RCPedia: Rtcs

Summary

Retrocopy Name	RNFT1P3	Plot displaying the genomic locations of a retrocopy (in scaffold_m29_p_14) and its respective parental gene (in scaffold_m29_p_20). Each line represents a retrocopy.
Species	Rhinolophus ferrumequinum
Coordinates	scaffold_m29_p_14:58934773-58935325 UCSC
Strand	+
Parental Sequence	RNFT1_x2
Parental seq. overlap	475 bp
Parental seq. overlap (%)	39.5%
Genomic Region	Intragenic (WDR35)
Retrocopy Summary	RNFT1P3, located on scaffold_m29_p_14:58934773-58935325, is a retrocopy of the parental gene RNFT1. 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	RNFT1
Full Name	N/A
Also known as	NULL
Coordinate	scaffold_m29_p_20:25939115-25949726
Strand	+
Gene summary	N/A

Homology

Species	Scientific Name	Retrocopy
Human	Homo sapiens	RNFT1P1
Chimpanzee	Pan troglodytes	RNFT1P1
Bonobo	Pan paniscus	RNFT1P1
Gorilla	Gorilla gorilla	RNFT1P1
Orangutan	Pongo abelii	RNFT1P1
Green monkey	Chlorocebus sabaeus	RNFT1P1
Rhesus	Macaca mulatta	RNFT1P1
Baboon	Papio anubis	RNFT1P1
Golden snub-nosed monkey	Rhinopithecus roxellana	RNFT1P2
Marmoset	Callithrix jacchus	RNFT1P2
Dolphin	Tursiops truncatus	RNFT1P3
Velvety free-tailed bat	Molossus molossus	RNFT1P2
Sloth	Choloepus didactylus	RNFT1P6
Gibbon	Nomascus leucogenys	Without Homology
Crab-eating macaque	Macaca fascicularis	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
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
Greater mouse-eared bat	Myotis myotis	Without Homology
Kuhl's pipistrelle	Pipistrellus kuhlii	Without Homology
Egyptian rousette	Rousettus aegyptiacus	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

>RNFT1P3
GGGATTGTTGGAATCACTGATTTCGTTCTGAAATTCCGCTGCCTGGTTCTAAATGCCTTATTTTATTGGTGTCTTCTTTCCTCATGCCTTTTAAATCCAAAGGTTACTGGCATGTGCTTTTCGAAGAATTATGTCAGTATTACCAGACTTTTGTTCCCATGCCAATTTGGTTTGTTACCTCACTGACCATGGGGAGATCAGTAATGTAACTCACTGTAGTCTGGGATATTGGTGGCTTTAGCCTTCTTCATTTAAAACTTTTGGCCTTTTTTGGAAATCAGAACTTTCAGATGGGTTTTGCAAATATCTTATGTGTGATCAAGTTACAGAGTTGCTGCCAGCAAGAGACAAATGTTCAAATGTGGATATTTTTTCAGTATGTAAAGCAGAATTTCAAAAATTTACTCGTCATCTGTCAGCATATGTTTTGTGAAGAGTTCCTGTACTTTATGGTTTAACAGAGAAAACGTGTCCGCTGTGCAGAACTGTGATTCAGACATATAAACAAATGGAAAGATGAAACAATGTACTTGATCACATTTTCAAATATATT

>RNFT1_x2
ATGCAAGCCAACTATAGCCCACTGCACAGTCCTCCAGGAGCTGCAGGCAGTGAAGATGCCTCAGCCTCCCAATGTGTCCATACAAGATTGACAGAAAGTTCTTGTCGTCATTCTGGAGATGTGCATATCCAGATAAACTCCATACCTAAAGAATGTGCTGAAAATCCAAGCTCCAGAAATACAAGGTCAGGTGTCCATAGCTGTACCCATGGATGTGTACACAGTCGCTCACGGATTCACTCCCATAACGAAGCAAGGCAGCCTGATGATACTGCCATGGAGTATGGAGATCATAATAGTAGCTCCTTCTCAGAATTCCGGTATCTCTTTAAGTGGCTGCAAAAAAGCCTTCCATATATTTTGATTCTGGGTGTCAAACTTGTTATGCAGCATATAACAGGAATTTCTGTTGGAATTGGGCTGCTTACAACTTTTATGTATGCAAACAAAAGCATTGTAAATCAGGTTTTTCTAAGAGAAAGGTGCTCAAAGATTCAATGTGCTTGGTTACTGGTATTCTTAGCAGGATCTTCTGTTCTTTTATATTACACCTTTCATTCTCAGTCACTTTATTACAGCTTAATTTTTTTAAATCCTGCTTTGGACCATTCAAGCTTCTGGGAAGTACTTTGGATTGTTGGAATTACAGACTTCATTCTGAAATTCCTCTTCATGGGCTTAAAATGCCTTATTTTATTGGTGCCTTCTTTCATCATGCCTTTTAAATCCAAGGGTTACTGGTATATGCTTTTAGAAGAATTATGTCAGTATTACCGAACTTTTGTTCCCATACCAGTTTGGTTTCGTTACCTTATAAGCTATGGGGACTTTGGTAATGTAACTAGATGGAGTCTTGGGATATTGCTGGCTTTACTCTACCTCATACTGAAACTTTTGGACTTTTTTGGACATCTAAGAACTTTCAGACGGGTTTTGCAAATATTTTTTATACGACCAAGTTACGGAGTGGCTGCCAGCAAGAGACAATGTGCAGATGTGGATGATATTTGTTCAATATGTCAAGCTGAATTTCAAAAGCCAGTTCTTCTCATCTGTCAGCATATATTTTGTGAAGAGTGCATTACCTTATGGTTTAACAGAGAGAAAACATGTCCACTGTGCAGAATTGTGATTTCAGACCATATAAACAAATGGAAAGATGGAGCTACTTCATCACACCTTCAAATATATTAA

>RNFT1_x2 

ATGCAAGCCAACTATAGCCCACTGCACAGTCCTCCAGGAGCTGCAGGCAGTGAAGATGCCTCAGCCTCCCAATGTGTCCATACAAGATTGACAGAAAGTTCTTGTCGTCATTCTGGAGATGTGCATATCCAGATAAACTCCATACCTAAAGAATGTGCTGAAAATCCAAGCTCCAGAAATACAAGGTCAGGTGTCCATAGCTGTACCCATGGATGTGTACACAGTCGCTCACGGATTCACTCCCATAACGAAGCAAGGCAGCCTGATGATACTGCCATGGAGTATGGAGATCATAATAGTAGCTCCTTCTCAGAATTCCGGTATCTCTTTAAGTGGCTGCAAAAAAGCCTTCCATATATTTTGATTCTGGGTGTCAAACTTGTTATGCAGCATATAACAGGAATTTCTGTTGGAATTGGGCTGCTTACAACTTTTATGTATGCAAACAAAAGCATTGTAAATCAGGTTTTTCTAAGAGAAAGGTGCTCAAAGATTCAATGTGCTTGGTTACTGGTATTCTTAGCAGGATCTTCTGTTCTTTTATATTACACCTTTCATTCTCAGTCACTTTATTACAGCTTAATTTTTTTAAATCCTGCTTTGGACCATTCAAGCTTCTGGGAAGTACTTTGGATTGTTGGAATTACAGACTTCATTCTGAAATTCCTCTTCATGGGCTTAAAATGCCTTATTTTATTGGTGCCTTCTTTCATCATGCCTTTTAAATCCAAGGGTTACTGGTATATGCTTTTAGAAGAATTATGTCAGTATTACCGAACTTTTGTTCCCATACCAGTTTGGTTTCGTTACCTTATAAGCTATGGGGACTTTGGTAATGTAACTAGATGGAGTCTTGGGATATTGCTGGCTTTACTCTACCTCATACTGAAACTTTTGGACTTTTTTGGACATCTAAGAACTTTCAGACGGGTTTTGCAAATATTTTTTATACGACCAAGTTACGGAGTGGCTGCCAGCAAGAGACAATGTGCAGATGTGGATGATATTTGTTCAATATGTCAAGCTGAATTTCAAAAGCCAGTTCTTCTCATCTGTCAGCATATATTTTGTGAAGAGTGCATTACCTTATGGTTTAACAGAGAGAAAACATGTCCACTGTGCAGAATTGTGATTTCAGACCATATAAACAAATGGAAAGATGGAGCTACTTCATCACACCTTCAAATATATTAA

Publications

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