RCPedia: Rtcs

Summary

Retrocopy Name	TM2D1P1	Plot displaying the genomic locations of a retrocopy (in chr3) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr3:106325764-106325925 UCSC
Coordinates (T2T)	chr3:109044725-109044886 UCSC
Coordinates (hg19)	chr3:106044611-106044772 UCSC
Strand	-
Parental Sequence	NM_032027.3
Parental seq. overlap	138 bp
Parental seq. overlap (%)	14.2%
Genomic Region	Intergenic
Retrocopy Summary	TM2D1P1, located on chr3:106325764-106325925, is a retrocopy of the parental gene TM2D1. 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	TM2D1
Full Name	TM2 domain containing 1
Also known as	BBP
Coordinate	chr1:61681046-61725141
Strand	-
Gene summary	The protein encoded by this gene is a beta-amyloid peptide-binding protein. It contains a structural module related to that of the seven transmembrane domain G protein-coupled receptor superfamily and known to be important in heterotrimeric G protein activation. Beta-amyloid peptide has been established to be a causative factor in neuron death and the consequent diminution of cognitive abilities observed in Alzheimer's disease. This protein may be a target of neurotoxic beta-amyloid peptide, and may mediate cellular vulnerability to beta-amyloid peptide toxicity through a G protein-regulated program of cell death. Several transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	TM2D1P1
Bonobo	Pan paniscus	TM2D1P1
Gorilla	Gorilla gorilla	TM2D1P1
Gibbon	Nomascus leucogenys	TM2D1P1
Green monkey	Chlorocebus sabaeus	TM2D1P1
Baboon	Papio anubis	TM2D1P1
Orangutan	Pongo abelii	Without Homology
Crab-eating macaque	Macaca fascicularis	Without Homology
Rhesus	Macaca mulatta	Without Homology
Golden snub-nosed monkey	Rhinopithecus roxellana	Without Homology
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

>TM2D1P1
TTGGATGTATGGGAACAGATGTATTTTACCTTGGATACTTTGCCTTGGGTGTGTTAAAGTTTTTCCTGTAGAGTTTTGTAAAATTGGGAACCTAATTGACATAGTTTTATTTCAATACAGATCGTTGTACCTTCACATAGAAGTACTTACATTATAGATTAT

>NM_032027.3
GAGAAAGTGTCGGTCTCCAAGATGGCGGCCGCCTGGCCGTCTGGTCCGTCTGCTCCGGAGGCCGTGACGGCCAGACTCGTTGGTGTCCTGTGGTTCGTCTCAGTCACTACAGGACCCTGGGGGGCTGTTGCCACCTCCGCCGGGGGCGAGGAGTCGCTTAAGTGCGAGGACCTCAAAGTGGGACAATATATTTGTAAAGATCCAAAAATAAATGACGCTACGCAAGAACCAGTTAACTGTACAAACTACACAGCTCATGTTTCCTGTTTTCCAGCACCCAACATAACTTGTAAGGATTCCAGTGGCAATGAAACACATTTTACTGGGAACGAAGTTGGTTTTTTCAAGCCCATATCTTGCCGAAATGTAAATGGCTATTCCTACAAAGTGGCAGTCGCATTGTCTCTTTTTCTTGGATGGTTGGGAGCAGATCGATTTTACCTTGGATACCCTGCTTTGGGTTTGTTAAAGTTTTGCACTGTAGGGTTTTGTGGAATTGGGAGCCTAATTGATTTCATTCTTATTTCAATGCAGATTGTTGGACCTTCAGATGGAAGTAGTTACATTATAGATTACTATGGAACCAGACTTACAAGACTGAGTATTACTAATGAAACATTTAGAAAAACGCAATTATATCCATAAATATTTTTTAAAAGAAACAGATTTGAGCCTCCTTGATTTTAATAGAGAACTTCTAGTGTATGGATTTAAAGATTTCTCTTTTTCATTCATATACCATTTTATGAGTTCTGTATAATTTTTTGTGGTTTTTGTTTTGTTGAGTTAAAGTATATTATTGTGAGATTTATTTAATAGGACTTCCTTTGAAAGCTGTATAATAGTGTTTCTCGGGCTTCTGTCTCTATGAGAGATAGCTTATTACTCTGATACTCTTTAATCTTTTACAAAGGCAAGTTGCCACTTGTCATTTTTGTTTCTGAAAAATAAAAGTATAACTTATTCACA

>NM_032027.3 

GAGAAAGTGTCGGTCTCCAAGATGGCGGCCGCCTGGCCGTCTGGTCCGTCTGCTCCGGAGGCCGTGACGGCCAGACTCGTTGGTGTCCTGTGGTTCGTCTCAGTCACTACAGGACCCTGGGGGGCTGTTGCCACCTCCGCCGGGGGCGAGGAGTCGCTTAAGTGCGAGGACCTCAAAGTGGGACAATATATTTGTAAAGATCCAAAAATAAATGACGCTACGCAAGAACCAGTTAACTGTACAAACTACACAGCTCATGTTTCCTGTTTTCCAGCACCCAACATAACTTGTAAGGATTCCAGTGGCAATGAAACACATTTTACTGGGAACGAAGTTGGTTTTTTCAAGCCCATATCTTGCCGAAATGTAAATGGCTATTCCTACAAAGTGGCAGTCGCATTGTCTCTTTTTCTTGGATGGTTGGGAGCAGATCGATTTTACCTTGGATACCCTGCTTTGGGTTTGTTAAAGTTTTGCACTGTAGGGTTTTGTGGAATTGGGAGCCTAATTGATTTCATTCTTATTTCAATGCAGATTGTTGGACCTTCAGATGGAAGTAGTTACATTATAGATTACTATGGAACCAGACTTACAAGACTGAGTATTACTAATGAAACATTTAGAAAAACGCAATTATATCCATAAATATTTTTTAAAAGAAACAGATTTGAGCCTCCTTGATTTTAATAGAGAACTTCTAGTGTATGGATTTAAAGATTTCTCTTTTTCATTCATATACCATTTTATGAGTTCTGTATAATTTTTTGTGGTTTTTGTTTTGTTGAGTTAAAGTATATTATTGTGAGATTTATTTAATAGGACTTCCTTTGAAAGCTGTATAATAGTGTTTCTCGGGCTTCTGTCTCTATGAGAGATAGCTTATTACTCTGATACTCTTTAATCTTTTACAAAGGCAAGTTGCCACTTGTCATTTTTGTTTCTGAAAAATAAAAGTATAACTTATTCACA

Publications

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