCAGGCTGCTGCTAAAAAAGCTGAGGCTAAGGAGGAATTTCAGGGTGAAGGGACTGCCCTGGCTCCTGAGTGTACTGCTACTCAGCCTGAGGTTGCAGCCTGCTTTGAAGGTGTGCAGGTCACACAGGTGCCCCCTGTGTCTGTTCAGCAGGTCCCTACTGAAGACTAGAGCACTCAGCCTGCCATGGAAGACTGGTCCACAGCTCCCACTGCTTGGGCCACTGAATGGGTATGAAAAACCACTGAGTGGTCGGTCTTAAGCCATTTTCCACAGGCTCCTAAGCAAAATGGAAATAAGGTTGTTGGAAAATAAACATCAGTTCTGGCATTGTTCTGGATTCCATTGTAACTTCAAGGGAAACTTTCACAACGTCT
>NM_001304288.2
CTTTTCCGTGCTACCTGCAGAGGGGTCCATACGGCGTTGTTCTGGATTCCCGTCGTAACTTAAAGGGAAATTTTCACAATGTCCggagcccttgatgtcctgcaaatgaaggagGAGGATGTCCTTAAGTTCCTTGCAGCAGGAACCCACTTAGGTGGCACCAATCTTGACTTCCAGATGGAACAGTACATCTATAAAAGGAAAAGTGATGGCATCTATATCATAAATCTCAAGAGGACCTGGGAGAAGCTTCTGCTGGCAGCTCGTGCAATTGTTGCCATTGAAAACCCTGCTGATGTCAGTGTTATATCCTCCAGGAATACTGGCCAGGTTTGTGGAACAGTGAGGGCTGTGCTGAAGTTTGCTGCTGCCACTGGAGCCACTCCAATTGCTGGCCGCTTCACTCCTGGAACCTTCACTAACCAGATCCAGGCAGCCTTCCGGGAGCCACGGCTTCTTGTGGTTACTGACCCCAGGGCTGACCACCAGCCTCTCACGGAGGCATCTTATGTTAACCTACCTACCATTGCGCTGTGTAACACAGATTCTCCTCTGCGCTATGTGGACATTGCCATCCCATGCAACAACAAGGGAGCTCACTCAGTGGGTTTGATGTGGTGGATGCTGGCTCGGGAAGTTCTGCGCATGCGTGGCACCATTTCCCGTGAACACCCATGGGAGGTCATGCCTGATCTGTACTTCTACAGAGATCCTGAAGAGATTGAAAAAGAAGAGCAGGCTGCTGCTGAGAAGGCAGTGACCAAGGAGGAATTTCAGGGTGAATGGACTGCTCCCGCTCCTGAGTTCACTGCTACTCAGCCTGAGGTTGCAGACTGGTCTGAAGGTGTACAGGTGCCCTCTGTGCCTATTCAGCAATTCCCTACTGAAGACTGGAGCGCTCAGCCTGCCACGGAAGACTGGTCTGCAGCTCCCACTGCTCAGGCCACTGAATGGGTAGGAGCAACCACTGACTGGTCTTAAGCTGTTCTTGCATAGGCTCTTAAGCAGCATGGAAAAATGGTTGATGGAAAATAAACATCAGTTTCTAAAAGTTGTCTTCATTTAGTTTGCTTTTTACTCCAGATCAGAATACCTGGGATTGCATATCAAAGCATAATAATAAATACATGTCTCGACATGAGTTGTACTTCTAAA

Publications

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