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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name CTNNA1P2
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Plot displaying the genomic locations of a retrocopy (in chr2) and its respective parental gene (in chr5). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr2:31651386-31651586  UCSC
Coordinates (T2T) chr2:31696145-31696345  UCSC
Coordinates (hg19) chr2:31876455-31876655  UCSC
Strand +
Parental Sequence NM_001323987.1
Parental seq. overlap 161 bp
Parental seq. overlap (%) 5.7%
Genomic Region Intragenic (SRD5A2)
Retrocopy Summary CTNNA1P2, located on chr2:31651386-31651586, is a retrocopy of the parental gene CTNNA1. 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 CTNNA1
Full Name catenin alpha 1
Also known as CAP102|MDPT2
Coordinate chr5:138753425-138935034
Strand +
Gene summary This gene encodes a member of the catenin family of proteins that play an important role in cell adhesion process by connecting cadherins located on the plasma membrane to the actin filaments inside the cell. The encoded mechanosensing protein contains three vinculin homology domains and undergoes conformational changes in response to cytoskeletal tension, resulting in the reconfiguration of cadherin-actin filament connections. Certain mutations in this gene cause butterfly-shaped pigment dystrophy. [provided by RefSeq, May 2016]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes CTNNA1P1
Bonobo Pan paniscus CTNNA1P1
Gorilla Gorilla gorilla CTNNA1P1
Orangutan Pongo abelii CTNNA1P1
Gibbon Nomascus leucogenys CTNNA1P2
Crab-eating macaque Macaca fascicularis CTNNA1P2
Rhesus Macaca mulatta CTNNA1P2
Green monkey Chlorocebus sabaeus Without Homology
Baboon Papio anubis Without Homology
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)

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 Medulla00.10.20.3
log10(TPM+1)

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

Related Sequence

>CTNNA1P2
CAAAAGAGCAATCTGGATGCTGACATGTCCAAATGGGGTAACAGTGGCAATGACATCATCATGCTGGCCAAGCAGACTTATGGTAATGTACATGCTAATGATAGAGATGACTGACTTTACCCAATGTGAAGGACTGCTCAAAAATTCATCAGACAAGATCAGTGCAGCCAAGAAAATTGCTAAGACAAGATCTAGGATGGA
>NM_001323987.1
CTTTTGTTTGGGTTTTCCAGAAGCTTTACTGTTATAAAGCACCATGCTTTGTAACAGCATCGGGGTCGTTGCAGGACCCCCTGATTACAATAAAGCGAGAAAGAAGAACTCCTGACTTAAAAACATGATATTCCTTCAGTGTAGGAAGCAGCAGTGAGGTTGTAATAAAGGCTGCATTCAAGAAGACCCATCTGAACAGCTGGACGTAAAGAAAGAAGTGATGCACTCAATTCTGCAATAGATAAAATGACCAAGAAGACCAGGGACTTGCGTAGACAGCTCCGCAAAGCTGTCATGGACCACGTTTCAGATTCTTTCCTGGAAACCAATGTTCCACTTTTGGTATTGATTGAAGCTGCAAAGAATGGAAATGAGAAAGAAGTTAAGGAGTATGCCCAAGTTTTCCGTGAACATGCCAACAAATTGATTGAGGTTGCCAACTTGGCCTGTTCCATCTCAAATAATGAAGAAGGTGTAAAGCTTGTTCGAATGTCTGCAAGCCAGTTAGAAGCCCTCTGTCCTCAGGTTATTAATGCTGCACTGGCTTTAGCAGCAAAACCACAGAGTAAACTGGCCCAAGAGAACATGGATCTTTTTAAAGAACAATGGGAAAAACAAGTCCGTGTTCTCACAGATGCTGTCGATGACATTACTTCCATTGATGACTTCTTGGCTGTCTCAGAGAATCACATTTTGGAAGATGTGAACAAATGTGTCATTGCTCTCCAAGAGAAGGATGTGGATGGCCTGGACCGCACAGCTGGTGCAATTCGAGGCCGGGCAGCCCGGGTCATTCACGTAGTCACCTCAGAGATGGACAACTATGAGCCAGGAGTCTACACAGAGAAGGTTCTGGAAGCCACTAAGCTGCTCTCCAACACAGTCATGCCACGTTTTACTGAGCAAGTAGAAGCAGCCGTGGAAGCCCTCAGCTCGGACCCTGCCCAGCCCATGGATGAGAATGAGTTTATCGATGCTTCCCGCCTGGTATATGATGGCATCCGGGACATCAGGAAAGCAGTGCTGATGATAAGGACCCCTGAGGAGTTGGATGACTCTGACTTTGAGACAGAAGATTTTGATGTCAGAAGCAGGACGAGCGTCCAGACAGAAGACGATCAGCTGATAGCTGGCCAGAGTGCCCGGGCGATCATGGCTCAGCTTCCCCAGGAGCAAAAAGCGAAGATTGCGGAACAGGTGGCCAGCTTCCAGGAAGAAAAGAGCAAGCTGGATGCTGAAGTGTCCAAATGGGACGACAGTGGCAATGACATCATTGTGCTGGCCAAGCAGATGTGCATGATTATGATGGAGATGACAGACTTTACCCGAGGTAAAGGACCACTCAAAAATACATCGGATGTCATCAGTGCTGCCAAGAAAATTGCTGAGGCAGGATCCAGGATGGACAAGCTTGGCCGCACCATTGCAGACCATTGCCCCGACTCGGCTTGCAAGCAGGACCTGCTGGCCTACCTGCAACGCATCGCCCTCTACTGCCACCAGCTGAACATCTGCAGCAAGGTCAAGGCCGAGGTGCAGAATCTCGGCGGGGAGCTTGTTGTCTCTGGGGTGGACAGCGCCATGTCCCTGATCCAGGCAGCCAAGAACTTGATGAATGCTGTGGTGCAGACAGTGAAGGCATCCTACGTCGCCTCTACCAAATACCAAAAGTCACAGGGTATGGCTTCCCTCAACCTTCCTGCTGTGTCATGGAAGATGAAGGCACCAGAGAAAAAGCCATTGGTGAAGAGAGAGAAACAGGATGAGACACAGACCAAGATTAAACGGGCATCTCAGAAGAAGCACGTGAACCCGGTGCAGGCCCTCAGCGAGTTCAAAGCTATGGACAGCATCTAAGTCTGCCCAGGCCGGCCGCCCCCACCCCTCGGGGCTCCTGAATATCAGTCACTGTTCGTCACTCAAATGAATTTGCTAAATACAACACTGATACTAGATTCCACAGGGAAATGGGCAGACTGAACCAGTCCAGGTGGTGAATTTTCCAAGAACATAGTTTAAGTTGATTAAAAATGCTTTTAGAATGCAGGAGCCTACTTCTAGCTGTATTTTTTGTATGCTTAAATAAAAATAAAAATTCATAACCAAAGAGAATCCCACATTAGCTTGTTAGTAATGCTCTGACCAAGCCGAGATGCCCATTCTCTTAGTGATGGCGGCGTTAGGGTTTGAGAGAAGGGAATTTGGCTCAACTTCAGTTGAGAGGGTGCAGTCCAGACAGCTTGACTGCTTTTAAATGACCAAAGATGACCTGTGGTAAGCAACCTGGGCATCTTAGGAAGCAGTCCCTGGAGAAGGCATGTTCCCAGAAAGGTCTCTGGAGGGACAAACTCACTCAGTAAAACATAATGTATCATGAAGAAAACTGATTCTCTATGACATGAAATGAAAATTTTAATGCATTGTTATAATTACTAATGTACGCTGCTGCAGGACATTAATAAAGTTGCTTTTTTAGGCTACAGTGTCTCGATGCCATAATCAGAACACACTTTTTTTCCTCTTTCTCCCAGCTTCAAATGCAAATTCATCATTGGGCTCACTTCTAATAACTGCAGTGTTTCCCGCCTTGGGCTTGCAGCAGAAAAACCTGACAACATAGTGTTTGCTAAGGCAGTAATTTAGACTTTACCTTATTTGtgattactgtagtgattgattgattgattACTATTAACTACAAGGTATAATTTACTATCACCTTATTTAAATTTTATGAATTAATTTGAATGTTTTTTACACTAACTAACTTTTCCCAATAAAGTCCACTATGAAACCACGACA

Publications

PMID - Link Title
No publications available for this retrocopy