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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name U2AF1P1
Plot displaying the genomic locations of a retrocopy (in chr15) and its respective parental gene (in chr21). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr15:35092457-35093302  UCSC
Coordinates (T2T) chr15:32897664-32898506  UCSC
Coordinates (hg19) chr15:35384658-35385503  UCSC
Strand +
Parental Sequence NM_006758.3
Parental seq. overlap 756 bp
Parental seq. overlap (%) 79.8%
Genomic Region Intergenic
Retrocopy Summary U2AF1P1, located on chr15:35092457-35093302, is a retrocopy of the parental gene U2AF1. 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 U2AF1
Full Name U2 small nuclear RNA auxiliary factor 1
Also known as FP793|RN|RNU2AF1|U2AF35|U2AFBP
Coordinate chr21:43092956-43108291
Strand -
Gene summary This gene belongs to the splicing factor SR family of genes. U2 auxiliary factor, comprising a large and a small subunit, is a non-snRNP protein required for the binding of U2 snRNP to the pre-mRNA branch site. This gene encodes the small subunit which plays a critical role in both constitutive and enhancer-dependent RNA splicing by directly mediating interactions between the large subunit and proteins bound to the enhancers. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes U2AF1P2
Bonobo Pan paniscus LOC100973922P2
Gorilla Gorilla gorilla U2AF1P2
Orangutan Pongo abelii LOC100459870P2
Gibbon Nomascus leucogenys U2AF1P1
Green monkey Chlorocebus sabaeus U2AF1P1
Crab-eating macaque Macaca fascicularis U2AF1P1
Rhesus Macaca mulatta U2AF1P1
Baboon Papio anubis U2AF1P1
Golden snub-nosed monkey Rhinopithecus roxellana LOC104677998P1
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

Related Sequence

>U2AF1P1
AGCAGGGGCGGCGGCGGGTGGGAAATGGCGGAGTGTCCAGCCTCCATCTTTGGCACCGAGAAAGTCAACTGTTCATTTGATTTCAAAATTGGAGCATGTCTTCATGGAGACAGGTGCTCTTGGTTGCACCATAAACCGACGTTTAGCCAGACCATTGCCCTCTTGAACATTTACTGTAACCCTCAAAACGCTTCCCAGTCGGCCGACGGTTTGCGCTGTGCCCTGAGCGATGTTGAGGTGCAGGAACACTCTGATGAATTTTTTGAGGAGGTTTTTATAGAACTGGGGGAGAAGTATGGGGAAGTTGAGGAGATGAATGTCTGTGACAACCTGGGAGACCACCTGGTGGGGAACGTGTACTTCAAGCTTCCCCGTGAGGAAGATGCGGAAAAGGCTGTGATTGACTTGAACAACCGTTGGTTTAACGGACAGCCGATCCACGCCGAGCTGTCACCTGTGACGGACTTCAGGGGAGCCTGCTGCCGTCAGTATGAGATGGGAGAATGCACACGAGGCGGCTTCTGCAACTTCATGCATTTGAAGCCCATTTCCAGAGAGCTGCGGCGGGAGCTGTGTGGGCAGCGTCGCAAGAAGCATAGATCAAGATCCCGATCCCGGGAGCGTCATTCTCGGTCTGGAGACCGTGGTCACCAGGCGGCGGCGGCGGACGGGAGCGTGACAGGAGGCGGTTGAGAGATCGTGAAAGATCTGGGCGATTCTGAGCCATGCCATTTTTACCTTACGTCTGCTAGAAAGTGTTGTAGTTGATTGACCAAACCAGTTCATAAGGGGATTTTTTTA
>NM_006758.3
GACGTCTCCCGAGggcgtcggcagggtcggcggcgtcggcagcagtgtcgacggcagcggcggcggcggGTGGGAAATGGCGGAGTATCTGGCCTCCATCTTCGGCACCGAGAAAGACAAAGTCAACTGTTCATTTTATTTCAAAATTGGAGCATGTCGTCATGGAGACAGGTGCTCTCGGTTGCACAATAAACCGACGTTTAGCCAGACCATTGCCCTCTTGAACATTTACCGTAACCCTCAAAACTCTTCCCAGTCTGCTGACGGTTTGCGCTGTGCCGTGAGCGATGTGGAGATGCAGGAACACTATGATGAGTTTTTTGAGGAGGTTTTTACAGAAATGGAGGAGAAGTATGGGGAAGTAGAGGAGATGAACGTCTGTGACAACCTGGGAGACCACCTGGTGGGGAACGTGTACGTCAAGTTTCGCCGTGAGGAAGATGCGGAAAAGGCTGTGATTGACTTGAATAACCGTTGGTTTAATGGACAGCCGATCCACGCCGAGCTGTCACCCGTGACGGACTTCAGAGAAGCCTGCTGCCGTCAGTATGAGATGGGAGAATGCACACGAGGCGGCTTCTGCAACTTCATGCATTTGAAGCCCATTTCCAGAGAGCTGCGGCGGGAGCTGTATGGCCGCCGTCGCAAGAAGCATAGATCAAGATCCCGATCCCGGGAGCGTCGTTCTCGGTCTAGAGACCgtggtcgtggcggtggcggtggcggtggtggaggtggcggcggacgggagcgtgacaggaggcggtCGAGAGATCGTGAAAGATCTGGGCGATTCTGAGCCATGCCATTTTTACCTTATGTCTGCTAGAAAGTGTTGTAGTTGATTGACCAAACCAGTTCATAAGGGGAATTTTTTTTaaaaaacaacaaaaaaaaaaacatacaaaGATGGGTTTCTGAATAAAATTTGTAGTGATAACAGTA

Publications

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