RCPedia: Rtcs

Summary

Retrocopy Name	SNAP23P1	Plot displaying the genomic locations of a retrocopy (in chr20) and its respective parental gene (in chr15). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr20:49038355-49038583 UCSC
Coordinates (T2T)	chr20:50807860-50808088 UCSC
Coordinates (hg19)	chr20:47654892-47655120 UCSC
Strand	-
Parental Sequence	NM_003825.4
Parental seq. overlap	203 bp
Parental seq. overlap (%)	8.8%
Genomic Region	Intergenic
Retrocopy Summary	SNAP23P1, located on chr20:49038355-49038583, is a retrocopy of the parental gene SNAP23. 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	SNAP23
Full Name	synaptosome associated protein 23
Also known as	HsT17016\|SNAP-23\|SNAP23A\|SNAP23B
Coordinate	chr15:42491244-42533058
Strand	+
Gene summary	Specificity of vesicular transport is regulated, in part, by the interaction of a vesicle-associated membrane protein termed synaptobrevin/VAMP with a target compartment membrane protein termed syntaxin. These proteins, together with SNAP25 (synaptosome-associated protein of 25 kDa), form a complex which serves as a binding site for the general membrane fusion machinery. Synaptobrevin/VAMP and syntaxin are believed to be involved in vesicular transport in most, if not all cells, while SNAP25 is present almost exclusively in the brain, suggesting that a ubiquitously expressed homolog of SNAP25 exists to facilitate transport vesicle/target membrane fusion in other tissues. The protein encoded by this gene is structurally and functionally similar to SNAP25 and binds tightly to multiple syntaxins and synaptobrevins/VAMPs. It is an essential component of the high affinity receptor for the general membrane fusion machinery and is an important regulator of transport vesicle docking and fusion. Two alternative transcript variants encoding different protein isoforms have been described for this gene. [provided by RefSeq, Jul 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	SNAP23P1
Bonobo	Pan paniscus	SNAP23P1
Gorilla	Gorilla gorilla	SNAP23P1
Orangutan	Pongo abelii	SNAP23P1
Gibbon	Nomascus leucogenys	SNAP23P1
Green monkey	Chlorocebus sabaeus	SNAP23P1
Rhesus	Macaca mulatta	SNAP23P1
Baboon	Papio anubis	SNAP23P1
Golden snub-nosed monkey	Rhinopithecus roxellana	SNAP23P2
Crab-eating macaque	Macaca fascicularis	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

>SNAP23P1
CTGATGAGTCTCTAGAAAGTACAAGGAGAATCCTGGGTTTAGCCATTGAGTCTCAGGATGCAGGAATCAAGATCATCACAATACTGGATAAACAAGGGGAACAACTCAACCACATAGAAGACATGGGCCACAAAAATACAGACATGAGAGAGGCAGAGAAGACTTTAACAGAACTTAACAAATGCCATGCCCTTCGTGTCTGTCCACATAATAGAACAAAGAACTTTg

>NM_003825.4
AGGCGCGACTAGGGTGCAGCGCCAGGTCCGGTGTTGGGGTGTCCGAGTTGCCGCCGGAGAGGAGTGGCCTCGCCCGCTTGAGTTTTGATTCATCATGGATAATCTGTCATCAGAAGAAATTCAACAGAGAGCTCACCAGATTACTGATGAGTCTCTGGAAAGTACGAGGAGAATCCTGGGTTTAGCCATTGAGTCTCAGGATGCAGGAATCAAGACCATCACTATGCTGGATGAACAAAAGGAACAACTAAACCGCATAGAAGAAGGCTTGGACCAAATAAATAAGGACATGAGAGAGACAGAGAAGACTTTAACAGAACTCAACAAATGCTGTGGCCTTTGTGTCTGCCCATGTAATAGAACAAAGAACTTTGAGTCTGGCAAGGCTTATAAGACAACATGGGGAGATGGTGGAGAAAACTCACCTTGCAATGTAGTATCTAAACAGCCAGGCCCGGTGACAAATGGTCAGCTTCAGCAACCAACAACGGGAGCAGCCAGTGGTGGATACATTAAACGCATAACTAATGATGCCAGAGAAGATGAAATGGAAGAGAACCTGACTCAAGTGGGCAGTATCCTGGGAAATCTAAAAGACATGGCCCTGAACATAGGCAATGAGATTGATGCTCAAAATCCACAAATAAAACGAATCACAGACAAGGCTGACACCAACAGAGATCGTATTGATATTGCCAATGCCAGAGCAAAGAAACTCATTGACAGCTAAAGCTACTGCTGTTCTTCTTTATCATTTATTCACTTCCGTAGCTCCTCCTTGAAAGTTATTACCTTTTCAGAGTTTAAGTTTTCGGTTCCACGCTCTTCTAATTGGGAGATAATATGGAAGAAGGGCCAGAGCAGTTACAGCCCTCCTTCTTTTTTGTTTTCTGTTGAGGGCCGACTGCTGCTCTGCCTTCCTTCTAGTATTTTCTTTCTCAATTCATACGCTTAGATTGGTTTTCATATGTCATGTTTAGTGTTTTCATCCTCCTCATATACTTCAGCAGGTTCTTTTGCTTTCAAGATTTGGAAGCATTGCCAAAGACAGCCATGAAGAAGGAAGCTGTAGAGgtgttttttgttgttgtttatttttgcttttgtGGTTGAGGGAAGGACAAGAGATAAGAGGTTGTTACCTCAGTAAAAACCTTCAGGCCACAAAGCAAAAAGTTGCATAGCCACAACGAAGATCTAGTTGGATATAGTTTTTGATTTAAGTTGCAGTTATAGCCAATTTAGGCTAATGCTTGGTTTTGGAGCTTTTATACACAACGTTTTTGTTAGGCATCACAGTTTTGCAACCTCTGCTCCAAAGAGAAAAATAGAATGAGttttctttcttttttttttttttggagtcagagtctcgctctcttgtccaggctggagtgcaatagcgcgatctgggctcactgcaacctccgcctccctggttcaagcaattctcctgccttgcctcctgagtagctgggattacaggcgtgtgtcaccacgctcggctaatttttgtatttttagtagagacagggtttcaccatgtcaagctggtcttggactcctgacgtcgtgatccacccgccttggcctcccaaagtactgggattacaggcgtgagccactgtgcctggcTGAGTTTTCTTAAAGTGAGCTTAATTTCTGAACTCTTAGTGATTCATATATGTACATAAATCTGTGATCCCATTTCTTATTGCACCATTCAGGAACACTTTATATAAATGAGTGGCTTTTTATTTCATATTATTAGTAGTATCATGGTTCCATTACAGGCCTATTAACATCATACATTGTCATTAGTCTTTGAAGAAAAAATATGTAAATATATATGTGTAACATGAGAATTTCTCTCTAAAGCAGGGCTTAAAATTTTTTGGAAAAGTTTGACAAAGCATACCACATGAATTCAGATTTACCTCAATGCTAAGAATTATGTTTAGTTAGGAAAAAGGAAAGTCATTTTGACCTCAGGTAGAAAAATAGATTGCTTTGAGTTTTATGTAGCTTTAGACTTTAAAAAGTTAGAATTTATTCTGTAACTAAAAATTATTTGAAAAAATTATGCCTCTGGTTTAATTATTGGTGATTACACACTCTTTCTCTTACCCTTGTGTATTGAACTATGTCCATAATCAAGTTGATGTGGATCCTGAAAAGTGTTATGAACATCTGATTGGTATTTGTCACATTTATTTTAAAATTAGCATCTGAACACTTCAAAGCTGTCAGTGTGTATTGGTTTCACCAATAACCACTGCTTGATCCTTACAATTAAATTTTTTAACTAAC

>NM_003825.4 

AGGCGCGACTAGGGTGCAGCGCCAGGTCCGGTGTTGGGGTGTCCGAGTTGCCGCCGGAGAGGAGTGGCCTCGCCCGCTTGAGTTTTGATTCATCATGGATAATCTGTCATCAGAAGAAATTCAACAGAGAGCTCACCAGATTACTGATGAGTCTCTGGAAAGTACGAGGAGAATCCTGGGTTTAGCCATTGAGTCTCAGGATGCAGGAATCAAGACCATCACTATGCTGGATGAACAAAAGGAACAACTAAACCGCATAGAAGAAGGCTTGGACCAAATAAATAAGGACATGAGAGAGACAGAGAAGACTTTAACAGAACTCAACAAATGCTGTGGCCTTTGTGTCTGCCCATGTAATAGAACAAAGAACTTTGAGTCTGGCAAGGCTTATAAGACAACATGGGGAGATGGTGGAGAAAACTCACCTTGCAATGTAGTATCTAAACAGCCAGGCCCGGTGACAAATGGTCAGCTTCAGCAACCAACAACGGGAGCAGCCAGTGGTGGATACATTAAACGCATAACTAATGATGCCAGAGAAGATGAAATGGAAGAGAACCTGACTCAAGTGGGCAGTATCCTGGGAAATCTAAAAGACATGGCCCTGAACATAGGCAATGAGATTGATGCTCAAAATCCACAAATAAAACGAATCACAGACAAGGCTGACACCAACAGAGATCGTATTGATATTGCCAATGCCAGAGCAAAGAAACTCATTGACAGCTAAAGCTACTGCTGTTCTTCTTTATCATTTATTCACTTCCGTAGCTCCTCCTTGAAAGTTATTACCTTTTCAGAGTTTAAGTTTTCGGTTCCACGCTCTTCTAATTGGGAGATAATATGGAAGAAGGGCCAGAGCAGTTACAGCCCTCCTTCTTTTTTGTTTTCTGTTGAGGGCCGACTGCTGCTCTGCCTTCCTTCTAGTATTTTCTTTCTCAATTCATACGCTTAGATTGGTTTTCATATGTCATGTTTAGTGTTTTCATCCTCCTCATATACTTCAGCAGGTTCTTTTGCTTTCAAGATTTGGAAGCATTGCCAAAGACAGCCATGAAGAAGGAAGCTGTAGAGgtgttttttgttgttgtttatttttgcttttgtGGTTGAGGGAAGGACAAGAGATAAGAGGTTGTTACCTCAGTAAAAACCTTCAGGCCACAAAGCAAAAAGTTGCATAGCCACAACGAAGATCTAGTTGGATATAGTTTTTGATTTAAGTTGCAGTTATAGCCAATTTAGGCTAATGCTTGGTTTTGGAGCTTTTATACACAACGTTTTTGTTAGGCATCACAGTTTTGCAACCTCTGCTCCAAAGAGAAAAATAGAATGAGttttctttcttttttttttttttggagtcagagtctcgctctcttgtccaggctggagtgcaatagcgcgatctgggctcactgcaacctccgcctccctggttcaagcaattctcctgccttgcctcctgagtagctgggattacaggcgtgtgtcaccacgctcggctaatttttgtatttttagtagagacagggtttcaccatgtcaagctggtcttggactcctgacgtcgtgatccacccgccttggcctcccaaagtactgggattacaggcgtgagccactgtgcctggcTGAGTTTTCTTAAAGTGAGCTTAATTTCTGAACTCTTAGTGATTCATATATGTACATAAATCTGTGATCCCATTTCTTATTGCACCATTCAGGAACACTTTATATAAATGAGTGGCTTTTTATTTCATATTATTAGTAGTATCATGGTTCCATTACAGGCCTATTAACATCATACATTGTCATTAGTCTTTGAAGAAAAAATATGTAAATATATATGTGTAACATGAGAATTTCTCTCTAAAGCAGGGCTTAAAATTTTTTGGAAAAGTTTGACAAAGCATACCACATGAATTCAGATTTACCTCAATGCTAAGAATTATGTTTAGTTAGGAAAAAGGAAAGTCATTTTGACCTCAGGTAGAAAAATAGATTGCTTTGAGTTTTATGTAGCTTTAGACTTTAAAAAGTTAGAATTTATTCTGTAACTAAAAATTATTTGAAAAAATTATGCCTCTGGTTTAATTATTGGTGATTACACACTCTTTCTCTTACCCTTGTGTATTGAACTATGTCCATAATCAAGTTGATGTGGATCCTGAAAAGTGTTATGAACATCTGATTGGTATTTGTCACATTTATTTTAAAATTAGCATCTGAACACTTCAAAGCTGTCAGTGTGTATTGGTTTCACCAATAACCACTGCTTGATCCTTACAATTAAATTTTTTAACTAAC

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