RCPedia: Rtcs

Summary

Retrocopy Name	LSM3P5	Plot displaying the genomic locations of a retrocopy (in chr16) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr16:78355522-78356060 UCSC
Coordinates (T2T)	chr16:84411724-84412262 UCSC
Coordinates (hg19)	chr16:78389419-78389957 UCSC
Strand	+
Parental Sequence	NM_014463.3
Parental seq. overlap	504 bp
Parental seq. overlap (%)	15%
Genomic Region	Intragenic (WWOX)
Retrocopy Summary	LSM3P5, located on chr16:78355522-78356060, is a retrocopy of the parental gene LSM3. 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	LSM3
Full Name	LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
Also known as	SMX4\|USS2\|YLR438C
Coordinate	chr3:14178817-14201122
Strand	+
Gene summary	Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.[supplied by OMIM, Apr 2004]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	LSM3P4
Bonobo	Pan paniscus	LSM3P5
Gorilla	Gorilla gorilla	LSM3P5
Orangutan	Pongo abelii	LSM3P5
Gibbon	Nomascus leucogenys	LSM3P1
Green monkey	Chlorocebus sabaeus	LSM3P1
Crab-eating macaque	Macaca fascicularis	LSM3P7
Rhesus	Macaca mulatta	LSM3P7
Baboon	Papio anubis	LSM3P7
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

>LSM3P5
ATGAAACATGGCAGACAACGTAGACCAGCAGCAAACTACCAACACTGTGGAGGATCCCCTGGATCTTAGGCTCAGCCCAGAGGAGCGAATTTGTGTGAAAATGAGAAACGACCGAGAGCTTCGAGGCAGATTACATACTTATGATCAACATTTAAATATGATCTTGGGAGACGTGGAAGAAACTGTGACTACTATAGAAATTGATGAGGAAACATATGAAGAGACATATGAATCAACAAAACAGAATATTCCAGTGTTCTTTCTCCGGGGAGATGGCATTTTCCTGGTTGCCCCTCCACTGAGAGTTGGCTGAAACAAAGAATTTGTCCTGTACGGAAAACAGGAGACTTTGTACAGTGGCCTCTCTAAATGTGCAAGATATTCAAAAGAGAAACCCGCATACATTTGGATATTAAGAAATAATTCTGGGGATTCTTCCACTCCTGAAATGAGTTGATTTGCAGATAATTCACAACTTCTTAAGCTAAATGGTATTTTCGTTTTTCTCAAGCTCTTCCAATAAATATGACCACCAAGAT

>NM_014463.3
CTTGTGTTCTCGCGAGAGGCGGGAAAGGGCGCAGGGTTTGAAACATGGCGGACGACGTAGACCAGcaacaaactaccAACACTGTAGAGGAGCCCCTGGATCTTATCAGGCTCAGCCTAGATGAGCGAATTTATGTGAAAATGAGAAATGACCGAGAGCTTCGAGGCAGATTACATGCTTATGATCAACATTTAAATATGATCTTGGGAGATGTGGAAGAAACTGTGACTACTATAGAAATTGATGAAGAAACATATGAAGAGATATATAAATCAACGAAACGGAATATTCCAATGCTCTTTGTCCGGGGAGATGGCGTTGTCCTGGTTGCCCCTCCACTGAGAGTTGGCTGAAACAAAGAATTTGTCCTGTATGGAAAACGGGAGACTTTGTACAGTGGCCTCTCTAAAAGTACAAAACATTCATAAGAGAAACCTGCATACATTTTGATATTAAGAAATAATTCCGGGGATTCTTCCACTCCTGAAATGAGTTGATTTGCAGATAACTCACAACTTCTTAAGCTAAATGGTATTTTCATTTTTCTCAAGCTCTCCAATAAATATGACCACCAAGATGCAGAACTCTTTCAGGACTTCTTTTGCTCCATTATTCTCACAGATACTTACTGATTTTTCTTTTCTTTAAATTGGTGTTTCCTTGTAGATTTTTTTAAGTGCGGTCTTCTGTCTTGTGAATTATTTAAAGTAAGCATGTCTTACCttcacttagcacacatttgcagtgcacctactgtgtttgaggcaccaggtttgagtgctgggaaccagagttttatcaaaatgctttctgggccagacatggtggctcatgcctgtaatcccagcactttgggaggccaaggtgggtggatcacctgaggtcaggcgtttgagaccagcctggccaacatggtgaaaccctttctctactgaaaatataaaaattagccaggcgtggtggcgcatacttgtaatcccagctactcaggaggctgaggcagtagacgcttgaacccaggaggcagaggttgcagtgagccaagatcacaccattgcacttcaacctggtcaacagagcgagactccgtgtcaaaaaaaaaaaaaaaaaagttttctgccctcaagtcttctggggaggcagatgtttaaaccaacaattgcaggcagtaagattagtgctgatagaatcatgcacatgcaggatgccataggagcatggggaagagcacccaaaTATGGGAGAAAGGGGCAGAGGGACATTGTAAACATCAACCCTGCAGTAGAAGACAGAGCAAAGCATGATTTCTCTTTTCTCTGGCCTGATTTAATTCTAAGGTCAGACGTTCAGCTTGATCATAACCTGTTTATAATTATGACTCAGACCATTTTTCCACTCTTGGATCATTGGCCATTAATGATGAGGGGTCTCAAACAACATGTCTCAGTGACACAGTAAAGCAGAAATTGGCTGAAAGCAAAGCTGTTTTTATTTCTAGCTTCAGTCAGCACATAATGCTTAAAACCTAAAGAGGAAAGTAAAAGCGTGTTACAATCTCTCAAACTTTATCAAGACAGGGCTTAGAACCTGACATCCTCCGCTATGGTCATTCCATTTTGAAATGTAGAAAATCCAACTTGTGGATGGTTTGTCTGTAAATGAGCTGAATGTGTGTGCGTGTTCATTATCAAGCACGATATGCTCACAAATGCACAGTACTTTAAGCCTTGTGCAAGAAAGATGCTTTCAGTAAACATATTTAAAAGGTTTTATTTTCCTTACTAATGGTACATGCCCCTGCAAGTTCATGGAGAAGAGAAAAACAAGTGTGGGTGAGCTGATGGAGGCTTCATCTTAGGTGAGGAGGCAGGAGAGACACCCTCCCTTCACTTGTGCCATCCCCACGCTTTGTCCTTAAGCTGTAGTGGTCCCAGGAGATAACCTGTTTACAGCAGCCCATTCAGTATTGAAAAATGAACTCCCTCCTGCAGAATGTTAGAAGAAACAACCTCAAAGACCTCAGGCCGCCTGTGGTCATTAGTATGTGGCAGCAAGATTGAACCTGCCTGCCTCCTACCTGTGTGAGCCTGTGGTGTGGGTGTGGTACCAAGGCCCTGGCTCTGGGCAGTCTGTTGGCTCCTGGTGTTCACTAAGGCGTGGGGTGACAGGCCATCTGGCCTCGCTCTGCCAGTCTGCAGTTCTCCCCAGCACTGCATTCATTTTTAGTGGTTTCTGATAGTCACACTGAATTCCTGGACACTTTCTTCTCTTCATTCTTAGTTATCTTTCTCCTTTTTCTCCTGGAACTGATAGTTTACACTAAAACTTTTGGCTGTGAGGACTTGATTATACACATTTCTAAAACCCATGAACCTTAATATCTGACACTGTTACTCTCATATGCACACACAACTAAAACATACCAACCTACTTCATTTCCTAGCTGCTAAGATACAAGGGGAGGGACAATAAAAGGTTAACTGCAGAATAGCCACCTATGTGTCAGGAAATGGAGGGAGGGGAGGCAATGTGTGAGTCCTTTTGGAGCTGGGACTCAATCCACAACAGAGACAGCTCAAGCAGGGCCCTGCCATGGTCCACACTGAGGTTTCCTCTGCAGTGGTGCTGTCCACTGAGGGGTTATGGTGTGAGGGCCCCTGGGAGCCACGCCTTGGACTTCTGAGTCTGCAGAGCACTCGGCTCCAGCCAGCTGGATGGCAGGTGGTCAGTGGAGCTGGTGACTGGTGGTTTCTGCAATGAGGTGTCAGATTAGCCTAAGGGAAGCCTCTTCAGCAAGTATCATGCCTGGATCCCGGTCTTGGTTGTTTTATGAGAGGCCGATATGAATTGCCATTGCCTCCCACAAAGAAAAATGGACAAAATATGGGACCACATCTTTGAGATGAAATGTGCCCAAAATGAAAAGTAACTTGAGTATCCCAAGTTAAACTTAATCATTAGCTGCAAATGGACGATTTTCAAATTTCAAATAGTGATTTTTGAAGATTTGCCCAAACTAGAGTACTATCCCTCTTCacactaagaggcagaaagtggtttcacacacccttttatttaatcagctaaagtgggtgcggtgacacacacctgtaaactcaaccactaaggagactgaggcgggaggattacttgagcccaggagttcgagatcagcctgagcaacataacaagaccctgtctcaaataatacttagctattacccatattgcttttagcctgctgccaggaggggagaaATGTTATTGTTTGAACAGATGTCAGATGTGAGTAATGCTCAGCTGTGTTCAATGTAGAAAATTAATAAAAGTTCCAGGAGTCATCCTGGCTAGATCAAGAA

>NM_014463.3 

CTTGTGTTCTCGCGAGAGGCGGGAAAGGGCGCAGGGTTTGAAACATGGCGGACGACGTAGACCAGcaacaaactaccAACACTGTAGAGGAGCCCCTGGATCTTATCAGGCTCAGCCTAGATGAGCGAATTTATGTGAAAATGAGAAATGACCGAGAGCTTCGAGGCAGATTACATGCTTATGATCAACATTTAAATATGATCTTGGGAGATGTGGAAGAAACTGTGACTACTATAGAAATTGATGAAGAAACATATGAAGAGATATATAAATCAACGAAACGGAATATTCCAATGCTCTTTGTCCGGGGAGATGGCGTTGTCCTGGTTGCCCCTCCACTGAGAGTTGGCTGAAACAAAGAATTTGTCCTGTATGGAAAACGGGAGACTTTGTACAGTGGCCTCTCTAAAAGTACAAAACATTCATAAGAGAAACCTGCATACATTTTGATATTAAGAAATAATTCCGGGGATTCTTCCACTCCTGAAATGAGTTGATTTGCAGATAACTCACAACTTCTTAAGCTAAATGGTATTTTCATTTTTCTCAAGCTCTCCAATAAATATGACCACCAAGATGCAGAACTCTTTCAGGACTTCTTTTGCTCCATTATTCTCACAGATACTTACTGATTTTTCTTTTCTTTAAATTGGTGTTTCCTTGTAGATTTTTTTAAGTGCGGTCTTCTGTCTTGTGAATTATTTAAAGTAAGCATGTCTTACCttcacttagcacacatttgcagtgcacctactgtgtttgaggcaccaggtttgagtgctgggaaccagagttttatcaaaatgctttctgggccagacatggtggctcatgcctgtaatcccagcactttgggaggccaaggtgggtggatcacctgaggtcaggcgtttgagaccagcctggccaacatggtgaaaccctttctctactgaaaatataaaaattagccaggcgtggtggcgcatacttgtaatcccagctactcaggaggctgaggcagtagacgcttgaacccaggaggcagaggttgcagtgagccaagatcacaccattgcacttcaacctggtcaacagagcgagactccgtgtcaaaaaaaaaaaaaaaaaagttttctgccctcaagtcttctggggaggcagatgtttaaaccaacaattgcaggcagtaagattagtgctgatagaatcatgcacatgcaggatgccataggagcatggggaagagcacccaaaTATGGGAGAAAGGGGCAGAGGGACATTGTAAACATCAACCCTGCAGTAGAAGACAGAGCAAAGCATGATTTCTCTTTTCTCTGGCCTGATTTAATTCTAAGGTCAGACGTTCAGCTTGATCATAACCTGTTTATAATTATGACTCAGACCATTTTTCCACTCTTGGATCATTGGCCATTAATGATGAGGGGTCTCAAACAACATGTCTCAGTGACACAGTAAAGCAGAAATTGGCTGAAAGCAAAGCTGTTTTTATTTCTAGCTTCAGTCAGCACATAATGCTTAAAACCTAAAGAGGAAAGTAAAAGCGTGTTACAATCTCTCAAACTTTATCAAGACAGGGCTTAGAACCTGACATCCTCCGCTATGGTCATTCCATTTTGAAATGTAGAAAATCCAACTTGTGGATGGTTTGTCTGTAAATGAGCTGAATGTGTGTGCGTGTTCATTATCAAGCACGATATGCTCACAAATGCACAGTACTTTAAGCCTTGTGCAAGAAAGATGCTTTCAGTAAACATATTTAAAAGGTTTTATTTTCCTTACTAATGGTACATGCCCCTGCAAGTTCATGGAGAAGAGAAAAACAAGTGTGGGTGAGCTGATGGAGGCTTCATCTTAGGTGAGGAGGCAGGAGAGACACCCTCCCTTCACTTGTGCCATCCCCACGCTTTGTCCTTAAGCTGTAGTGGTCCCAGGAGATAACCTGTTTACAGCAGCCCATTCAGTATTGAAAAATGAACTCCCTCCTGCAGAATGTTAGAAGAAACAACCTCAAAGACCTCAGGCCGCCTGTGGTCATTAGTATGTGGCAGCAAGATTGAACCTGCCTGCCTCCTACCTGTGTGAGCCTGTGGTGTGGGTGTGGTACCAAGGCCCTGGCTCTGGGCAGTCTGTTGGCTCCTGGTGTTCACTAAGGCGTGGGGTGACAGGCCATCTGGCCTCGCTCTGCCAGTCTGCAGTTCTCCCCAGCACTGCATTCATTTTTAGTGGTTTCTGATAGTCACACTGAATTCCTGGACACTTTCTTCTCTTCATTCTTAGTTATCTTTCTCCTTTTTCTCCTGGAACTGATAGTTTACACTAAAACTTTTGGCTGTGAGGACTTGATTATACACATTTCTAAAACCCATGAACCTTAATATCTGACACTGTTACTCTCATATGCACACACAACTAAAACATACCAACCTACTTCATTTCCTAGCTGCTAAGATACAAGGGGAGGGACAATAAAAGGTTAACTGCAGAATAGCCACCTATGTGTCAGGAAATGGAGGGAGGGGAGGCAATGTGTGAGTCCTTTTGGAGCTGGGACTCAATCCACAACAGAGACAGCTCAAGCAGGGCCCTGCCATGGTCCACACTGAGGTTTCCTCTGCAGTGGTGCTGTCCACTGAGGGGTTATGGTGTGAGGGCCCCTGGGAGCCACGCCTTGGACTTCTGAGTCTGCAGAGCACTCGGCTCCAGCCAGCTGGATGGCAGGTGGTCAGTGGAGCTGGTGACTGGTGGTTTCTGCAATGAGGTGTCAGATTAGCCTAAGGGAAGCCTCTTCAGCAAGTATCATGCCTGGATCCCGGTCTTGGTTGTTTTATGAGAGGCCGATATGAATTGCCATTGCCTCCCACAAAGAAAAATGGACAAAATATGGGACCACATCTTTGAGATGAAATGTGCCCAAAATGAAAAGTAACTTGAGTATCCCAAGTTAAACTTAATCATTAGCTGCAAATGGACGATTTTCAAATTTCAAATAGTGATTTTTGAAGATTTGCCCAAACTAGAGTACTATCCCTCTTCacactaagaggcagaaagtggtttcacacacccttttatttaatcagctaaagtgggtgcggtgacacacacctgtaaactcaaccactaaggagactgaggcgggaggattacttgagcccaggagttcgagatcagcctgagcaacataacaagaccctgtctcaaataatacttagctattacccatattgcttttagcctgctgccaggaggggagaaATGTTATTGTTTGAACAGATGTCAGATGTGAGTAATGCTCAGCTGTGTTCAATGTAGAAAATTAATAAAAGTTCCAGGAGTCATCCTGGCTAGATCAAGAA

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