RCPedia: Rtcs

Summary

Retrocopy Name	CALM2P2	Plot displaying the genomic locations of a retrocopy (in chr10) and its respective parental gene (in chr2). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr10:70163630-70164741 UCSC
Coordinates (T2T)	chr10:71032572-71033683 UCSC
Coordinates (hg19)	chr10:71923386-71924497 UCSC
Strand	+
Parental Sequence	NM_001743.6
Parental seq. overlap	1041 bp
Parental seq. overlap (%)	84.6%
Genomic Region	Intragenic (SAR1A)
Retrocopy Summary	CALM2P2, located on chr10:70163630-70164741, is a retrocopy of the parental gene CALM2. 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	CALM2
Full Name	calmodulin 2
Also known as	CALM\|CALML2\|CAM1\|CAM3\|CAMC\|CAMII\|CAMIII\|LQT15\|PHKD\|PHKD2\|caM
Coordinate	chr2:47160082-47176936
Strand	-
Gene summary	This gene is a member of the calmodulin gene family. There are three distinct calmodulin genes dispersed throughout the genome that encode the identical protein, but differ at the nucleotide level. Calmodulin is a calcium binding protein that plays a role in signaling pathways, cell cycle progression and proliferation. Several infants with severe forms of long-QT syndrome (LQTS) who displayed life-threatening ventricular arrhythmias together with delayed neurodevelopment and epilepsy were found to have mutations in either this gene or another member of the calmodulin gene family (PMID:23388215). Mutations in this gene have also been identified in patients with less severe forms of LQTS (PMID:24917665), while mutations in another calmodulin gene family member have been associated with catecholaminergic polymorphic ventricular tachycardia (CPVT)(PMID:23040497), a rare disorder thought to be the cause of a significant fraction of sudden cardiac deaths in young individuals. Pseudogenes of this gene are found on chromosomes 10, 13, and 17. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	CALM2P2
Bonobo	Pan paniscus	CALM2P1
Gorilla	Gorilla gorilla	CALM2P2
Orangutan	Pongo abelii	CALM2P5
Gibbon	Nomascus leucogenys	CALM2P6
Green monkey	Chlorocebus sabaeus	CALM2P3
Crab-eating macaque	Macaca fascicularis	CALM2P5
Rhesus	Macaca mulatta	CALM2P5
Baboon	Papio anubis	CALM2P4
Golden snub-nosed monkey	Rhinopithecus roxellana	CALM2P6
Marmoset	Callithrix jacchus	CALM2P3
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

>CALM2P2
TGAGCGAGCAGAGTGGTTGTGTGGTTGCGTCTCGGAAACCAGTAGCACTTGCAGCATGGCTGACCAACTGACTGAGGAGCAGATTGTAGAATTCAAAGAAGTTTTTTCACTATTTGACAAAGATGGTGATGGAACTATAACAACAAAGAAACTAGGAACTGTAATGAGGTCTCAGGCAGAATCCCACAGAAGCAGAGTTACAGGACATGATTAATGAAGTAGATGCTGATGGTAATGGCACAATTGACTTCCCTGAATTTCTGACAATGATGGCAAGAAAAATGAAAGACACAGACAGTGAAGAAGAAATTAGAGAAACATTCTGTGTGTTTGATAAGGATGGCAATGGCTATATTAGTGGTGTAGAACTTCACCATGTGATGACAAACCTTGGAGTGAAGTTAACAGATGAAGAAGTTGATTAAATGATCAGGGAAGCAGATCCTGATGGTGATGGTCAAGTAAACTATGAGTTTGTACAAATGATGACAGCATAATGAAGACCTTGTACAGAATGTGTTAAATTTCTTGCACAAAACTGTTTATTTGCCTTTTGTTTGTAACTTATCTGTAAAAGGCTTCTCCCTACTGTCAAAAAAAAATATGCATGTATGGTAATCAGGACTTCATTCCTCCATGTGTTCTTCCCTTACTGTCATTGCCCTGAAACCTTATTTTAGAAAACTGATGAAGTAACATGTTGCCTGTGGCTTACTCCGGATATATCTAAGCCCTTCTGCACATCTAAACTTAGGTGGAGTTGGTCAAATAAGGGAACATCCGGGTTATGCCTTTTTTTAAAGTAGTTTTCTTTAGGAACTGTCAGCATGGTGTTGAAGTATGGAGTTGTAACTCTGTGTGGACTACGGACAGCCAACAATATGTACTTAAAAGTTGCACTACTGCAGAATGGGTGTATTATCCAGGTACTCCCAGGTACCTCACACACTGTTTTTTCTGTACTGCTGGTCCTGTACCAGAAACATTTTCTTTTACTGTTACTTGCTTTTTAAACTTTGTTTAGCCACTTAAAGAAAATGTGCTTATGGCACAATTTGCCTCAAATCCATTCCAAGTTGTGTATTTGTTTTCCAATTAAAAAAATTACAATT

>NM_001743.6
AGTCCGAGTGGAGAGAGCGAGCTGAGTGGTTGTGTGGTCGCGTCTCGGAAACCGGTAGCGCTTGCAGCATGGCTGACCAACTGACTGAAGAGCAGATTGCAGAATTCAAAGAAGCTTTTTCACTATTTGACAAAGATGGTGATGGAACTATAACAACAAAGGAATTGGGAACTGTAATGAGATCTCTTGGGCAGAATCCCACAGAAGCAGAGTTACAGGACATGATTAATGAAGTAGATGCTGATGGTAATGGCACAATTGACTTCCCTGAATTTCTGACAATGATGGCAAGAAAAATGAAAGACACAGACAGTGAAGAAGAAATTAGAGAAGCATTCCGTGTGTTTGATAAGGATGGCAATGGCTATATTAGTGCTGCAGAACTTCGCCATGTGATGACAAACCTTGGAGAGAAGTTAACAGATGAAGAAGTTGATGAAATGATCAGGGAAGCAGATATTGATGGTGATGGTCAAGTAAACTATGAAGAGTTTGTACAAATGATGACAGCAAAGTGAAGACCTTGTACAGAATGTGTTAAATTTCTTGTACAAAATTGTTTATTTGCCTTTTCTTTGTTTGTAACTTATCTGTAAAAGGTTTCTCCCTACTGTCAAAAAAATATGCATGTATAGTAATTAGGACTTCATTCCTCCATGTTTTCTTCCCTTATCTTACTGTCATTGTCCTAAAACCTTATTTTAGAAAATTGATCAAGTAACATGTTGCATGTGGCTTACTCTGGATATATCTAAGCCCTTCTGCACATCTAAACTTAGATGGAGTTGGTCAAATGAGGGAACATCTGGGTTATGCCTTTTTTAAAGTAGTTTTCTTTAGGAACTGTCAGCATGTTGTTGTTGAAGTGTGGAGTTGTAACTCTGCGTGGACTATGGACAGTCAACAATATGTACTTAAAAGTTGCACTATTGCAAAACGGGTGTATTATCCAGGTACTCGTACACTATTTTTTTGTACTGCTGGTCCTGTACCAGAAACATTTTCTTTTATTGTTACTTGCTTTTTAAACTTTGTTTAGCCACTTAAAATCTGCTTATGGCACAATTTGCCTCAAAATCCATTCCAAGTTGTATATTTGTTTTCCAATAAAAAAATTACAATTTACCCAATGGTTGCTCTGCATCTGAGTCATTTAACTGTTGAAGTCTAATAATTTTGAAAATAAAATATGGCATTGGTTTCTGCTTGG

>NM_001743.6 

AGTCCGAGTGGAGAGAGCGAGCTGAGTGGTTGTGTGGTCGCGTCTCGGAAACCGGTAGCGCTTGCAGCATGGCTGACCAACTGACTGAAGAGCAGATTGCAGAATTCAAAGAAGCTTTTTCACTATTTGACAAAGATGGTGATGGAACTATAACAACAAAGGAATTGGGAACTGTAATGAGATCTCTTGGGCAGAATCCCACAGAAGCAGAGTTACAGGACATGATTAATGAAGTAGATGCTGATGGTAATGGCACAATTGACTTCCCTGAATTTCTGACAATGATGGCAAGAAAAATGAAAGACACAGACAGTGAAGAAGAAATTAGAGAAGCATTCCGTGTGTTTGATAAGGATGGCAATGGCTATATTAGTGCTGCAGAACTTCGCCATGTGATGACAAACCTTGGAGAGAAGTTAACAGATGAAGAAGTTGATGAAATGATCAGGGAAGCAGATATTGATGGTGATGGTCAAGTAAACTATGAAGAGTTTGTACAAATGATGACAGCAAAGTGAAGACCTTGTACAGAATGTGTTAAATTTCTTGTACAAAATTGTTTATTTGCCTTTTCTTTGTTTGTAACTTATCTGTAAAAGGTTTCTCCCTACTGTCAAAAAAATATGCATGTATAGTAATTAGGACTTCATTCCTCCATGTTTTCTTCCCTTATCTTACTGTCATTGTCCTAAAACCTTATTTTAGAAAATTGATCAAGTAACATGTTGCATGTGGCTTACTCTGGATATATCTAAGCCCTTCTGCACATCTAAACTTAGATGGAGTTGGTCAAATGAGGGAACATCTGGGTTATGCCTTTTTTAAAGTAGTTTTCTTTAGGAACTGTCAGCATGTTGTTGTTGAAGTGTGGAGTTGTAACTCTGCGTGGACTATGGACAGTCAACAATATGTACTTAAAAGTTGCACTATTGCAAAACGGGTGTATTATCCAGGTACTCGTACACTATTTTTTTGTACTGCTGGTCCTGTACCAGAAACATTTTCTTTTATTGTTACTTGCTTTTTAAACTTTGTTTAGCCACTTAAAATCTGCTTATGGCACAATTTGCCTCAAAATCCATTCCAAGTTGTATATTTGTTTTCCAATAAAAAAATTACAATTTACCCAATGGTTGCTCTGCATCTGAGTCATTTAACTGTTGAAGTCTAATAATTTTGAAAATAAAATATGGCATTGGTTTCTGCTTGG

Publications

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