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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name RPL3P4
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Plot displaying the genomic locations of a retrocopy (in chr14) and its respective parental gene (in chr22). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr14:98972822-98973301  UCSC
Coordinates (T2T) chr14:93204525-93205004  UCSC
Coordinates (hg19) chr14:99439159-99439638  UCSC
Strand -
Parental Sequence NM_000967.4
Parental seq. overlap 477 bp
Parental seq. overlap (%) 36.8%
Genomic Region Intergenic
Retrocopy Summary RPL3P4, located on chr14:98972822-98973301, is a retrocopy of the parental gene RPL3. 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 RPL3
Full Name ribosomal protein L3
Also known as ASC-1|L3|TARBP-B
Coordinate chr22:39312882-39319623
Strand -
Gene summary Ribosomes, the complexes that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 60S subunit. The protein belongs to the L3P family of ribosomal proteins and it is located in the cytoplasm. The protein can bind to the HIV-1 TAR mRNA, and it has been suggested that the protein contributes to tat-mediated transactivation. This gene is co-transcribed with several small nucleolar RNA genes, which are located in several of this gene's introns. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes Without Homology
Bonobo Pan paniscus Without Homology
Gorilla Gorilla gorilla Without Homology
Orangutan Pongo abelii Without Homology
Gibbon Nomascus leucogenys Without Homology
Green monkey Chlorocebus sabaeus Without Homology
Crab-eating macaque Macaca fascicularis Without Homology
Rhesus Macaca mulatta 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 Medulla123
log10(TPM+1)

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

Related Sequence

>RPL3P4
TTCTCTGTGGCACGCGCTGGGCAGAAAGGCTACCATCACCGCACTGAGATCAACAAGAAGATCTATAAGATTGGCCAGGGCTACCTTATCAAGGATGGCAAGCTGATCAAGAACAATGCCTCCACTGACTATGACCTATCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACTATGGTGAAGTGACCAATGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGGGTGCTCACCCTCCGCAAGTCCTTGCTGGTGCAGACGAAGCGGCGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATGGCCGCTTCCAGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTGAAGAAAGACCGAATTGCAAAGGAAGAAGGAGCTTAATGCCAGGAACAGATTTTGCAGTTGGTGGGGTCTCAATAAAAGTTATTTTCCACTGa
>NM_000967.4
CTCTACCGGCGGGATTTGATGGCGTGATGTCTCACAGAAAGTTCTCCGCTCCCAGACATGGGTCCCTCGGCTTCCTGCCTCGGAAGCGCAGCAGCAGGCATCGTGGGAAGGTGAAGAGCTTCCCTAAGGATGACCCGTCCAAGCCGGTCCACCTCACAGCCTTCCTGGGATACAAGGCTGGCATGACTCACATCGTGCGGGAAGTCGACAGGCCGGGATCCAAGGTGAACAAGAAGGAGGTGGTGGAGGCTGTGACCATTGTAGAGACACCACCCATGGTGGTTGTGGGCATTGTGGGCTACGTGGAAACCCCTCGAGGCCTCCGGACCTTCAAGACTGTCTTTGCTGAGCACATCAGTGATGAATGCAAGAGGCGTTTCTATAAGAATTGGCATAAATCTAAGAAGAAGGCCTTTACCAAGTACTGCAAGAAATGGCAGGATGAGGATGGCAAGAAGCAGCTGGAGAAGGACTTCAGCAGCATGAAGAAGTACTGCCAAGTCATCCGTGTCATTGCCCACACCCAGATGCGCCTGCTTCCTCTGCGCCAGAAGAAGGCCCACCTGATGGAGATCCAGGTGAACGGAGGCACTGTGGCCGAGAAGCTGGACTGGGCCCGCGAGAGGCTTGAGCAGCAGGTACCTGTGAACCAAGTGTTTGGGCAGGATGAGATGATCGACGTCATCGGGGTGACCAAGGGCAAAGGCTACAAAGGGGTCACCAGTCGTTGGCACACCAAGAAGCTGCCCCGCAAGACCCACCGAGGCCTGCGCAAGGTGGCCTGTATTGGGGCATGGCATCCTGCTCGTGTAGCCTTCTCTGTGGCACGCGCTGGGCAGAAAGGCTACCATCACCGCACTGAGATCAACAAGAAGATTTATAAGATTGGCCAGGGCTACCTTATCAAGGACGGCAAGCTGATCAAGAACAATGCCTCCACTGACTATGACCTATCTGACAAGAGCATCAACCCTCTGGGTGGCTTTGTCCACTATGGTGAAGTGACCAATGACTTTGTCATGCTGAAAGGCTGTGTGGTGGGAACCAAGAAGCGGGTGCTCACCCTCCGCAAGTCCTTGCTGGTGCAGACGAAGCGGCGGGCTCTGGAGAAGATTGACCTTAAGTTCATTGACACCACCTCCAAGTTTGGCCATGGCCGCTTCCAGACCATGGAGGAGAAGAAAGCATTCATGGGACCACTGAAGAAAGACCGAATTGCAAAGGAAGAAGGAGCTTAATGCCAGGAACAGATTTTGCAGTTGGTGGGGTCTCAATAAAAGTTATTTTCCACTGACA

Publications

PMID - Link Title
No publications available for this retrocopy