RCPedia: Rtcs

Summary

Retrocopy Name	SS18L2P1	Plot displaying the genomic locations of a retrocopy (in chr10) and its respective parental gene (in chr3). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr10:34875208-34876225 UCSC
Coordinates (T2T)	chr10:34903726-34904743 UCSC
Coordinates (hg19)	chr10:35164136-35165153 UCSC
Strand	+
Parental Sequence	NM_001370300.1
Parental seq. overlap	650 bp
Parental seq. overlap (%)	23.9%
Genomic Region	Intergenic
Retrocopy Summary	SS18L2P1, located on chr10:34875208-34876225, is a retrocopy of the parental gene SS18L2. 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	SS18L2
Full Name	SS18 like 2
Also known as	KIAA-iso
Coordinate	chr3:42581840-42596934
Strand	+
Gene summary	Synovial sarcomas occur most frequently in the extremities around large joints. More than 90% of cases have a recurrent and specific chromosomal translocation, t(X;18)(p11.2;q11.2), in which the 5-prime end of the SS18 gene (MIM 600192) is fused in-frame to the 3-prime end of the SSX1 (MIM 312820), SSX2 (MIM 300192), or SSX4 (MIM 300326) gene. The SS18L2 gene is homologous to SS18.[supplied by OMIM, Jul 2002]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	SS18L2P1
Bonobo	Pan paniscus	SS18L2P1
Gorilla	Gorilla gorilla	SS18L2P1
Orangutan	Pongo abelii	SS18L2P1
Gibbon	Nomascus leucogenys	SS18L2P2
Green monkey	Chlorocebus sabaeus	SS18L2P1
Crab-eating macaque	Macaca fascicularis	SS18L2P1
Rhesus	Macaca mulatta	SS18L2P1
Baboon	Papio anubis	SS18L2P1
Golden snub-nosed monkey	Rhinopithecus roxellana	SS18L2P1
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

>SS18L2P1
TGGACTGGCTGAGGGGCAAGGTGGAAGTCAATCAAGAGACTATCCAGCGGCTCCTTGAGGAGAATGACCAACTGATCCGCTGTATCGTGGAGTATCAGAACAAGGGCGGAGCGAACGAGTGCGTCCAGTGCCAGCTTGTGTTACACAGAAATCTCATTTATTTGGCTACCATCGCAGATGCCAGCCCAACCAGTACTTCAAAAGCAATGGAATAATCTTTCAAAAGCAATGGAATAACCTTCCAGTTGGCTGTTGTGAGTAGTAATTGAATGTAATCCATCTCTTACAAAATGGAGACAGGATCTTTACCAACTTAACTGCTTAAAACGTGAATGACACTTCTGTGGCTCTATTTAAAAATGTGAAAATGTGGAAAaGTGAAAATGTGAAGAAAGCTACCAACTTAACTGTATTCTCAATGTAAATATTTTTAAAATAATTAAGCAAATCCCTCAATAAGTTGAGACCAGATGTCCTCTTTCCTGAACTTGGAGCATATTTGGATAACTAAGACATTACTAGGATGTTCAAGCCTACTTTTTAGTTTCAACCTGAAGAGGAAGCTGAGTAGGTGTTGGGCAGGAATTGGTGAGACTCCTTGACTTGAGACCTTGCTAAATGGACATTTATCTGCGTGCTCCTTCCTAACAGTTGTAAATGTGGTCCCCCGACTGCTGTTTTCAGATTGCTTTGAAATAAAGCTTAGTTTTCTACAAAA

>NM_001370300.1
GAGTTGCTTGGCGGTCGTGGTTCCGGAGGTTCCTCGGGATGTCGGTGGCCTTCGTACCGGACTGGCTGAGGGGCAAGGCGGAAGTCAATCAAGAGACTATCCAGCGGCTCCTTGAGGAGAATGACCAGCTGATCCGCTGTATTGTGGAGTATCAGAACAAGGGCCGCGGGAACGAGTGCGTGCAGTACCAGCATGTGTTACATAGAAATCTCATTTATTTGGCTACCATTGCAGATGCCAGTCCAACCAGCACTTCAAAAGCAATGGAATAATCTTTCAAAAGCAATAGAATAATCTTCCATTTGGCTGTCGTGAGGAGTAATTGAATGTAATCCATCTCTTACAAAATGGAGACAGGGTCTTTACCAACTCAACTGGTTAAAACATGAATGAAACCTCTGTGGCTCTTTCGAAACGTGAAAATGTGAAGAAAGCTACTAACTTAGCTGTATTCTCATGTAAATATTTTTTAAATAATTAAGCAAATCCCTCAATAAGTTGAGCCCAGGTGTCCTCTTTCCTGAACTTGGAGCATGTTTGGATAACAAAGACATCACTGGGATGTTCAAGTCTACTTTTTAGTTTCAACCTGAAGAGGAAACTCAGTAGGTGTTGGGCAGGAATTGGTGAGATTCCTGACTTGATACCTTGCTAAATGGACATGTAACTGTGTGCTCCTTCCTATCAGTTTGTAAATGTGGTCCCCCTGACTGCTGTTTTCAGATTGCTTTGAAATAAAGCTTATTTTTCTATAAAATACTGATGTGGAGGTATAGAAGTTTTCATGTAATAAGTATTCCATTTGGTTTTCAAGAATAACTGTGAGGACTTAACCAtaaagtatataaaaacaatactattatcattgccaacaaaatgaatagtgatttctaattattatctaatatcatctgataatagatgatgtttaattttcttcagttatcagatagtctttttgttgatttgtctgaaccagaatccaaataagattcacatgttgtattttgttgatgttcctttaagtcacttaaagaatacttaatagttcctttttttctttatttgttgaaataactaggtgtttaccctagaattctctcgtgttctacatacagttgtatctctgtagtgttgttaattatgtgccactatcatccacttttcctgtaaactagtagatctagaggctcatgcagactcatgttctaatatttttagcaggaatatattagaaggtgataagtacttgcttttgcatcacataaggagtgacctgacttttaagttcccaaccagcctttcacttaaattatgatccacccagctttgatgtggtaattcattagggattacataatgaggattttctaatttatcattctttctgactttattagctgtattctataaaaaactttcactcTTGGAGATTTATCTGAAAGATGAGGCAAAGGGATTCTTGTAAGTATATCCAAAATTAGAAGCCCAGGTCCCTGCTCCTTTTTTTGGAGTCAAGGGTTGCAACCTAGGGCAACTGTAAAATACATGTAAATAGTGAAGAGATAACTCATTTTGAATCCCAGCTCTAtcccttaacctctgaaagctctgtttcctcacctctaaagtgaggataatgaaaatagcatctgcctcctgaggttgtgagactgagataacgtggttgagaacTGGGCACATGTTAATCTATGTTAGCACTAATGTGCTGAGGGCTCTGGCTCtttcttttttctttttcttcttttttttggttttgttttgttttgtttttgtttttgtttttttttgagacggaatctcgctctgtcggagtgcagtggtgcaattttggctcactgcaacctctacctcctgggttcaagtgattctcctgcctcagcctcccaagtagctgggattacaggcatgtggcaccatgcctggctaattttggtatttttagtagagacggggtttctccatgttggtcaggctggtctcgtactcacgacctcaggtgatccacctgcctcagcctcctagagtgctgggattacaggcgtaagccaccgcgcccagccgatcatttctgttttctAGAAAATTATTTTGTCTGTTTCCCCACTAGCATTCCTGATGGTTTTCCAGAGTCCTATCCCCTGAAGTTCTAATTGCTGGCATAATCACACTCTAAAAGGCTGAACCCCAGAATCATTACCTGAAAATTCGTACTACCAGTGGTTCTTCTTCATGATAAATCATGGACAAATTAAGCCTGAGTTTGTAAACTCTTTGGATACCAACTTTCTACCACTCTTGGAAGAGATGGAGGAGGTGTCAGTCATTTTGGTTGATACTAGCCCTAGGCCTGCCTTGTCCCAGGAGTTTCTTCACCTTAATCACAGACCAAATTGCATACTTTTATCTTCGAATCATCTAAAATATAATTTCAAATCACAAGACAGAATAAaataatctttgagagaggcagaaccttagaaaggagatattttatctcatttattttacagatgaagaaagtaaacttcagagagatcaaagtgatttgtctcaggtcacataaccagtggcagaAAGAAGAGAATTGCTGGAATGTCAAGATAAGAATGAATTCTAGGTTTAAAGTTGTTTAAGTATATCCCAAATTAAATATTTCATTCCTGAGCTCTAAAA

>NM_001370300.1 

GAGTTGCTTGGCGGTCGTGGTTCCGGAGGTTCCTCGGGATGTCGGTGGCCTTCGTACCGGACTGGCTGAGGGGCAAGGCGGAAGTCAATCAAGAGACTATCCAGCGGCTCCTTGAGGAGAATGACCAGCTGATCCGCTGTATTGTGGAGTATCAGAACAAGGGCCGCGGGAACGAGTGCGTGCAGTACCAGCATGTGTTACATAGAAATCTCATTTATTTGGCTACCATTGCAGATGCCAGTCCAACCAGCACTTCAAAAGCAATGGAATAATCTTTCAAAAGCAATAGAATAATCTTCCATTTGGCTGTCGTGAGGAGTAATTGAATGTAATCCATCTCTTACAAAATGGAGACAGGGTCTTTACCAACTCAACTGGTTAAAACATGAATGAAACCTCTGTGGCTCTTTCGAAACGTGAAAATGTGAAGAAAGCTACTAACTTAGCTGTATTCTCATGTAAATATTTTTTAAATAATTAAGCAAATCCCTCAATAAGTTGAGCCCAGGTGTCCTCTTTCCTGAACTTGGAGCATGTTTGGATAACAAAGACATCACTGGGATGTTCAAGTCTACTTTTTAGTTTCAACCTGAAGAGGAAACTCAGTAGGTGTTGGGCAGGAATTGGTGAGATTCCTGACTTGATACCTTGCTAAATGGACATGTAACTGTGTGCTCCTTCCTATCAGTTTGTAAATGTGGTCCCCCTGACTGCTGTTTTCAGATTGCTTTGAAATAAAGCTTATTTTTCTATAAAATACTGATGTGGAGGTATAGAAGTTTTCATGTAATAAGTATTCCATTTGGTTTTCAAGAATAACTGTGAGGACTTAACCAtaaagtatataaaaacaatactattatcattgccaacaaaatgaatagtgatttctaattattatctaatatcatctgataatagatgatgtttaattttcttcagttatcagatagtctttttgttgatttgtctgaaccagaatccaaataagattcacatgttgtattttgttgatgttcctttaagtcacttaaagaatacttaatagttcctttttttctttatttgttgaaataactaggtgtttaccctagaattctctcgtgttctacatacagttgtatctctgtagtgttgttaattatgtgccactatcatccacttttcctgtaaactagtagatctagaggctcatgcagactcatgttctaatatttttagcaggaatatattagaaggtgataagtacttgcttttgcatcacataaggagtgacctgacttttaagttcccaaccagcctttcacttaaattatgatccacccagctttgatgtggtaattcattagggattacataatgaggattttctaatttatcattctttctgactttattagctgtattctataaaaaactttcactcTTGGAGATTTATCTGAAAGATGAGGCAAAGGGATTCTTGTAAGTATATCCAAAATTAGAAGCCCAGGTCCCTGCTCCTTTTTTTGGAGTCAAGGGTTGCAACCTAGGGCAACTGTAAAATACATGTAAATAGTGAAGAGATAACTCATTTTGAATCCCAGCTCTAtcccttaacctctgaaagctctgtttcctcacctctaaagtgaggataatgaaaatagcatctgcctcctgaggttgtgagactgagataacgtggttgagaacTGGGCACATGTTAATCTATGTTAGCACTAATGTGCTGAGGGCTCTGGCTCtttcttttttctttttcttcttttttttggttttgttttgttttgtttttgtttttgtttttttttgagacggaatctcgctctgtcggagtgcagtggtgcaattttggctcactgcaacctctacctcctgggttcaagtgattctcctgcctcagcctcccaagtagctgggattacaggcatgtggcaccatgcctggctaattttggtatttttagtagagacggggtttctccatgttggtcaggctggtctcgtactcacgacctcaggtgatccacctgcctcagcctcctagagtgctgggattacaggcgtaagccaccgcgcccagccgatcatttctgttttctAGAAAATTATTTTGTCTGTTTCCCCACTAGCATTCCTGATGGTTTTCCAGAGTCCTATCCCCTGAAGTTCTAATTGCTGGCATAATCACACTCTAAAAGGCTGAACCCCAGAATCATTACCTGAAAATTCGTACTACCAGTGGTTCTTCTTCATGATAAATCATGGACAAATTAAGCCTGAGTTTGTAAACTCTTTGGATACCAACTTTCTACCACTCTTGGAAGAGATGGAGGAGGTGTCAGTCATTTTGGTTGATACTAGCCCTAGGCCTGCCTTGTCCCAGGAGTTTCTTCACCTTAATCACAGACCAAATTGCATACTTTTATCTTCGAATCATCTAAAATATAATTTCAAATCACAAGACAGAATAAaataatctttgagagaggcagaaccttagaaaggagatattttatctcatttattttacagatgaagaaagtaaacttcagagagatcaaagtgatttgtctcaggtcacataaccagtggcagaAAGAAGAGAATTGCTGGAATGTCAAGATAAGAATGAATTCTAGGTTTAAAGTTGTTTAAGTATATCCCAAATTAAATATTTCATTCCTGAGCTCTAAAA

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