RCPedia: Rtcs

Summary

Retrocopy Name	AMTP1	Plot displaying the genomic locations of a retrocopy (in chr4) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr4:83247170-83248964 UCSC
Coordinates (T2T)	chr4:86577265-86579059 UCSC
Coordinates (hg19)	chr4:84168323-84170117 UCSC
Strand	+
Parental Sequence	NM_001164711.2
Parental seq. overlap	1541 bp
Parental seq. overlap (%)	83.4%
Genomic Region	Intergenic
Retrocopy Summary	AMTP1, located on chr4:83247170-83248964, is a retrocopy of the parental gene AMT. 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	AMT
Full Name	aminomethyltransferase
Also known as	GCE\|GCST\|GCVT\|NKH
Coordinate	chr3:49416778-49422473
Strand	-
Gene summary	This gene encodes one of four critical components of the glycine cleavage system. Mutations in this gene have been associated with glycine encephalopathy. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	AMTP1
Bonobo	Pan paniscus	AMTP1
Gorilla	Gorilla gorilla	AMTP1
Orangutan	Pongo abelii	AMTP1
Gibbon	Nomascus leucogenys	AMTP1
Green monkey	Chlorocebus sabaeus	AMTP1
Crab-eating macaque	Macaca fascicularis	AMTP1
Rhesus	Macaca mulatta	AMTP1
Baboon	Papio anubis	AMTP1
Golden snub-nosed monkey	Rhinopithecus roxellana	AMTP1
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

The Genotype-Tissue Expression project - (GTEx)

Related Sequence

>AMTP1
GAGGCGACAATGCAGTGGGCTGTGAGCACGGTGGCCAATCGGGGTTTTCTCCTGCAGGCATTCCCTCCTGCCTTGTGTCATCTGCTTAGTTGTGCACAGACCGAGATACGTGGTGGTGACCCGGTGAAGCTGATGCAGAGTCTAGTGGTTGGAGACACTGCAGAGCTGAGGCCAAACCAGAGGACACTGTTGCTGTTTACCAATGAGGCTGGAGGCACCTTAGATGACTTGATTGTGACCAGCACTTCTGAGGGGCACCTACATGTGATGTCCAACACTGGCTGCTGGGAAAAAGACTTGGCCTTCATGCAGGACAAGGTCAGAGAACTTTAGAGGCAGGGCAGAGATGTGGGCCTGGAGGTAGTGGATACTGCCCTGCTAGCCCTGAAAGGGCCCCCTGTGGCCCAGGTGCTACAGGCCAGCACGGCAGCTGACCTGAGGAAACTGCCTTCATGACTAGTGCTGTGATGGAGGTGTTTGACGTGTCTGGCCGCCACCTTACACACTGTGGCTGCACAGGAGAGAATGGTGTGGACATCTTGGTGCCAGCAGCGGGGGCAGTTCACCCCGCATCAGCTCTTCTGGAAAACCCAGAGGCAAAGCTGGCAGTGCTGGCAGCTTGCGCCTGGAGGCAGGCCTCCGGCTGTACAGGAGTGACACTGATGAACACACTACCCCTGTGGAGGGCAGCCTCAGTTGGACATTGGGGAAGTGCCACTGAGCTGCTCTCGACTTCCCTGGAGCCAAGGTCATTGTTCCCCAGCTGAAGGGAAAGTGCAGTGGAGGCGTGTGGGGTTGATGTGTGAGGGGGCCCTGATGCAGGCACACAGTCCCACCTGAGCATGGAGGGCCCATGATTGGTACTGTGACCAGTGGCTGTCCCTTGCCCTACCTGAAGAAGACTGTGGCAATGAGTTACATGCCCTGCCAGTAGTCAGCCAGGGATAATGCTGCTGGTAGAGGTGCGGCAGAAGCAGCAGATGGGCGCAGTCAGCAAGATGCCCTTTGCGCCCATGAACTGCTCTACCCTCATGTGAGGATGGCTCAGGGCAGGACCATCCCCTCCAGAAGTCTTGCCCTAGAGGGCATTCTACAAGGGCTTAGGCAGGAAGCTGAGGCAGAACTCACTGGGGGTGGGCAGCTAAGGGGCAGGTTGGTTTTAGTTGTCTGGTTAAGGGGGCCATACCACCTACTCTCTCCACCCAACCCATGGCCACTCCAGCTCCAGGACCCTGTTTCTGAGCGACAGACCAGCCATTCAATGTCTTCTTTCGGTCCATGATCCCACTGACCCACTCTAGCCTGATGGAGGGAAATGAGCAGCTCTGGTTCTGCTATCTCTCCCACTCTGCCAGGTGCTGGCTGTGGCACAAAGGCTCGCCTTTGTGGGGAGGATAAAACCTGCCCAACCTGCCTCACCTTGGTTATTCGCATTGCAAGGAGTCATTACCATGGGCAATATGGGCTCAGGCCACTCCTTCCAGTTTGCTTTCCATAAATGCAAACTGTCCCTACCGTGAGTCAGGAATGACTCCTGACTCACAGTGGGGCTGCTGTAAACTTGGGGATGGTTGAGGGAACACAGACACAGTCTTCCATGCTCCCCAGGTGGTCCAGCCTGCTGCCCAGAAGCAAACCATGGCAGGCTCACCACCGGTTCTATGCCGCAGGGCTGTTGTAGGACAGGCTGGGCTTTCTCCTGGACTCACCTTACCCTGGGCTGACCTTTGCCCCTGGTATCCAATAATGGCCTCCACTAAATCCTGAAAAAAAAATTAAACACACTTCCTTCTTA

>NM_001164711.2
GTCTGCACTCGTTGCAGGCGACGATGCAGAGGGCTGTAAGTGTGGTGGCCCGTCTGGGCTTTCGCCTGCAGGCATTCCCCCCGGCCTTGTGTCGTCCACTTAGTTGCGCACAGACCAAGATACTTGGTAGTGACCGGGTGAAGCTGATGGAGAGTCTAGTGGTTGGAGACATTGCAGAGCTAAGACCAAACCAGGGGACACTGTCGCTGTTTACCAACGAGGCTGGAGGCATCTTAGATGACTTGATTGTAACCAATACTTCTGAGGGCCACCTGTATGTGGTGTCCAACGCTGGCTGCTGGGAGAAAGATTTGGCCCTCATGCAGGACAAGGTCAGGGAGCTTCAGAACCAGGGCAGAGATGTGGGCCTGGAGGTGTTGGATAATGCCCTGCTAGCTCTGCAAGGCCCCACTGCAGCCCAGGTACTACAGGCCGGCGTGGCAGATGACCTGAGGAAACTGCCCTTCATGACCAGTGCTGTGATGGAGGTGTTTGGCGTGTCTGGCTGCCGCGTGACCCGCTGTGGCTACACAGGAGAGGATGGTGTGGAGATCTCGGTGCCGGTAGCGGGGGCAGTTCACCTGGCAACAGCTATTCTGAAAAACCCAGAGGTGAAGCTGGCAGGGCTGGCAGCCAGGGACAGCCTGCGCCTGGAGGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACACCTGTGGAGGGCAGCCTCAGTTGGACACTGGGGAAGCGCCGCCGAGCTGCTATGGACTTCCCTGGAGCCAAGGTCATTGTTCCCCAGCTGAAGGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGGGGGCCCCCATGCGGGCACACAGTCCCATCCTGAACATGGAGGGTACCAAGATTGGTACTGTGACTAGTGGCTGCCCCTCCCCCTCTCTGAAGAAGAATGTGGCGATGGGTTATGTGCCCTGCGAGTACAGTCGTCCAGGGACAATGCTGCTGGTAGAGGTGCGGCGGAAGCAGCAGATGGCTGTAGTCAGCAAGATGCCCTTTGTGCCCACAAACTACTATACCCTCAAGTGAAGCTGGCTCAGGGTGGGGCTGTCCCTTCCAGGAGTTTTGCCCCTACAAGGGGTTAGTCAAGAAGCTGAGGCAGAACTCACTGGGGGTGGGCAGTTAAGGTGGAGGCTGATTCTAATTGTCTGGTTGAGGGGCCACACCACCTATTCCCCCCACCTAACTCATGCCATTCCAGCTTCCTTCAGGACCCTGCTTCTGAGTGACGGACCAGCTCACACAATGTCTTGTTTCAGTCCATGATCCCACTGACCTACTCTTGCCTGCTGGAGGGTAATGAGAAGCTTTGGTTCTGCCATCTCTCCCACTCTGCCAGGTGCTGGCTGTGGAGCAAAGGctcacctttgtggagaggataaaacctgcccaacctacctcaccatggtttttCACATTGCAAAGGGTAATAACATGGGCAGTGCGGACTTAGGCTACCCCCTCCAGTTTGCTTTCCGTAAATGCAAATTGTCCTTACTGCAAGTCAGGAATGATTGCTGACTCACAGTAGGGCTGCTATGCCTGTGTGTAAACTTGGGGATGGCTGAGGGAACATAGACTCACTCTTCCACATTCCCAAGTTGGTCTAGTGTGCTGCCCAGTAGCAAACCATGGCAGACTCACCACCTATTCTGAGTTCCAGGGCTGCTGTAGGGCAGGGTGGGCTTCCTCCCAGACTTGCCTTACCCTGGGCTGATCTTTGCCCCTGGTATGCATTAATGGACTCCACTGAATCCTGAAAAAAAAATTAAACTTCCTTCTTACTTGCCA

>NM_001164711.2 

GTCTGCACTCGTTGCAGGCGACGATGCAGAGGGCTGTAAGTGTGGTGGCCCGTCTGGGCTTTCGCCTGCAGGCATTCCCCCCGGCCTTGTGTCGTCCACTTAGTTGCGCACAGACCAAGATACTTGGTAGTGACCGGGTGAAGCTGATGGAGAGTCTAGTGGTTGGAGACATTGCAGAGCTAAGACCAAACCAGGGGACACTGTCGCTGTTTACCAACGAGGCTGGAGGCATCTTAGATGACTTGATTGTAACCAATACTTCTGAGGGCCACCTGTATGTGGTGTCCAACGCTGGCTGCTGGGAGAAAGATTTGGCCCTCATGCAGGACAAGGTCAGGGAGCTTCAGAACCAGGGCAGAGATGTGGGCCTGGAGGTGTTGGATAATGCCCTGCTAGCTCTGCAAGGCCCCACTGCAGCCCAGGTACTACAGGCCGGCGTGGCAGATGACCTGAGGAAACTGCCCTTCATGACCAGTGCTGTGATGGAGGTGTTTGGCGTGTCTGGCTGCCGCGTGACCCGCTGTGGCTACACAGGAGAGGATGGTGTGGAGATCTCGGTGCCGGTAGCGGGGGCAGTTCACCTGGCAACAGCTATTCTGAAAAACCCAGAGGTGAAGCTGGCAGGGCTGGCAGCCAGGGACAGCCTGCGCCTGGAGGCAGGCCTCTGCCTGTATGGGAATGACATTGATGAACACACTACACCTGTGGAGGGCAGCCTCAGTTGGACACTGGGGAAGCGCCGCCGAGCTGCTATGGACTTCCCTGGAGCCAAGGTCATTGTTCCCCAGCTGAAGGGCAGGGTGCAGCGGAGGCGTGTGGGGTTGATGTGTGAGGGGGCCCCCATGCGGGCACACAGTCCCATCCTGAACATGGAGGGTACCAAGATTGGTACTGTGACTAGTGGCTGCCCCTCCCCCTCTCTGAAGAAGAATGTGGCGATGGGTTATGTGCCCTGCGAGTACAGTCGTCCAGGGACAATGCTGCTGGTAGAGGTGCGGCGGAAGCAGCAGATGGCTGTAGTCAGCAAGATGCCCTTTGTGCCCACAAACTACTATACCCTCAAGTGAAGCTGGCTCAGGGTGGGGCTGTCCCTTCCAGGAGTTTTGCCCCTACAAGGGGTTAGTCAAGAAGCTGAGGCAGAACTCACTGGGGGTGGGCAGTTAAGGTGGAGGCTGATTCTAATTGTCTGGTTGAGGGGCCACACCACCTATTCCCCCCACCTAACTCATGCCATTCCAGCTTCCTTCAGGACCCTGCTTCTGAGTGACGGACCAGCTCACACAATGTCTTGTTTCAGTCCATGATCCCACTGACCTACTCTTGCCTGCTGGAGGGTAATGAGAAGCTTTGGTTCTGCCATCTCTCCCACTCTGCCAGGTGCTGGCTGTGGAGCAAAGGctcacctttgtggagaggataaaacctgcccaacctacctcaccatggtttttCACATTGCAAAGGGTAATAACATGGGCAGTGCGGACTTAGGCTACCCCCTCCAGTTTGCTTTCCGTAAATGCAAATTGTCCTTACTGCAAGTCAGGAATGATTGCTGACTCACAGTAGGGCTGCTATGCCTGTGTGTAAACTTGGGGATGGCTGAGGGAACATAGACTCACTCTTCCACATTCCCAAGTTGGTCTAGTGTGCTGCCCAGTAGCAAACCATGGCAGACTCACCACCTATTCTGAGTTCCAGGGCTGCTGTAGGGCAGGGTGGGCTTCCTCCCAGACTTGCCTTACCCTGGGCTGATCTTTGCCCCTGGTATGCATTAATGGACTCCACTGAATCCTGAAAAAAAAATTAAACTTCCTTCTTACTTGCCA

Publications

PMID - Link	Title
No publications available for this retrocopy