RCPedia: Rtcs

Summary

Retrocopy Name	TPM3P2	Plot displaying the genomic locations of a retrocopy (in chr20) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr20:33910747-33913397 UCSC
Coordinates (T2T)	chr20:35637102-35639759 UCSC
Coordinates (hg19)	chr20:32498553-32501203 UCSC
Strand	-
Parental Sequence	NM_153649.4
Parental seq. overlap	1401 bp
Parental seq. overlap (%)	39.1%
Genomic Region	Intergenic
Retrocopy Summary	TPM3P2, located on chr20:33910747-33913397, is a retrocopy of the parental gene TPM3. 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	TPM3
Full Name	tropomyosin 3
Also known as	CAPM1\|CFTD\|HEL-189\|HEL-S-82p\|NEM1\|OK/SW-cl.5\|TM-5\|TM3\|TM30\|TM30nm\|TM5\|TPM3nu\|TPMsk3\|TRK\|hscp30
Coordinate	chr1:154155308-154192100
Strand	-
Gene summary	This gene encodes a member of the tropomyosin family of actin-binding proteins. Tropomyosins are dimers of coiled-coil proteins that provide stability to actin filaments and regulate access of other actin-binding proteins. Mutations in this gene result in autosomal dominant nemaline myopathy and other muscle disorders. This locus is involved in translocations with other loci, including anaplastic lymphoma receptor tyrosine kinase (ALK) and neurotrophic tyrosine kinase receptor type 1 (NTRK1), which result in the formation of fusion proteins that act as oncogenes. There are numerous pseudogenes for this gene on different chromosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2013]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	TPM3P9
Bonobo	Pan paniscus	TPM3P9
Gorilla	Gorilla gorilla	TPM3P9
Orangutan	Pongo abelii	TPM3P9
Gibbon	Nomascus leucogenys	TPM3P3
Green monkey	Chlorocebus sabaeus	TPM3P1
Crab-eating macaque	Macaca fascicularis	TPM3P5
Rhesus	Macaca mulatta	TPM3P5
Baboon	Papio anubis	TPM3P7
Golden snub-nosed monkey	Rhinopithecus roxellana	TPM3P8
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

>TPM3P2
GTGACCAAATTAAGACGGTGAGACCTCTGAGACCAAATTTCTGTCCCATCTCCACCCCATTCCCAGCCGCTTACAGAGTGGATCATGTGCCCCTTACATTGAGGTGACCACTTGATTGCTCTCCTGCCTCCTTGAAAGAAAGAAGATTATGTTTTTGCCACTGATTTAGCCACATGAAACTCATCTCATCACCCTTTTCTGGGTTTGAAGCTGCTGTCTCTAAAAGTGCCATGTCATTGTGCTTTGTATCAGTCAGTGAGAAATCTTGAATAGCTTGTGTACAAAACTTTTTAAATGTCATATTATTTTGAAACTTTGCTTCTTTGGGTTTCTGGCACCCTGGCTACCCCCTCTGGCTGTGAGAGCTCTCCACAGTCTGTAGGCTGGCAGGTTGCTGATCTTTTAAAGTTTCTTTCCCTACCTAATCCCCACTTTTTGGTAAAGTTTCTAGGAGGTCTGTTAGGCGTACAAACTGCAGCTTATTGGCTTACAATGTACTCTCCTTTGATGCCTCTTTGACGACAACTGGGAGAAAAAGAAATCAATAGTGCAACTGTTTTGATACTGAAGACTGATGAGTGTCTTTTTGAAATAAAGAACCACTCCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGATAGGTAGGAAGCATGAAGATGGGGCTCGGCTCATAAGTTGGTGGTTGTTGAAGGAAACTTGGGACGCAGAGAGGAACAACCTGAGCTGGCAGAGTCCTGTGGCTGAGAGATGGAGGAGCAGATCAGATCGATGGACCAGAACCTGAAGTGGCTGAGTGCTGCCGAAGAAAAGGACTCTCAAAAAGAAGACAGATATGAGGAAGCAACTGAGATTCTTACTGATAAACGCAAGGAGGCAGAGACCCGGGCTGAGTTTGCCGAGAGATCGGTAGCCAAGCTGGAAGAGACAATTGATGACTTGGAAGATAAACTGAAATGCACCAAGGAGGAGCACCTCTGTACACAAAGGATGCCAGACCAGACCTGCTTAACTGAATGAGATGCAGAGCACCCCAGTCCCACCTTGCCACTGCTCCTCCCTCTGACCCCAACTCCAACTAGGCCAGCCTGCCCAAAGCTGCCCTTTAACTGAGGGTTGATCTTTAACTGGAAGGCTGCTTTCTCCTTTCACCACCCCTACCTCCCCCACGTGTCTTTTTTGCCAAACTGTCTCTGCCTCTTCCCAGAGATTCCAGCTGCGCTAGAGGCTGAGCACCTTTGGGAACAACATTTAAGCGAATGTGAGTGCAACACATAATGTCTTTAAAAGCATGTTGTGTTGTATACATTTAGTAATTACCTTTTTTGTTGTTTTATAGCAACCATTTGTAAAACATTCCAAATAGTTCCACAGCTCTGAAGCAGCAATCTAATCCCTTTCTCCCTTTTGGAAGGTGACTGTTTAGCTTACTGTATATTGCTTTCTCTAGAAAAAAGGGAAAAAGGTATGAGCCTGCCTTACTGAGAACCAAACAGAGCCCGGGGAAAGACTCCACTCTGGGAAATCATAGCTTTGCACAAAGTACCAGCCAAACCAGAAAGGTGATTCCAGGAGTTAGCCCAAAAACAACAGCAACAAAAAATGTGCTGTTCAGGTTTTCAGCTTTAAGATATCTTTGGACAAAGTTATTTTTACTTTTTTGTTTTTTCATTAGAAGTGACCAAATTAAGAGGCAGGACCTGGAGCACAAGCAGGGGCTGGGTGGGCACCGTGGCTGGGATCGCCACCATCAAGGCAGTAAAGCGCAAGAGCCAGGTTCAGCAGCAGCAGGCAGATGATGCAGAGGAGAGAGCTAAGCGCCTCCAGCGGGGAGTAGAGGGAGCAAGGTGGGCCCGGAACAGGCTGAGGCCAAGGTGGCCTCCTTGAACCATAGGATCCAGCTGGTTGAAAAGGAGCTGGACAGTGCTCAGGCGTGCCTGGCCACTGCTCTGCAAAAGCTGGAAGAAGTGGTAAAAGCTGCTGATTGAGAGTGGGAGAGGTAGGAAGGTTATTGAAAATCGAGCCTTAAAAGATGAAGAAAAg

>NM_153649.4
ATTTCAGGGCGTAGCAGGCGGAAGTAAGGGTGAGAGGAGGCTGCAACGCCGAGCGGAGGAGGCAGGAACCGGAGCGCGAGCAGTAGCTGGGTGGGCACCATGGCTGGGATCACCACCATCGAGGCGGTGAAGCGCAAGATCCAGGTTCTGCAGCAGCAGGCAGATGATGCAGAGGAGCGAGCTGAGCGCCTCCAGCGAGAAGTTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACCGTAGGATCCAGCTGGTTGAAGAAGAGCTGGACCGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCTGAAAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGGCCTTAAAAGATGAAGAAAAGATGGAACTCCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAGTATGAAGAGGTGGCTCGTAAGTTGGTGATCATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCAGATTAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGATAAATATGAGGAAGAAATCAAGATTCTTACTGATAAACTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTGAGAGATCGGTAGCCAAGCTGGAAAAGACAATTGATGACCTGGAAGATAAACTGAAATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGCTGGACCAGACCCTGCTTGACCTGAATGAGATGTAGAACGCCCCAGTCCCACCCTGCTGCTGCTCCTCCCTCTGACCCAGACTCCGCCTGAGGCCAGCCTGCGGGAAGCTGACCTTTAACTGAGGGCTGATCTTTAACTGGAAGGCTGCTTTCTCCTTTCACCACCCCCTCCTTCCCTGTGTCTTTTTCGCCAAACTGTCTCTGCCTCTTCCCGGAGAATCCAGCTGGGCTAGAGGCTGAGCACCTTTGGAAACAACATTTAAGGGAATGTGAGCACAATGCATAATGTCTTTAAAAAGCATGTTGTGATGTACACATTTTGTAATTACCTTTTTTGTTGTTTTGTAGCAACCATTTGTAAAACATTCCAAATAATTCCACAGTCCTGAAGCAGCAATCGAATCCCTTTCTCACTTTTGGAAGGTGACTTTTCACCTTAATGCATATTCCCCTCTCCATAGAGGAGAGGAAAAGGTGTAGGCCTGCCTTACCGAGAGCCAAACAGAGCCCAGGGAGACTCCGCTGTGGGAAACCTCATTGTTCTGTACAAAGTACTAGCTAAACCAGAAAGGTGATTCCAGGAGGAGTTAGCCAAACAACAACAAAAACAAAAAATGTGCTGTTCAAGTTTTCAGCTTTAAGATATCTTTGGATAATGTTATTTCTATTTTTTATTTTTTTCATTAGAAGTTACCAAATTAAGATGGTAAGACCTCTGAGACCAAAATTTTGTCCCATCTCTACCCCCTCACAACTGCTTACAGAATGGATCATGTCCCCCTTATGTTGAGGTGACCACTTAATTGCTTTCCTGCCTCCTTGAAAGAAAGAAAGAAAGAAGACTGTGTTTTTGCCACTGATTTAGCCATGTGAAACTCATCTCATTACCCTTTTCTGGGTTTGAAGCTGCTGTCTCTAGAAGTGCCATCTCAATTGTGCTTTGTATCAGTCAGTGCTGGAGAAATCTTGAATAGCTTATGTACAAAACTTTTTAAATTTTATATTATTTTGAAACTTTGCTTTGGGTTTGTGGCACCCTGGCCACCCCATCTGGCTGTGACAGCCTCTGCAGTCCGTGGGCTGGCAGTTTGTTGATCTTTTAAGTTTCCTTCCCTACCCAGTCCCCATTTTCTGGTAAGGTTTCTAGGAGGTCTGTTAGGTGTACATCCTGCAGCTTATTGGCTTAAAATGTACTCTCCTTTTATGTGGTCTCTTTGGGGCCGATTGGGAGAAAGAGAAATCAATAGTGCAACTGTTTTGATACTGAATATTGACAAGTGTCTTTTTGAAATAAAGAACCAGTCCCTCCAACCCTCAGACCTATTTGACTTTTATTTATTAAAACTAAATGTGCTTTCTCCACAGAAGCTATGAGGTTTGGGTTAAAAATAGCATCTTTGTGGGTGGTAGCAACAGGAtttattctttattattattatttttgagatgaagtttcattcttgttgcctgggctggagcgtaatggctcgatctcggctcactgcaacctccgcctcctggttcaagagattctcctgcctcagcctcccgagtagctgggattacaggcacctgccaccatgcccgggtaattttttatattttaagtagagacagggcttcaccatgttggccaggctggtctcgaactcctgaccttcaggtgatccacctgcctcagcttcccaaaatgctgggattacgggcgtgagccaccgcacccagcTGGAGCAACAGGATTTAATATAGAGCAAATGTTTAGTTTTATCATCTGTAAAATGGAGATAAGTATTGTCAGAGTAAACATGAAGATTAGAAAGAACACTTAATGTGCTGGGCCTTTTATAGGTTAACACTGACATCTCAGGCTGAACTATATACATTTTCCTTCACAACCATATCAATCCTTATAAACTATGGATTTATGCTCCTTAAAACAATATATAATGCTGATCACTACTATAAATGCGTGGTTTTAACCAACTGTACTGAAACAGCTTTGAGTTTATATTCTGTTTGGATATTTGGAGAAAACAACAAGTGCTCTCAAGAGTATTTGCTTAGAGGCCGGCTGTGTGAGTGGATAACTTTGAAAGCTGCTTTTGAGACGCCAGTGTCTGGCATTTCCTGCATTCTGGCCTGGAGGCCGGACGTGAATCTGACTTCTAGTAAAAATACACGGTTCCCTTGACAAAGTCGAGCTGTTTATCCCAGAGACTGCACAATTTTCCGTTGATAGGCATGGACCAATGCTAACTGGAAATCATTGCAAAAAGTTTTTTTGTCGGGCGGAGGGTGTGGTGTTAAGATAAACAGTGTGCAACAGAAGAAATTAAAACTGGAAGAAATTAAAGGGTTTTTTTTAGA

>NM_153649.4 

ATTTCAGGGCGTAGCAGGCGGAAGTAAGGGTGAGAGGAGGCTGCAACGCCGAGCGGAGGAGGCAGGAACCGGAGCGCGAGCAGTAGCTGGGTGGGCACCATGGCTGGGATCACCACCATCGAGGCGGTGAAGCGCAAGATCCAGGTTCTGCAGCAGCAGGCAGATGATGCAGAGGAGCGAGCTGAGCGCCTCCAGCGAGAAGTTGAGGGAGAAAGGCGGGCCCGGGAACAGGCTGAGGCTGAGGTGGCCTCCTTGAACCGTAGGATCCAGCTGGTTGAAGAAGAGCTGGACCGTGCTCAGGAGCGCCTGGCCACTGCCCTGCAAAAGCTGGAAGAAGCTGAAAAAGCTGCTGATGAGAGTGAGAGAGGTATGAAGGTTATTGAAAACCGGGCCTTAAAAGATGAAGAAAAGATGGAACTCCAGGAAATCCAACTCAAAGAAGCTAAGCACATTGCAGAAGAGGCAGATAGGAAGTATGAAGAGGTGGCTCGTAAGTTGGTGATCATTGAAGGAGACTTGGAACGCACAGAGGAACGAGCTGAGCTGGCAGAGTCCCGTTGCCGAGAGATGGATGAGCAGATTAGACTGATGGACCAGAACCTGAAGTGTCTGAGTGCTGCTGAAGAAAAGTACTCTCAAAAAGAAGATAAATATGAGGAAGAAATCAAGATTCTTACTGATAAACTCAAGGAGGCAGAGACCCGTGCTGAGTTTGCTGAGAGATCGGTAGCCAAGCTGGAAAAGACAATTGATGACCTGGAAGATAAACTGAAATGCACCAAAGAGGAGCACCTCTGTACACAAAGGATGCTGGACCAGACCCTGCTTGACCTGAATGAGATGTAGAACGCCCCAGTCCCACCCTGCTGCTGCTCCTCCCTCTGACCCAGACTCCGCCTGAGGCCAGCCTGCGGGAAGCTGACCTTTAACTGAGGGCTGATCTTTAACTGGAAGGCTGCTTTCTCCTTTCACCACCCCCTCCTTCCCTGTGTCTTTTTCGCCAAACTGTCTCTGCCTCTTCCCGGAGAATCCAGCTGGGCTAGAGGCTGAGCACCTTTGGAAACAACATTTAAGGGAATGTGAGCACAATGCATAATGTCTTTAAAAAGCATGTTGTGATGTACACATTTTGTAATTACCTTTTTTGTTGTTTTGTAGCAACCATTTGTAAAACATTCCAAATAATTCCACAGTCCTGAAGCAGCAATCGAATCCCTTTCTCACTTTTGGAAGGTGACTTTTCACCTTAATGCATATTCCCCTCTCCATAGAGGAGAGGAAAAGGTGTAGGCCTGCCTTACCGAGAGCCAAACAGAGCCCAGGGAGACTCCGCTGTGGGAAACCTCATTGTTCTGTACAAAGTACTAGCTAAACCAGAAAGGTGATTCCAGGAGGAGTTAGCCAAACAACAACAAAAACAAAAAATGTGCTGTTCAAGTTTTCAGCTTTAAGATATCTTTGGATAATGTTATTTCTATTTTTTATTTTTTTCATTAGAAGTTACCAAATTAAGATGGTAAGACCTCTGAGACCAAAATTTTGTCCCATCTCTACCCCCTCACAACTGCTTACAGAATGGATCATGTCCCCCTTATGTTGAGGTGACCACTTAATTGCTTTCCTGCCTCCTTGAAAGAAAGAAAGAAAGAAGACTGTGTTTTTGCCACTGATTTAGCCATGTGAAACTCATCTCATTACCCTTTTCTGGGTTTGAAGCTGCTGTCTCTAGAAGTGCCATCTCAATTGTGCTTTGTATCAGTCAGTGCTGGAGAAATCTTGAATAGCTTATGTACAAAACTTTTTAAATTTTATATTATTTTGAAACTTTGCTTTGGGTTTGTGGCACCCTGGCCACCCCATCTGGCTGTGACAGCCTCTGCAGTCCGTGGGCTGGCAGTTTGTTGATCTTTTAAGTTTCCTTCCCTACCCAGTCCCCATTTTCTGGTAAGGTTTCTAGGAGGTCTGTTAGGTGTACATCCTGCAGCTTATTGGCTTAAAATGTACTCTCCTTTTATGTGGTCTCTTTGGGGCCGATTGGGAGAAAGAGAAATCAATAGTGCAACTGTTTTGATACTGAATATTGACAAGTGTCTTTTTGAAATAAAGAACCAGTCCCTCCAACCCTCAGACCTATTTGACTTTTATTTATTAAAACTAAATGTGCTTTCTCCACAGAAGCTATGAGGTTTGGGTTAAAAATAGCATCTTTGTGGGTGGTAGCAACAGGAtttattctttattattattatttttgagatgaagtttcattcttgttgcctgggctggagcgtaatggctcgatctcggctcactgcaacctccgcctcctggttcaagagattctcctgcctcagcctcccgagtagctgggattacaggcacctgccaccatgcccgggtaattttttatattttaagtagagacagggcttcaccatgttggccaggctggtctcgaactcctgaccttcaggtgatccacctgcctcagcttcccaaaatgctgggattacgggcgtgagccaccgcacccagcTGGAGCAACAGGATTTAATATAGAGCAAATGTTTAGTTTTATCATCTGTAAAATGGAGATAAGTATTGTCAGAGTAAACATGAAGATTAGAAAGAACACTTAATGTGCTGGGCCTTTTATAGGTTAACACTGACATCTCAGGCTGAACTATATACATTTTCCTTCACAACCATATCAATCCTTATAAACTATGGATTTATGCTCCTTAAAACAATATATAATGCTGATCACTACTATAAATGCGTGGTTTTAACCAACTGTACTGAAACAGCTTTGAGTTTATATTCTGTTTGGATATTTGGAGAAAACAACAAGTGCTCTCAAGAGTATTTGCTTAGAGGCCGGCTGTGTGAGTGGATAACTTTGAAAGCTGCTTTTGAGACGCCAGTGTCTGGCATTTCCTGCATTCTGGCCTGGAGGCCGGACGTGAATCTGACTTCTAGTAAAAATACACGGTTCCCTTGACAAAGTCGAGCTGTTTATCCCAGAGACTGCACAATTTTCCGTTGATAGGCATGGACCAATGCTAACTGGAAATCATTGCAAAAAGTTTTTTTGTCGGGCGGAGGGTGTGGTGTTAAGATAAACAGTGTGCAACAGAAGAAATTAAAACTGGAAGAAATTAAAGGGTTTTTTTTAGA

Publications

PMID - Link	Title
No publications available for this retrocopy