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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name EIF4A3P1
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Plot displaying the genomic locations of a retrocopy (in chr18) and its respective parental gene (in chr17). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr18:24522307-24522908  UCSC
Coordinates (T2T) chr18:24716645-24717246  UCSC
Coordinates (hg19) chr18:22102271-22102872  UCSC
Strand -
Parental Sequence NM_014740.4
Parental seq. overlap 500 bp
Parental seq. overlap (%) 19.8%
Genomic Region Intergenic
Retrocopy Summary EIF4A3P1, located on chr18:24522307-24522908, is a retrocopy of the parental gene EIF4A3. 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 EIF4A3
Full Name eukaryotic translation initiation factor 4A3
Also known as DDX48|Fal1|MUK34|NMP265|NUK34|RCPS|eIF-4A-III|eIF4A-III|eIF4AIII
Coordinate chr17:80134369-80147128
Strand -
Gene summary This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene is a nuclear matrix protein. Its amino acid sequence is highly similar to the amino acid sequences of the translation initiation factors eIF4AI and eIF4AII, two other members of the DEAD box protein family. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes LOC742589P1
Bonobo Pan paniscus EIF4A3P1
Gorilla Gorilla gorilla EIF4A3P1
Orangutan Pongo abelii EIF4A3P1
Gibbon Nomascus leucogenys EIF4A3P1
Crab-eating macaque Macaca fascicularis EIF4A3P2
Rhesus Macaca mulatta EIF4A3P2
Baboon Papio anubis EIF4A3P3
Golden snub-nosed monkey Rhinopithecus roxellana EIF4A3P2
Marmoset Callithrix jacchus EIF4A3P2
Green monkey Chlorocebus sabaeus 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 Medulla00.10.20.30.4
log10(TPM+1)

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

Related Sequence

>EIF4A3P1
TTTCAAAGATCAGATTTGCGACATGTTCAGGTACTTGCCTCCAGTCACACAAGTAGTTCTCATCAGTGTTACACTGCCTCGCGAAATCCTAGAGATGACCAACAAGTACATGATGGACCCAATCCACATCTTGGTGAATTGACTCTGGAAGGCATCAAACAGCCTTTTGTGGCAGTGGAAAGAGAAGAGTGGAAATTCGACATCCCATGTGATCTCTACGAAATGCTAACTGTTATTCAGGTGGTCATCTTCTGTAACACCAAAAGGAAAGTTGACTGGCTGATGGAGAAAATGAGAGATGCTGCTCTCACCGTGTCCTCGATGCACAGAGACACACCTCAGAAAGGGCCACAGTCCGTCAGTAAGGAGTTCCCATCCGGCACCAGCACAGGGCTCATTTCCACAGATGTCTGGGCCGGGAGGTCAGATGTCCCTCAGGTGTCCGTCATCATTAACTATGACCTGCCCAAAAAACAGAATTGTACTCACACAGAATTTGGAGATCAGGTCGATATGGCTGGAAGGCTGTGGCCATTAACTTTGTAAAGAATGACCAACATCTGCATCCTGAGAGACATTGAACAGTACTATTCCACTCAGAC
>NM_014740.4
ACAGCGAGGTCGGCAGCGGCACAGCGAGGTCGGCAGCGGCACAGCGAGGTCGGCAGCGGCACAGCGAGGTCGGCAGCGGCAGCGAGGTCGGCAGCGGCACAGCGAGGTCGGCAGCGGCAGCGAGGTCGGCAGCGGCGCGCGCTGTGCTCTTCCGCGGACTCTGAATCATGGCGACCACGGCCACGATGGCGACCTCGGGCTCGGCGCGAAAGCGGCTGCTCAAAGAGGAAGACATGACTAAAGTGGAATTCGAGACCAGCGAGGAGGTGGATGTGACCCCCACGTTCGACACCATGGGCCTGCGGGAGGACCTGCTGCGGGGCATCTACGCTTACGGTTTTGAAAAACCATCAGCAATCCAGCAACGAGCAATCAAGCAGATCATCAAAGGGAGAGATGTCATCGCACAGTCTCAGTCCGGCACAGGAAAAACAGCCACCTTCAGTATCTCAGTCCTCCAGTGTTTGGATATTCAGGTTCGTGAAACTCAAGCTTTGATCTTGGCTCCCACAAGAGAGTTGGCTGTGCAGATCCAGAAGGGGCTGCTTGCTCTCGGTGACTACATGAATGTCCAGTGCCATGCCTGCATTGGAGGCACCAATGTTGGCGAGGACATCAGGAAGCTGGATTACGGACAGCATGTTGTCGCGGGCACTCCAGGGCGTGTTTTTGATATGATTCGTCGCAGAAGCCTAAGGACACGTGCTATCAAAATGTTGGTTTTGGATGAAGCTGATGAAATGTTGAATAAAGGTTTCAAAGAGCAGATTTACGATGTATACAGGTACCTGCCTCCAGCCACACAGGTGGTTCTCATCAGTGCCACGCTGCCACACGAGATTCTGGAGATGACCAACAAGTTCATGACCGACCCAATCCGCATCTTGGTGAAACGTGATGAATTGACTCTGGAAGGCATCAAGCAATTTTTCGTGGCAGTGGAGAGGGAAGAGTGGAAATTTGACACTCTGTGTGACCTCTACGACACACTGACCATCACTCAGGCGGTCATCTTCTGCAACACCAAAAGAAAGGTGGACTGGCTGACGGAGAAAATGAGGGAAGCCAACTTCACTGTATCCTCAATGCATGGAGACATGCCCCAGAAAGAGCGGGAGTCCATCATGAAGGAGTTCCGGTCGGGCGCCAGCCGAGTGCTTATTTCTACAGATGTCTGGGCCAGGGGGTTGGATGTCCCTCAGGTGTCCCTCATCATTAACTATGATCTCCCTAATAACAGAGAATTGTACATACACAGAATTGGGAGATCAGGTCGATACGGCCGGAAGGGTGTGGCCATTAACTTTGTAAAGAATGACGACATCCGCATCCTCAGAGATATCGAGCAGTACTATTCCACTCAGATTGATGAGATGCCGATGAACGTTGCTGATCTTATCTGAAGCAGCAGATCAGTGGGATGAGGGAGACTGTTCACCTGCTGTGTACTCCTGTTTGGAAGTATTTAGATCCAGATTCTACTTAATGGGGTTTATATGGACTTTCTTCTCATAAATGGCCTGCCGTCTCCCTTCCTTTGAAGAGGATATGGGGATTCTGCTCTCTTTTCTTATTTACATGTAAATAATACATTGTTCTAAGTCTTTTTCATTAAAAATTTAAAACTTTTCCCATAAACTCTATACTTCTAAGGTGCCACCACCTTCTCTAGTAACTTACTGTGTAGTCTTGGGTCATTTCACTCACTTTTCTttttttcttttctttttcttttttttttttgagacagtctccctctgttgcccaggcaggagcgcagtggcgtgatctcctctcaccgcaagctccacttcctgggttcatgccattctcctacctcagcctcccacgtagctgggagtacaggcggccgccaccatgccaggctaatttttttgtattttcagtagagacggggtttcaccgtgttagccaagatggtctcgatctcctgacctcgtgatccacccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacccggccCATTTCACTCACTTTTCTAATCTTTTTTTTTGGAAAGAGTTTCATCGTTGATgagttttgctctgctgcccaggctgaagagcagtggcaccatcacaactcattgcagccacaacctcctgggctcaagcgatcctctcacctcaccctcctgagtagctgggactacaggtgcatgccagcacatctggctaatatttaaattttttgtagagacagggtctcactttgtggcctaggctggtctgtcactcatgggtttaagtgattctcccatcttggccttacaaagtgctgggataacaggtgtgagccaccatgcctggccTCAtttttctaattttttttttttgttgtttttttgagagcccaggatctccctgtcgcccaggcaggagtatagtggcaggatcatgacttaccacaatgttgacAAACTAAAACAGATAATTATCTGTTTAAATATTTAAATTATTAAAGTATTTAAGTTATCTGTTGAAA

Publications

PMID - Link Title
No publications available for this retrocopy