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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name PABPC4P3
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Plot displaying the genomic locations of a retrocopy (in chr15) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr15:94033719-94034499  UCSC
Coordinates (T2T) chr15:91795616-91796396  UCSC
Coordinates (hg19) chr15:94576948-94577728  UCSC
Strand +
Parental Sequence NM_001135653.2
Parental seq. overlap 721 bp
Parental seq. overlap (%) 22.9%
Genomic Region Intergenic
Retrocopy Summary PABPC4P3, located on chr15:94033719-94034499, is a retrocopy of the parental gene PABPC4. 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 PABPC4
Full Name poly(A) binding protein cytoplasmic 4
Also known as APP-1|APP1|PABP4|iPABP
Coordinate chr1:39560816-39576790
Strand -
Gene summary Poly(A)-binding proteins (PABPs) bind to the poly(A) tail present at the 3-prime ends of most eukaryotic mRNAs. PABPC4 or IPABP (inducible PABP) was isolated as an activation-induced T-cell mRNA encoding a protein. Activation of T cells increased PABPC4 mRNA levels in T cells approximately 5-fold. PABPC4 contains 4 RNA-binding domains and proline-rich C terminus. PABPC4 is localized primarily to the cytoplasm. It is suggested that PABPC4 might be necessary for regulation of stability of labile mRNA species in activated T cells. PABPC4 was also identified as an antigen, APP1 (activated-platelet protein-1), expressed on thrombin-activated rabbit platelets. PABPC4 may also be involved in the regulation of protein translation in platelets and megakaryocytes or may participate in the binding or stabilization of polyadenylates in platelet dense granules. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. This protein has also been found to interact with coronavirus nucleocapsid proteins and is thought to inhibit coronavirus replication. [provided by RefSeq, Nov 2021]

Homology

Species Scientific Name Retrocopy
Gorilla Gorilla gorilla PABPC4P3
Orangutan Pongo abelii PABPC4P3
Gibbon Nomascus leucogenys PABPC4P2
Green monkey Chlorocebus sabaeus PABPC4P3
Crab-eating macaque Macaca fascicularis PABPC4P1
Rhesus Macaca mulatta PABPC4P1
Baboon Papio anubis PABPC4P1
Golden snub-nosed monkey Rhinopithecus roxellana PABPC4P1
Chimpanzee Pan troglodytes Without Homology
Bonobo Pan paniscus 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

>PABPC4P3
CCAGCTGCCAATCTGGAGGCGTTCCCACAGCTGGGCAGAATTTTGCGCCGCGCtCCCCAGGATGTTGCCCCCTACAAATACGCCTCCTGTGTCCGCAGCCCTCATCCTGCCATACAGCCTCAGCCGGCGCCCCAGCCTGCGGTCCGTGTGCAGGGGCGGGAGCCACTCACTGCCTCCATGTTGGCTGCAGCACCCCCGCACGGAACAGAAGCAGATGCTGGGAGAACGCGTGTTCCCACTCATCCAAACAATGCATTCAAACCTGGCTGGGAAGATCACGGGAATGCTGCTGGAGATCGACAACTCTGAGCTGCTGCACGTGTTAGAGTCCCCCGAGTCTCTCCGCTCCAAGGTGGATGAAGCTGTAGCAGTTCTACAGGCTCATCATGCCAAGAAAGAAGCTGCCCAGAAGGTGGGCGCTGTTGCTGCTGCTACCACTCAGACAAGGAAAAACCGATTCAAAAGCCAAATAACCCCTCATGGAATTCAGCTCAAGGCTTGAAGTCTTCCTAGCTTGTCCTATGGACCTCAACACCAAGAACTACAAATTGCAAATTTAATAGGTCATTTTGTATCAAAAGGTCAATTGTGAAGCGCCTAGAATTTTTCAATGATACGAATATGTTCTCTGGGTTCTGCTGTGGCCCAGACAGTGTTAACTTTTTTTTTTCTATTGTGGGTTTTGATTTTTTCCCCCCAGAAATTGGTTTCATTTGATTACCCAAGTCTTACGTTTCTCAATAAAGAAAAAAAATCTCCAT
>NM_001135653.2
ctctctccgccccgggtcgctgccgcctccgccgcTTTCGGGCTTCGCAGCCTGaggaaaaaaagagaaaaagataaaaaaaatctgaaaacgcttcaaaatcctgaaaaaaaaaaaggaaaagaaaaaaCGAATCCTCGGAGAACCCGCGGGGAAGTCACTTTCGTACGCTTCCGGCCTGCCCCGCGCCCGCCGCCGCAGCGCTTGGcgtccgtcggtctccgtccgtcggtccgggggtgagccgcccgcccggcccgccgtgccctccccccgctcgggccccgagccccgcgccccgcgcctgccccggcgcaccacgtgtccgtgctgcccttcgccgcccgcccGGGGCTCGCCGAGTCGGCGCCCACAAAGATTTGGTTTCCCTCTGCCCCGGCGGTTGTAATCTTAAACCGCCGGAGCCCGAGGCCTATATTTATAGAGAAACGCGTGTCCCCGAGGCCGCCGTGGGCAGCGTCCGGTCGCCTCTTAAAGGATTTTTACCCTTCGGAAGGGGATTCCCCGTTTAATTTTTTTCCTACTTTGATTTTTTGAAATTTGGAGCTTCGCACCAGGACCGCGGAGAAGTGCAAAGTCGCGGGGAGGGCCGTATTGTGCGGAGAGCCTTTTGTCTGCGGTGCTGCGGCCGTGGGAGCCGGCCCCCGCCTCCCGTTTCCGTCCCGTCTCCAAGCCCGCCGACTCCAGCTCGTCCTCGCCGCGCCGGTGCCACCTGTGAGCCGCGGCGCGGGCCCGGGCTCCGAAGGCGCCCCTTTGTCCTGCGGCGGGCCCGATAAGAAGTCCTCCTGGCGGGGCTCGGGGTGGTGGGGGGCGGGGAGATGAACGCTGCGGCCAGCAGCTACCCCATGGCCTCCCTGTACGTGGGCGACCTGCATTCGGACGTCACCGAGGCCATGCTGTACGAAAAGTTCAGCCCCGCGGGGCCTGTGCTGTCCATCCGGGTCTGCCGCGATATGATCACCCGCCGCTCCCTGGGCTATGCCTACGTCAACTTCCAGCAGCCGGCCGACGCTGAGCGGGCTTTGGACACCATGAACTTTGATGTGATTAAGGGAAAGCCAATCCGCATCATGTGGTCTCAGAGGGATCCCTCTTTGAGAAAATCTGGTGTGGGAAACGTCTTCATCAAGAACCTGGACAAATCTATAGATAACAAGGCACTTTATGATACTTTTTCTGCTTTTGGAAACATACTGTCCTGCAAGGTGGTGTGTGATGAGAACGGCTCTAAGGGTTATGCCTTTGTCCACTTCGAGACCCAAGAGGCTGCCGACAAGGCCATCGAGAAGATGAATGGCATGCTCCTCAATGACCGCAAAGTATTTGTGGGCAGATTCAAGTCTCGCAAAGAGCGGGAAGCTGAGCTTGGAGCCAAAGCCAAGGAATTCACCAATGTTTATATCAAAAACTTTGGGGAAGAGGTGGATGATGAGAGTCTGAAAGAGCTATTCAGTCAGTTTGGTAAGACCCTAAGTGTCAAGGTGATGAGAGATCCCAATGGGAAATCCAAAGGCTTTGGCTTTGTGAGTTACGAAAAACACGAGGATGCCAATAAGGCTGTGGAAGAGATGAATGGAAAAGAAATAAGTGGTAAAATCATATTTGTAGGCCGTGCACAAAAGAAAGTAGAACGGCAGGCAGAGTTAAAACGGAAATTTGAACAGTTGAAACAGGAGAGAATTAGTCGATATCAGGGGGTGAATCTCTACATTAAGAACTTGGATGACACTATTGATGATGAGAAATTAAGGAAAGAATTTTCTCCTTTTGGATCAATTACCAGTGCTAAGGTAATGCTGGAGGATGGAAGAAGCAAAGGGTTTGGCTTCGTCTGCTTCTCATCTCCTGAAGAAGCAACCAAAGCAGTCACTGAGATGAATGGACGCATTGTGGGCTCCAAGCCACTATATGTTGCCCTGGCCCAGAGGAAGGAAGAGAGAAAGGCTCACCTGACCAACCAGTATATGCAACGAGTGGCTGGAATGAGAGCACTTCCTGCCAATGCCATCTTAAATCAGTTCCAGCCTGCAGCGGGTGGCTACTTTGTGCCAGCAGTCCCACAGGCTCAGGGAAGGCCTCCATATTATACACCTAACCAGTTAGCACAGATGAGGCCTAATCCACGCTGGCAGCAAGGTGGGAGACCTCAAGGCTTCCAAGGAATGCCAAGTGCTATACGCCAGTCTGGGCCTCGTCCAACTCTTCGCCATCTGGCTCCAACTGGTAATGCTCCGGCCTCTCGTGGCCTCCCTACTACCACTCAGAGAGTCGGGTCTGAGTGCCCGGACCGCTTGGCTATGGACTTTGGTGGGGCTGGTGCCGCCCAGCAAGGGCTGACTGACAGCTGCCAGTCTGGAGGCGTTCCCACAGCTGTGCAGAACTTAGCGCCACGCgctgctgttgctgctgctgctCCCCGGGCTGTTGCCCCCTACAAATACGCCTCCAGTGTCCGCAGCCCTCATCCTGCCATACAGCCTCTGCAGGCACCCCAGCCTGCGGTCCATGTGCAGGGGCAGGAGCCACTGACTGCCTCCATGCTGGCTGCAGCACCCCCCCAGGAACAGAAGCAGATGCTGGGAGAACGCTTGTTCCCACTCATCCAAACAATGCATTCAAATCTGGCTGGGAAGATCACGGGAATGCTGCTGGAGATAGACAACTCTGAGCTGCTGCACATGTTAGAGTCCCCCGAGTCTCTCCGCTCCAAGGTGGATGAAGCTGTAGCAGTTCTACAGGCTCATCATGCCAAGAAAGAAGCTGCCCAGAAGGTGGGCGCTGTTGCTGCTGCTACCTCTTAGACAAGGAAAAACCGATTCAAAAGCCAAATAACCCCTTATGGAATTCAACTCAAGGTTTGAAGACTTCCTAGCTTGTCCTATGGACCTCAACACCAAGGATTACAAATTGCAAATTTAATAGGTCATTTTGTATCAAAAGGTCAATTATGAAGCACCTAGAATTTTTCAATTATACGAATATGTTCTTTGGGTTCTGCTGTGGCCCAGACAGTGTTAACTTTTTTTTTATTGTGGGTTTTGATTTTTTCCCCCAGAAATTGGTTTTATTTGATGTACCCAAGTCTTACGTTTCCCAATAAAGAAAAAAAATCTCCATAAAA

Publications

PMID - Link Title
No publications available for this retrocopy