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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name CBX3P5
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Plot displaying the genomic locations of a retrocopy (in chr12) and its respective parental gene (in chr7). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr12:95285778-95286902  UCSC
Coordinates (T2T) chr12:95266548-95267673  UCSC
Coordinates (hg19) chr12:95679554-95680678  UCSC
Strand -
Parental Sequence NM_016587.4
Parental seq. overlap 582 bp
Parental seq. overlap (%) 26.1%
Genomic Region Intragenic (VEZT)
Retrocopy Summary CBX3P5, located on chr12:95285778-95286902, is a retrocopy of the parental gene CBX3. 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 CBX3
Full Name chromobox 3
Also known as HECH|HP1-GAMMA|HP1Hs-gamma
Coordinate chr7:26201443-26213607
Strand +
Gene summary At the nuclear envelope, the nuclear lamina and heterochromatin are adjacent to the inner nuclear membrane. The protein encoded by this gene binds DNA and is a component of heterochromatin. This protein also can bind lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the encoded protein may explain the association of heterochromatin with the inner nuclear membrane. This protein binds histone H3 tails methylated at Lys-9 sites. This protein is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. Two transcript variants encoding the same protein but differing in the 5' UTR, have been found for this gene.[provided by RefSeq, Mar 2011]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes CBX3P10
Bonobo Pan paniscus CBX3P10
Gorilla Gorilla gorilla CBX3P8
Orangutan Pongo abelii CBX3P9
Gibbon Nomascus leucogenys CBX3P6
Green monkey Chlorocebus sabaeus CBX3P7
Baboon Papio anubis CBX3P6
Golden snub-nosed monkey Rhinopithecus roxellana CBX3P6
Marmoset Callithrix jacchus CBX3P8
Crab-eating macaque Macaca fascicularis Without Homology
Rhesus Macaca mulatta 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 Medulla00.20.40.6
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 Smooth0123
log10(TPM+1)

Related Sequence

>CBX3P5
GAAGGGGTCGGGGGGAGCGTCTTGGTTTTTTATTTACTAGTATGACAAAATAACTACACTCTAATGAAAATCAAGTTTTATATGCTCATTTTGAAAGCAGTGTTGGAAGAATTGTTGGGTTTTTCTTTTTTGCATCAATAGCACTGGTTACTTTGAATAAATAAATACAAGCTTTCTGTAGTTGCTTTCTTTATCAGAAAAGAAACAGACCCATGACCCAGAGCAGCTTGGAGGCAGTGAATAATAGCTCTTCAGGTCTGCAATAAAAAATGGCCTCCAACAAAACCACATTGCAAAACATGGGAAAGAAACAGAATGGAAAAGTAAAAAAGTTGAAGAGGCAGAGCCTGAAGAATTTGTGGTGGAAAATGTACTAGATAGACACGCAGGGAATGGGAAAGTGGAATATTTCCTGAAGGAATTTACAGATGCTGACAATACTTTGGAACCTGAAGAAAATTTAGATTGTCCAGAGTTAATTGAAGCATTTCTTAATTCTCAAAAAGCTGGTGAAGAAAAAGATGGTACAAAAAGAAAACCTTTATCTGGCAGTGAATCTGATGACAGCAAATCAAAGAAGAGATGCTGTTGACAAACCAAGAGGAATTGCCAGAGGTCTTGATCCTGAAAGAATAATTGGTGCCACAGATGGCAGTGAAGAATTGATGTTGCTCATGAAATGGAAGGATTCAGATGAGGCAGACTTGGTGCTGGCACAAAAGGCAAATATGAAGTATCCTCAAATTGAAATTGCTTTTTATGAAGAAAGACTAACTTGGTATTCTTGTTACATACATACATACATGTAAAATTTGCg
>NM_016587.4
CTTCGGATGTGGCTTGAGCTGTAGGCGCGGAGGGCCGGAGACGCTGCAGACCCGCGACCCGGAGCAGCTCGGAGGCGGTGAATAATAGCTCTTCAAGTCTGCAATAAAAAATGGCCTCCAACAAAACTACATTGCAAAAAATGGGAAAAAAACAGAATGGAAAGAGTAAAAAAGTTGAAGAGGCAGAGCCTGAAGAATTTGTCGTGGAAAAAGTACTAGATCGACGTGTAGTGAATGGGAAAGTGGAATATTTCCTGAAGTGGAAGGGATTTACAGATGCTGACAATACTTGGGAACCTGAAGAAAATTTAGATTGTCCAGAATTGATTGAAGCGTTTCTTAACTCTCAGAAAGCTGGCAAAGAAAAAGATGGTACAAAAAGAAAATCTTTATCTGACAGTGAATCTGATGACAGCAAATCAAAGAAGAAAAGAGATGCTGCTGACAAACCAAGAGGATTTGCCAGAGGTCTTGATCCTGAAAGAATAATTGGTGCCACAGACAGCAGTGGAGAATTGATGTTTCTCATGAAATGGAAAGATTCAGATGAGGCAGACTTGGTGCTGGCGAAAGAGGCAAATATGAAGTGTCCTCAAATTGTAATTGCTTTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAAGATGAAGCTCAATAATTGTTCACATTGTTCTTTtatatatatttatatatatatataAAAATTGGGTCTTAGATTTTGATTTACTAGTGTGACAAAATAACTACATCCTAATGAAAATCAAGTTTGATATGTTTGTTTTGAAAGTAGCGTTGGAAGAGTTGTTGGGGGTTTTTTGCATCCATAGCACTGGTTACTTTGAACAAATAAATAAAAGCTTTCTGTAGTTGCTTCCTTTATCAGAAAAGAACATTTGATACCATGGTATATCATTTCCTCTTCATTAAAGAACAGCTTTTCTAAATGTTGGGGGAAATGTCCATAGTCATTACTCAGTCAAAACTTGTGTTCTCATGAGCCTAAGGACCATTCTAGATTTATTACGTGTTTTTtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtATCCATAAAATGCATATGTAAATTTTTTTTTGTTTTTAAGCATTCACCCAAACAAAAAAATCACAGGTAAACCCATGTTTCTGAGATGCCATTATTCCAAGCAAAATAAGAGATAATCCCTTCAAGTTAAATTGAAAATTTTCCTGAAACCATACATTTCAAGTGAAATAAGTAATTCTAGATAGGACAATTTAAATTGGATAATTTTAAAGTGTCTATAATTGCAGTGGTTTATTTGCAAAATTCCTAAAAGGAAAAATTTTATCACTGCCATCACAGCAGGTTTCCTCATCCAGATGAGGAAACTAGACAAATGCTAGTGTGTTTTAACTAGCTAAACAAAACTAAGTTAAATGAACATTTAAAAGTTTCCCTAGCGGGCCATTCCTTAGCAAAATGTTGGAATCCCTGTTGCTACATTGACTAAAAGGTCATGATGAATGGAATATGTAAGACTTGGCTCATAGAAACCTAATCAGATGGTTAGAGGTGTTGGCAGTTTAGGACCTGCTGTCATAAATGTGTGAACAACCTTTTGTAACCTAACCTATTGACCTGCATGTTTTTTCTTTACCCCAATTCATTACATGGAGGCTCAATCTTGAGTTTGCTTTACTGGTTCAGCAAAAGCCAGGAAGAACAACTTTGTAGTAATCAAAATGTTATCCAACTGTATATTGTTTACTTTATTGTAAATACTGGTGAACAGTGGTTAATAAATAGTTTTATATTCCTTTATGCAATTATTAGACTTTTTTCTTTATTTGATATGCCTTTACAGTAGAAATAGAAATGCCCACACTCATTGGATTATCTTTGTTTATAAGTTAGATGATACCAGTAAGGCATTACAGTACATATCCTAGATCTTTTGAGCTTACGAGTTTTAAACTTGAATATGTATTTCCACAGGAATGTTTCCACAGTTGGGAAATAAAAGTTTCATGTGATGCCTAGGGTCAATTGTCTCATTAAAATGAGGTTTTAAATTCTG

Publications

PMID - Link Title
No publications available for this retrocopy