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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name SOD1P2
Plot displaying the genomic locations of a retrocopy (in chr16) and its respective parental gene (in chr21). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr16:51107601-51108118  UCSC
Coordinates (T2T) chr16:56905452-56905969  UCSC
Coordinates (hg19) chr16:51141512-51142029  UCSC
Strand +
Parental Sequence NM_000454.5
Parental seq. overlap 442 bp
Parental seq. overlap (%) 49.4%
Genomic Region Intergenic
Retrocopy Summary SOD1P2, located on chr16:51107601-51108118, is a retrocopy of the parental gene SOD1. 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 SOD1
Full Name superoxide dismutase 1
Also known as ALS|ALS1|HEL-S-44|IPOA|SOD|STAHP|hSod1|homodimer
Coordinate chr21:31659693-31668931
Strand +
Gene summary The protein encoded by this gene binds copper and zinc ions and is one of two isozymes responsible for destroying free superoxide radicals in the body. The encoded isozyme is a soluble cytoplasmic protein, acting as a homodimer to convert naturally-occuring but harmful superoxide radicals to molecular oxygen and hydrogen peroxide. The other isozyme is a mitochondrial protein. In addition, this protein contains an antimicrobial peptide that displays antibacterial, antifungal, and anti-MRSA activity against E. coli, E. faecalis, S. aureus, S. aureus MRSA LPV+, S. agalactiae, and yeast C. krusei. Mutations in this gene have been implicated as causes of familial amyotrophic lateral sclerosis. Rare transcript variants have been reported for this gene. [provided by RefSeq, Jul 2020]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes SOD1P3
Bonobo Pan paniscus SOD1P4
Gorilla Gorilla gorilla SOD1P3
Orangutan Pongo abelii SOD1P2
Gibbon Nomascus leucogenys SOD1P1
Green monkey Chlorocebus sabaeus SOD1P2
Crab-eating macaque Macaca fascicularis SOD1P1
Rhesus Macaca mulatta SOD1P1
Baboon Papio anubis SOD1P3
Golden snub-nosed monkey Rhinopithecus roxellana SOD1P3
Marmoset Callithrix jacchus SOD1P3
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

Related Sequence

>SOD1P2
AGCCCGGTGCAGGGCACCATCCACTTTGAGCAGAAGGAAAATGAACCATTTATGGTGTCAGAATGCATTACAGGATTGACTGAACGCCAGCACAGATTCCATGTTCATCAGTTTGGAGATAATACACCAGGCTGTACCAGGGCAGTTCCTTACTTTAATCCTTTAACCAAAAACCACAGTGGGCCAAGGATCAAGAGAGGCAGGTTGGAGACCTGGGTAATGTGGCCGCTGGCAAAGATGTGTCGCCAACATGTCTGTTGAAGATTCTCTGGTCTCACTCTCAGGACACTATTCCATCACTGCCCACACAATGGTGTCCATGACAAACCAGATGACTTGGGCAAAGGTGAAAATGAAGAAAGTACAAACACAGGAAATGCTAGAAGTTGTTTGGTTTGTGGTGTAATTGGGATTGCCCAATAAACATTCTCTTAAATGTGGTCTGAGTTCCATTAACTCATCTATTATCCTGCTAGCTGTAGAGATGAAATTTGATAAACATTAAACACTGAAATC
>NM_000454.5
GCGTCGTAGTCTCCTGCAGCGTCTGGGGTTTCCGTTGCAGTCCTCGGAACCAGGACCTCGGCGTGGCCTAGCGAGTTATGGCGACGAAGGCCGTGTGCGTGCTGAAGGGCGACGGCCCAGTGCAGGGCATCATCAATTTCGAGCAGAAGGAAAGTAATGGACCAGTGAAGGTGTGGGGAAGCATTAAAGGACTGACTGAAGGCCTGCATGGATTCCATGTTCATGAGTTTGGAGATAATACAGCAGGCTGTACCAGTGCAGGTCCTCACTTTAATCCTCTATCCAGAAAACACGGTGGGCCAAAGGATGAAGAGAGGCATGTTGGAGACTTGGGCAATGTGACTGCTGACAAAGATGGTGTGGCCGATGTGTCTATTGAAGATTCTGTGATCTCACTCTCAGGAGACCATTGCATCATTGGCCGCACACTGGTGGTCCATGAAAAAGCAGATGACTTGGGCAAAGGTGGAAATGAAGAAAGTACAAAGACAGGAAACGCTGGAAGTCGTTTGGCTTGTGGTGTAATTGGGATCGCCCAATAAACATTCCCTTGGATGTAGTCTGAGGCCCCTTAACTCATCTGTTATCCTGCTAGCTGTAGAAATGTATCCTGATAAACATTAAACACTGTAATCTTAAAAGTGTAATTGTGTGACTTTTTCAGAGTTGCTTTAAAGTACCTGTAGTGAGAAACTGATTTATGATCACTTGGAAGATTTGTATAGTTTTATAAAACTCAGTTAAAATGTCTGTTTCAATGACCTGTATTTTGCCAGACTTAAATCACAGATGGGTATTAAACTTGTCAGAATTTCTTTGTCATTCAAGCCTGTGAATAAAAACCCTGTATGGCACTTATTATGAGGCTATTAAAAGAATCCAAATTCAAACTAAA

Publications

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