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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name TPI1P2
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Plot displaying the genomic locations of a retrocopy (in chr7) and its respective parental gene (in chr12). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr7:129055980-129057212  UCSC
Coordinates (T2T) chr7:130368850-130370082  UCSC
Coordinates (hg19) chr7:128696034-128697266  UCSC
Strand +
Parental Sequence NM_001159287.1
Parental seq. overlap 1101 bp
Parental seq. overlap (%) 74.6%
Genomic Region Intergenic
Retrocopy Summary TPI1P2, located on chr7:129055980-129057212, is a retrocopy of the parental gene TPI1. 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 TPI1
Full Name triosephosphate isomerase 1
Also known as HEL-S-49|TIM|TPI|TPID
Coordinate chr12:6867420-6870948
Strand +
Gene summary This gene encodes an enzyme, consisting of two identical proteins, which catalyzes the isomerization of glyceraldehydes 3-phosphate (G3P) and dihydroxy-acetone phosphate (DHAP) in glycolysis and gluconeogenesis. Mutations in this gene are associated with triosephosphate isomerase deficiency. Pseudogenes have been identified on chromosomes 1, 4, 6 and 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes TPI1P4
Bonobo Pan paniscus TPI1P4
Gorilla Gorilla gorilla TPI1P4
Orangutan Pongo abelii TPI1P3
Gibbon Nomascus leucogenys TPI1P2
Green monkey Chlorocebus sabaeus TPI1P3
Crab-eating macaque Macaca fascicularis TPI1P1
Rhesus Macaca mulatta TPI1P1
Baboon Papio anubis TPI1P2
Golden snub-nosed monkey Rhinopithecus roxellana TPI1P4
Marmoset Callithrix jacchus TPI1P3
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 Medulla00.51
log10(TPM+1)

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

Related Sequence

>TPI1P2
gCGCCTCAGCTCCAGCGCCATGGCGCCCTCCAGGAAGTTCTTCGTGGGGAGGAACTGGAAGATGAACGGGCGGAAGAAATGTCTGGGGGAGCTCATCGGCACTCAGAACGCGGCCACTGTGCCTGCCGACACCAAGGTGATTTGTGCTCTCGCCACTGCGTATAACGAGTTGGCCCGGCAGAAGCTAGCTCCCAAGATTGCTGTGGCTCCGCAGAACTGCTACAAAGTGACTAATGGGGCCTTTACTGGGGAGATCAGCCCTGGCATGGTCAAAGACTTAGGAGTCACGTGGGTGGTGTGGTCCTGGGGCACTCAGAAGGCGTGTCTTTGGGGAGTCAGATGAGCTGATTGGGCAGAAAAGTGGCCCATGCTCTGGCAGAGAGACTCGGAGTAATCGCCTGCATTGGGGAGAAGCTAGATGAAAGGGAAGCTGGCATCACTGAGAAGGTTGTTTTTGAGCAGACAAAGGTCATCGCAGATAATGTGAAGGACTGGAGCAAGGTCATCTTGGCCTATGATCCCGTGTGGGCCACTGGTACTGGCAAGACTGCAACACCCCAACAGGCCCAGGAGGTACACAAGAAGCTCCGAGGATGGCTTAAGTCCAACATCTCTGATGCAGTGGCTCAGAGCACTGGTATCATTTATGGAGGCTCTGTGACCAAGGCAACCTGCAAGGAGCTGGCCAGCCAGCCTGACGTGGCTGCCTTCCTCATGAGTGGTGTTTCCCTCAAGCCCGAATTCGTAGACATCATCAATGCCAAACAATGAGCCCCATCCGTCTTCCCTACCCTTCCTGCCAACCCAGGAACTAAGCAGCCCAGAAGCTGAGTGACTGCCCCTCCCCTGCACATGCTTCTGATGGTGTCATCTGCACCCTATTGTGGCCTCATCCAAACTGTATCTTCCTTTACTATGTATACCTTCACCGTGTAATGGTCGGGACCAGACCAATCCCTTCTCCACTTACTGTAATTGTTGGAACTAAATGTCACCAATGTGGCTTCTCCTTGGCTGAGAGGTGAAAGGGATGGAATTTGCTCCTGGGTCCCCTAGGCCCTAGTGAGGGGAGGAGAGAGAACCCATCCTCTCCCTTCTTACACTGTGAGGCCAAGCAGAAGCCAGGGGTGCTGCCCTCTCCCACGGTGCCAACGCCTTTGTGTGTTGTGTATGTGAGCCATCCCACATGTGAGGGAAATAAACCCCTGGCACT
>NM_001159287.1
GGGCGGGGGGCAGGGCTCCGGGGGACTGGGCGGGCCATGGCGGAGGACGGCGAGGAGGCGGAGTTCCACTTCGCGGCGCTCTATATAAGTGGGCAGTGGCCGCGACTGCGCGCAGACACTGACCTTCAGCGCCTCGGCTCCAGCGCCATGGCGCCCTCCAGGAAGTTCTTCGTTGGGGGAAACTGGAAGATGAACGGGCGGAAGCAGAGTCTGGGGGAGCTCATCGGCACTCTGAACGCGGCCAAGGTGCCGGCCGACACCGAGGTGGTTTGTGCTCCCCCTACTGCCTATATCGACTTCGCCCGGCAGAAGCTAGATCCCAAGATTGCTGTGGCTGCGCAGAACTGCTACAAAGTGACTAATGGGGCTTTTACTGGGGAGATCAGCCCTGGCATGATCAAAGACTGCGGAGCCACGTGGGTGGTCCTGGGGCACTCAGAGAGAAGGCATGTCTTTGGGGAGTCAGATGAGCTGATTGGGCAGAAAGTGGCCCATGCTCTGGCAGAGGGACTCGGAGTAATCGCCTGCATTGGGGAGAAGCTAGATGAAAGGGAAGCTGGCATCACTGAGAAGGTTGTTTTCGAGCAGACAAAGGTCATCGCAGATAACGTGAAGGACTGGAGCAAGGTCGTCCTGGCCTATGAGCCTGTGTGGGCCATTGGTACTGGCAAGACTGCAACACCCCAACAGGCCCAGGAAGTACACGAGAAGCTCCGAGGATGGCTGAAGTCCAACGTCTCTGATGCGGTGGCTCAGAGCACCCGTATCATTTATGGAGGCTCTGTGACTGGGGCAACCTGCAAGGAGCTGGCCAGCCAGCCTGATGTGGATGGCTTCCTTGTGGGTGGTGCTTCCCTCAAGCCCGAATTCGTGGACATCATCAATGCCAAACAATGAGCCCCATCCATCTTCCCTACCCTTCCTGCCAAGCCAGGGACTAAGCAGCCCAGAAGCCCAGTAACTGCCCTTTCCCTGCATATGCTTCTGATGGTGTCATCTGCTCCTTCCTGTGGCCTCATCCAAACTGTATCTTCCTTTACTGTTTATATCTTCACCCTGTAATGGTTGGGACCAGGCCAATCCCTTCTCCACTTACTATAATGGTTGGAACTAAACGTCACCAAGGTGGCTTCTCCTTGGCTGAGAGATGGAAGGCGTGGTGGGATTTGCTCCTGGGTTCCCTAGGCCCTAGTGAGGGCAGAAGAGAAACCATCCTCTCCCTTCTTACACCGTGAGGCCAAGATCCCCTCAGAAGGCAGGAGTGCTGCCCTCTCCCATGGTGCCCGTGCCTCTGTGCTGTGTATGTGAACCACCCATGTGAGGGAATAAACCTGGCACTAGGTCTTGTGGTTTGTCTGCCTTCACTGGACTTGCCCAGATAATCTTCCTTTTTGAGGCAGCTATATAAATGATCATTTGTGCAAGAAAAAAAAAAAAACAAGAACAGGTTTCTATAACAA

Publications

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