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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name PHF5AP3
Plot displaying the genomic locations of a retrocopy (in chr3) and its respective parental gene (in chr22). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr3:141307246-141307943  UCSC
Coordinates (T2T) chr3:144054839-144055536  UCSC
Coordinates (hg19) chr3:141026088-141026785  UCSC
Strand -
Parental Sequence NM_032758.4
Parental seq. overlap 581 bp
Parental seq. overlap (%) 55%
Genomic Region Intergenic
Retrocopy Summary PHF5AP3, located on chr3:141307246-141307943, is a retrocopy of the parental gene PHF5A. 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 PHF5A
Full Name PHD finger protein 5A
Also known as INI|Rds3|SAP14b|SF3B7|SF3b14b|bK223H9.2
Coordinate chr22:41459717-41468692
Strand -
Gene summary This gene encodes a subunit of the splicing factor 3b protein complex. Splicing factor 3b, together with splicing factor 3a and a 12S RNA unit, forms the U2 small nuclear ribonucleoproteins complex (U2 snRNP). The splicing factor 3b/3a complex binds pre-mRNA upstream of the intron's branch site in a sequence-independent manner and may anchor the U2 snRNP to the pre-mRNA. The protein encoded by this gene contains a PHD-finger-like domain that is flanked by highly basic N- and C-termini. This protein belongs to the PHD-finger superfamily and may act as a chromatin-associated protein. This gene has several pseudogenes on different chromosomes. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes PHF5AP3
Bonobo Pan paniscus PHF5AP3
Gorilla Gorilla gorilla PHF5AP3
Orangutan Pongo abelii PHF5AP2
Gibbon Nomascus leucogenys PHF5AP2
Green monkey Chlorocebus sabaeus PHF5AP3
Crab-eating macaque Macaca fascicularis PHF5AP2
Rhesus Macaca mulatta PHF5AP3
Baboon Papio anubis PHF5AP1
Golden snub-nosed monkey Rhinopithecus roxellana PHF5AP1
Marmoset Callithrix jacchus PHF5AP6
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

>PHF5AP3
AGGAGCTACGGCTGAACATTATCTGGGTTTGATCTTTTGCTGCAAGCAGGCTGATGTTGCCATCGGAAGATTGTGTGAAAACTGACGGCAAGTGTGTGATTTGTGACCGCTGTGTCTGTCCCTTCACCCTGGTATGCTTATATGATGAGTGTAACTATGGCTTTTACCAGGGACACTGTGAGATCTGTGGAGGCCATGGGAGTCTCTGATGCCTATTATTGTAAGGAGTGCACCAGCCAGGAGAAGAATAGAGATGGCTGCCCAAAGATTGTCAGCTTAGGGAGCTCTGAGACAGGCCTCTTCCATGAACGTCAAAAATGTGGCATCAGAAAGAGGTGATTGGTGGGTGGCCCCTTCCTTCCCTGCATCGAGCTGCAGCAGCTGCCAGAAATGACGCCTACAACTATCAACAGAAAGGGAGCGGAGCCCCGGGCATCGCCGAAGTGCCTGCCGGTGTACTGGGACCCTGCCACCTCTCCCTCCCCTTTCGTACAAATGTGTGATAGGGATGGAAAAGGATTCTTTACAGAACACCCTGGCAGACTGAATCACAGAAGAATCGATAGATTAGTTACTGTTTTTTCTTGAATTTGAAAAGCAAGGTTCTGTCCTGCATATGGATATGTCCTCCCTACCCGGAGAGCTTCTAAAAACAAGTCACGGTTCAGTCTTCTGCTTGAGGAGCTGACTGTGAAGCT
>NM_032758.4
AGTTCCCGAAGCTTCCGGTGGCCGGCTTAGTTAGGAGCTATGGCTAAACATCATCCTGATTTGATCTTTTGCCGCAAGCAGGCTGGTGTTGCCATCGGAAGACTGTGTGAAAAATGTGATGGCAAGTGTGTGATTTGTGACTCCTATGTGCGTCCCTGCACTCTGGTGCGCATATGTGATGAGTGTAACTATGGATCTTACCAGGGGCGCTGTGTGATCTGTGGAGGACCTGGGGTCTCTGATGCCTATTATTGTAAGGAGTGCACCATCCAGGAGAAGGACAGAGATGGCTGCCCAAAGATTGTCAATCTGGGGAGCTCTAAGACAGACCTCTTCTATGAACGCAAAAAATACGGCTTCAAGAAGAGGTGATTGGTGGGTGGCCCCTTCCTCCCCCCAACATCAGTCTGCTGCAGCTGCCAGAAAACATGCCTACTACTACCAGCAGAAAGGGAGCAGAGCCCAGAGCATCACCAGGAGTGCCTGCTAGTGTACTGGCAGCTTGCCACCCCCTCCTCTCCCTTCACCCAGACACGTGGTAGGGATGGAAAAGGATTCTTCACAGAGCACTCTGGCACACCATATCGGAGAAAACTTGATAGATTAGTTAATGGTTTTTCTTGAATTCGAGAAGCAAAGATCTGTTCTCCATATTGGTATGTTCTCCCTCAACCAAGATCTTCTAAAAAGAAATAATATTTTAGTCTTCTGCTTGAGGAACTGACTGTGAAGCGACGCCCAGTGAAAAACATGTTCTTGCAGCAGCTCTGGTGGCAGCTGTCCTTGAGGAACCTTTGGTGTGTGGTGGGAAGCTATCAGAACAAGAAATGTAGGCATTTCCCGTTTTTTTTGGGGGGGGGGTGGGGGGGCAGGGCTCTGCCCTCTTGAAAGGCATTTACTTGTTTAACACTTGTCCAGCTACAGTGGGGTACAGTAGCTGGCTATTCACAGGCATCATCATAGCCCACTAGTCTCATATTATTTTCCTTTTGAGAAATTGGAAACTCTTTCTGTTGCTATTATATTAATAAAGTTGGTGTTTATTTTCTGGTA

Publications

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