RCPedia: Rtcs

Summary

Retrocopy Name	NENFP2	Plot displaying the genomic locations of a retrocopy (in chr12) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr12:101963999-101964473 UCSC
Coordinates (T2T)	chr12:101925119-101925593 UCSC
Coordinates (hg19)	chr12:102357777-102358251 UCSC
Strand	+
Parental Sequence	NM_013349.5
Parental seq. overlap	399 bp
Parental seq. overlap (%)	43.4%
Genomic Region	Intergenic
Retrocopy Summary	NENFP2, located on chr12:101963999-101964473, is a retrocopy of the parental gene NENF. 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	NENF
Full Name	neudesin neurotrophic factor
Also known as	CIR2\|SCIRP10\|SPUF
Coordinate	chr1:212432920-212446379
Strand	+
Gene summary	This gene encodes a neurotrophic factor that may play a role in neuron differentiation and development. A pseudogene of this gene is found on chromosome 12. Alternate splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2009]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	NENFP3
Bonobo	Pan paniscus	NENFP3
Gorilla	Gorilla gorilla	NENFP2
Orangutan	Pongo abelii	NENFP3
Gibbon	Nomascus leucogenys	NENFP1
Green monkey	Chlorocebus sabaeus	NENFP1
Crab-eating macaque	Macaca fascicularis	NENFP3
Rhesus	Macaca mulatta	NENFP3
Baboon	Papio anubis	NENFP3
Golden snub-nosed monkey	Rhinopithecus roxellana	NENFP1
Marmoset	Callithrix jacchus	NENFP2
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

>NENFP2
GGATCAGCCCATCTATTTGGCAGTGAAGGGAGTGGGGCTTGATGTCACCTCTGGAAAGGGGTTTTATGGACAAAGAGCCCCCTACAATGCCTTGACCAGGAAGGACTCTGCTAGAGGGGTAGCCAAGGTGTCCTTGGATCATGTAGACCTTACCTGTGACACACCACAGGTCTCATAGCCAAGAAGTTGTAGTCCATGGATGATGTCTTCACCAGTGTGTACAAAGCCAAACACCCAATTGTCAGCTACAGGGCTCAGACAATTCTCAATGAGTTTGGCAGCCCCAACCTGGACTTCAAGGCTGAAGACCAGCCCCTTTTTGACAAGAAGGAGGGGTTCTGAGGTTTCATCTGCAGGAGCAGGTTCTTGGGAGAGTGAGGTAGGAAGACATTCCAGCACTAAATTTCCTGCAAAACAGGCTGCCTAAAGCTTCTGACTTACCCAGGTTTGAATAAAACAGATGCTTAACCTGGAA

>NM_013349.5
cttgccttgcgctgcgcgctcaccatggtgggccccgcgccgcggcggcggctgcggccgctggcagcgctggccctggtcctggcgctggccccggggctgcccacagcccgggccGGGCAGACACCGCGCCCTGCCGAGCGGGGGCCCCCAGTGCGGCTTTTCACCGAGGAGGAGCTGGCCCGCTATGGCGGGGAGGAGGAAGATCAGCCCATCTACTTGGCAGTGAAGGGAGTGGTGTTTGATGTCACCTCCGGAAAGGAGTTTTATGGACGAGGAGCCCCCTACAATGCCTTGACGGGGAAGGACTCCACTAGAGGGGTAGCCAAGATGTCCTTGGATCCTGCAGACCTCACCCATGACACTACGGGTCTCACGGCCAAGGAACTGGAGGCCCTGGATGAGGTCTTCACCAAAGTGTACAAAGCCAAATACCCCATCGTCGGCTACACTGCCCGGAGAATTCTCAATGAGGATGGCAGCCCTAACCTGGACTTCAAGCCTGAAGACCAGCCCCATTTTGACATCAAGGATGAGTTCTGATGTTCCCCCTGCAGGAGCAGGTTCTTGGGAGCGTGAGGCAGGAAGACACTAGGTGCTGAATCTCCTGCAAAACTGGCTGCCTGGAGGCCCTGAGCCACCCAGATCTGAATAAAACAGATGCTTACCCTGGAAGAGCAAATGCCTCCTGTTGTCCTTGGTCAGGGGTTCTGTCTACCTGGGGACCCCTGTCTGCACACCAGGGATCAATAAGAGCCAAAGTGGGACACCTCCTAGATGTCAGTATCAGCTGGctgggcagtggaattttgagcgacctttactttatacttttctgtgcttgacagattttcagccatgaccatgttcactttataatcaaaacaaaaataaaggtcccatttttacaaaaGGA

>NM_013349.5 

cttgccttgcgctgcgcgctcaccatggtgggccccgcgccgcggcggcggctgcggccgctggcagcgctggccctggtcctggcgctggccccggggctgcccacagcccgggccGGGCAGACACCGCGCCCTGCCGAGCGGGGGCCCCCAGTGCGGCTTTTCACCGAGGAGGAGCTGGCCCGCTATGGCGGGGAGGAGGAAGATCAGCCCATCTACTTGGCAGTGAAGGGAGTGGTGTTTGATGTCACCTCCGGAAAGGAGTTTTATGGACGAGGAGCCCCCTACAATGCCTTGACGGGGAAGGACTCCACTAGAGGGGTAGCCAAGATGTCCTTGGATCCTGCAGACCTCACCCATGACACTACGGGTCTCACGGCCAAGGAACTGGAGGCCCTGGATGAGGTCTTCACCAAAGTGTACAAAGCCAAATACCCCATCGTCGGCTACACTGCCCGGAGAATTCTCAATGAGGATGGCAGCCCTAACCTGGACTTCAAGCCTGAAGACCAGCCCCATTTTGACATCAAGGATGAGTTCTGATGTTCCCCCTGCAGGAGCAGGTTCTTGGGAGCGTGAGGCAGGAAGACACTAGGTGCTGAATCTCCTGCAAAACTGGCTGCCTGGAGGCCCTGAGCCACCCAGATCTGAATAAAACAGATGCTTACCCTGGAAGAGCAAATGCCTCCTGTTGTCCTTGGTCAGGGGTTCTGTCTACCTGGGGACCCCTGTCTGCACACCAGGGATCAATAAGAGCCAAAGTGGGACACCTCCTAGATGTCAGTATCAGCTGGctgggcagtggaattttgagcgacctttactttatacttttctgtgcttgacagattttcagccatgaccatgttcactttataatcaaaacaaaaataaaggtcccatttttacaaaaGGA

Publications

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