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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name CLTAP2
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Plot displaying the genomic locations of a retrocopy (in chr12) and its respective parental gene (in chr9). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr12:7606898-7607621  UCSC
Coordinates (T2T) chr12:7620689-7621412  UCSC
Coordinates (hg19) chr12:7759494-7760217  UCSC
Strand +
Parental Sequence NM_001833.4
Parental seq. overlap 662 bp
Parental seq. overlap (%) 60.9%
Genomic Region Intergenic
Retrocopy Summary CLTAP2, located on chr12:7606898-7607621, is a retrocopy of the parental gene CLTA. 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 CLTA
Full Name clathrin light chain A
Also known as LCA
Coordinate chr9:36190855-36212059
Strand +
Gene summary Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes CLTAP2
Bonobo Pan paniscus CLTAP1
Gorilla Gorilla gorilla CLTAP2
Orangutan Pongo abelii CLTAP2
Green monkey Chlorocebus sabaeus CLTAP2
Crab-eating macaque Macaca fascicularis CLTAP2
Rhesus Macaca mulatta CLTAP2
Baboon Papio anubis CLTAP2
Gibbon Nomascus leucogenys 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 Medulla00.20.4
log10(TPM+1)

Related Sequence

>CLTAP2
TGGATGCTGTTGATGGAGTAATGAATGGTAAATACTACCAGGAAAGTAATAGTCCAACAGACAGTTGTGCAGCATTTCACAAGTGGATAGATTGCAGTCAGAGCCTGAAAGTATCCGTAAATGGAGAGAAGAGCAAACAGAACGCTTGGAAGCCCTTGATGCCAATTCTCAGAAGCAAGAAGCAGAGTGGAAAGAAAAGGCAATAAAGGAGCTAGAGGTGTGATATGTGAGATAGGATGAGCAACTACAGAAAACAAAAGCAAACAGGGCAGCAGAAGAAGCCTTTGTAAATGACATTGACCAGTTCTTCCCAGGCACTGAGTGGGAAAGTGTGGCCTGGCTGTGTAACTTTAACCCCAAGTCCAGAAGGCAGGCTAAAGACATCTCCCAGAGGTGCTCAGTCCTCATCTCCCTCAAGCAGGCCCCGCTGGTGCACTGAAGAGCCACCCTGTGGAAACATGTGCAGGAAACATCTGCAATATCTTAATCCTACTCAGCAAAGTTCTTCACAGTTATTGGATTAATTATGTTGAGTTATTTTGGACCAAACCTTTTTGTCTTTAGAGTTGATCATTGTTTGTGATTGCATGTTTCCTTCAACTGTGTTCTACCTGGCATTCAGAGAGTAGGGGGAGTAGGAAGAGGAAGAGAGAGAAGCCTCCCAACAGTAGCCTCGACCTATGCTTTTGTGCATTATTCTGAGAATAAATTTCTGTTTCAAACT
>NM_001833.4
CCGCTTTACCCGTCTCCCTCCTGGCGCTTGTCCTCCTCTCCCAGTCGGCACCACAGCGGTGGCTGCCGGGCGTGGTGTCGGTGGGTCGGTTGGTTTTTGTCTCACCGTTGGTGTCCGTGCCGTTCAGTTGCCCGCCATGGCTGAGCTGGATCCGTTCGGCGCCCCTGCCGGCGCCCCTGGCGGTCCCGCGCTGGGGAACGGAGTGGCCGGCGCCGGCGAAGAAGACCCGGCTGCGGCCTTCTTGGCGCAGCAAGAGAGCGAGATTGCGGGCATCGAGAACGACGAGGCCTTCGCCATCCTGGACGGCGGCGCCCCCGGGCCCCAGCCGCACGGCGAGCCGCCGGGGGGTCCGGATGCTGTTGATGGAGTAATGAATGGTGAATACTACCAGGAAAGTAATGGTCCAACAGACAGTTATGCAGCTATTTCACAAGTGGATCGATTGCAGTCAGAGCCTGAAAGTATCCGTAAATGGAGAGAAGAACAAATGGAACGCTTGGAAGCCCTTGATGCCAATTCTCGGAAGCAAGAAGCAGAGTGGAAAGAAAAGGCAATAAAGGAGCTAGAAGAATGGTATGCAAGACAGGACGAGCAGCTACAGAAAACAAAAGCAAACAACAGGGCAGCAGAAGAAGCCTTTGTAAATGACATTGACGAGTCGTCCCCAGGCACTGAGTGGGAACGGGTGGCCCGGCTGTGTGACTTTAACCCCAAGTCTAGCAAGCAGGCCAAAGATGTCTCCCGCATGCGCTCAGTCCTCATCTCCCTCAAGCAGGCCCCGCTGGTGCACTGAAGAGCCACCCTGTGGAAACACTACATCTGCAATATCTTAATCCTACTCAGTGAAGCTCTTCACAGTCATTGGATTAATTATGTTGAGTTCTTTTGGACCAAACCTTTTTGTCTTTAGAGTTGTTCATTGTTTGTGATTGCATGTTTCCTTCCTTCAACTGTGTTCTCCCTGGCATTCAGagaggagggagaggaggaagaggaaggggagggaagCTTCCCAAGAGTAGCCTCAACCTGTGCTTCTGTGCATTATTCTGAGAATAAATTTCTGTTTCAAACTGTA

Publications

PMID - Link Title
No publications available for this retrocopy