RCPedia: Rtcs

Summary

Retrocopy Name	BLOC1S2P1	Plot displaying the genomic locations of a retrocopy (in chrX) and its respective parental gene (in chr10). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chrX:64726513-64727104 UCSC
Coordinates (T2T)	chrX:63151795-63152386 UCSC
Coordinates (hg19)	chrX:63946393-63946984 UCSC
Strand	-
Parental Sequence	NM_001282437.2
Parental seq. overlap	510 bp
Parental seq. overlap (%)	18.6%
Genomic Region	Intergenic
Retrocopy Summary	BLOC1S2P1, located on chrX:64726513-64727104, is a retrocopy of the parental gene BLOC1S2. 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	BLOC1S2
Full Name	biogenesis of lysosomal organelles complex 1 subunit 2
Also known as	BLOS2\|BORCS2\|CEAP\|CEAP11
Coordinate	chr10:100273278-100286692
Strand	-
Gene summary	This gene encodes a protein with multiple functions. The encoded protein has been found in association with the centrosome, shown to co-localize with gamma-tubulin, and also found to be one of the proteins in the BLOC-1 complex which functions in the formation of lysosome-related organelles. A pseudogene of this gene is located on the X chromosome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	BLOC1S2P1
Bonobo	Pan paniscus	BLOC1S2P1
Gorilla	Gorilla gorilla	BLOC1S2P1
Orangutan	Pongo abelii	BLOC1S2P1
Green monkey	Chlorocebus sabaeus	BLOC1S2P1
Crab-eating macaque	Macaca fascicularis	BLOC1S2P1
Rhesus	Macaca mulatta	BLOC1S2P1
Gibbon	Nomascus leucogenys	Without Homology
Baboon	Papio anubis	Without Homology
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

>BLOC1S2P1
ACAGCTGAGGAAACAAAGGAACCTGCTGAAGCTGAGATCACTGAGCTGTGCTGGGACATGTTCTCCAAAATGGACATTTATCTTACTGGAGAATTGACGACCACCAATGAAGACTATAAGCTCCCAGAAAATGAATAAACTACTCAGCTTGAAGTATCTTGAAATAAAAGATATTTCTATAAACATTAGTAGATACTTAAAGGACTTAAGTTTAAGTTCAGTAGTATGCTGGACTGCAGCCTTATCTGGATCAGATCAATGTCATTGAAGAGCAGGTAGCAGCTCTTGAGCAGACAGCTTAAAAGTTAAATGCATTTTTTTAAAACTGGAAGCCAAGTACAAGAAGTTGGAGAAGCGATGAAAAACTTATTTGTATGGGACAAAGTCTTTTTTAATGTGGAAGATGTTTTATAAGATGTGAATACTGAGGCTGATGAATTGTCAAATCTCCGCAAAATGAAACTGTGCTGAACTTTCTAGGAAGATCTCAATGTTGGAATAAACTGTAGGACTGGGGCTACTTCTGTACCTCCTTTGAGGCAGTAACCCTTGAAAACTCACACATAACTTCTTATTTTTACCTGAATGCTTC

>NM_001282437.2
GGAAACAGCGCGGGGTCCGCTATGGCGGCGGCAGCCGAGGGCGTACTGGCGACCCGGAGTGATGAGCCCGCCCGAGATGGAGAATGGAGCCGACTTGATGGAATGAAGGCAAGTGGAGGGATGTCGGAACAGGCTGCTTTGGCTGGATTAGCACCGGGTGTAGGCGGGACACTTAGTCATTCTCCCTTGGCCCAGACGATGCCGCCGTGGAGACAGCTGAGGAAGCAAAGGAGCCTGCTGAAGCTGACATCACTGAGCTCTGCCGGGACATGTTCTCCAAAATGGCCACTTACCTGACTGGGGAACTGACGGCCACCAGTGAAGACTATAAGCTCCTGGAAAATATGAATAAACTCACCAGCTTGAAGTATCTTGAAATGAAAGATATTGCTATAAACATTAGTAGGAACTTAAAGGACTTAAACCAGAAATATGCTGGACTGCAGCCTTATCTGGATCAGATCAATGTCATTGAAGAGCAGGTAGCAGCTCTTGAGCAGGCAGCTTACAAGTTGGATGCATATTCAAAAAAACTGGAAGCCAAGTACAAGAAGCTGGAGAAGCGATGAGAAACTTATTTCTATGGGACAGAGTCTTTTTTTTTTAATGTGGAAGAATGTCTTATAAAACCTGAATCCTGAGGCTGATGAATTGTGAAAATTCCTCAAAAGGAAATTATGCTGGTCATCACAGGAACATCTCAACGTTCGAGTAAACTGGAGGACTGTGGCTATTCCTGAACCTTCTTTGAGACAGAATCCCTCAGAATCTCACACTTATAACTTCCTACCTTTTACTTGAATGCTTTGCCATATTCAGGACAGAGACTCTCACAAAGTTCAGAAAACAGCTGGACTTACCAGTAAAATCAAATGAGAGGACCTATTTTCTCTGGTAGTGGTTGATTACTACATTATTTTCTTAAGTGGCTGGTTTTTTAGTTACTATGTAAATGGTCGTTTTTCTGTTAATGATGCTAATGTGTTGTAAACAAGATTCTAAATTTAAAAAGGAAAACAAAACAAACTTGTTCTTTGCAGCTTATCACCTTGTGAATGTCGGTAACTTACTTTTCCATAATATTGCAAATAACATAAAATCTTAAAATAATTCCAAGCTGAGTCTTCTAGATTGAGCAGAAATGGTGAAAGGAGTATTGATAACTTGGCGTATGTGATGGGCCCCTCTTGTTTATTTTCTATGTGAGTCACATTGACATGCGATCAGTTTGGGAAATGTGATGAAAACAAAGACTAGATGGGTATGTGTGTTTATGTGTTGGGTAGGGAGGTGACGATTGCCACTCATAAAATAAAGGATTTTATAAAATACCTTCCTACTGTGTATGTAGGATTTGGGGGGATCTTAGGGACCTAATCGACTTCTTTGCACACTAAAAACATCAGACAATGGGACATACTGACTGACCAGTCTAGGTTGAAAGATAGGCAGCCTTACCCAGAACACAACATTAGCAGCTGGGAAGGTGTCTGAGGTCCCCAATTACATATCCCAAAGAGTttcttacttctgtttctgtcatttcccctctgttccagacagtcatcatttatcctctgttcttcctggactgttgctgtggtctcttctcatcttaactgtcccttccaaccaccctccacactgctgccagagcaatcttaaaaatgtaaactggccctattactcctgcttagaaccctgtagtgacttatcatggcctctgaaaaatctagactttcattatgcatacaagtccctTGTGtttttttgtttgtttatagacagggtctctattgtcacccaggctggagtgtggtggtgtgataatagctcaccttgacctcctaggctcaactgatcttcccacctcagcctcctgaatagctgggactaccagcacgctccaccatgccttgctaattattttttatacagatggagtctcactatgttgtccaggctggtcttgaactggcctcaagtgattctcttaccacagcctgccagagtgctgagattgtaggcatgaaccaccgtgccTAACATAAGGCCCCTATTTAAACATTTTTCTTAAATAAAAAACAAAAGAATTAAACTGTAACTCTACTATCTTAACATAGAATCAGTCTTACCCCTTCTTCCAACCCTTTTCCTTTTCCGTGCATGTATTGATCTAttttttttttttttttgagatgaagtcttgctctgtcgcctgggctggagtgcagtggtgcgatcttagctcactgcaacctctgtttcctgggttcaagcgattctcctgcctcagcctcccgagtagttgagatttacaggtgcccaccaccatgccaggctaatttttgtatttttagtagagacggggtttcaccatgttggccaggctggtctcgaactcctgaccccaaatgatccacccacctcggcctcccaaagtgctgggattacaggtgtgagccaccgcacccagccATGTTGATCTATTTTTAAAAAGTTTTTATTTCCTGTTACACTGTGTTCAGCTATCTTCAGCCACCTTAAATTCCCATGGATGAGTTTTCataaactttttgaaaatagatttagatttacgggaaagttgcaaagataatacagaATTTAATGGATGAGtttttttattgatgtgtaatagatgtatgtattttcagagtacaagtgataatttaatacatgtatataatgtgtaaatattaaatcaagagttattggga

>NM_001282437.2 

GGAAACAGCGCGGGGTCCGCTATGGCGGCGGCAGCCGAGGGCGTACTGGCGACCCGGAGTGATGAGCCCGCCCGAGATGGAGAATGGAGCCGACTTGATGGAATGAAGGCAAGTGGAGGGATGTCGGAACAGGCTGCTTTGGCTGGATTAGCACCGGGTGTAGGCGGGACACTTAGTCATTCTCCCTTGGCCCAGACGATGCCGCCGTGGAGACAGCTGAGGAAGCAAAGGAGCCTGCTGAAGCTGACATCACTGAGCTCTGCCGGGACATGTTCTCCAAAATGGCCACTTACCTGACTGGGGAACTGACGGCCACCAGTGAAGACTATAAGCTCCTGGAAAATATGAATAAACTCACCAGCTTGAAGTATCTTGAAATGAAAGATATTGCTATAAACATTAGTAGGAACTTAAAGGACTTAAACCAGAAATATGCTGGACTGCAGCCTTATCTGGATCAGATCAATGTCATTGAAGAGCAGGTAGCAGCTCTTGAGCAGGCAGCTTACAAGTTGGATGCATATTCAAAAAAACTGGAAGCCAAGTACAAGAAGCTGGAGAAGCGATGAGAAACTTATTTCTATGGGACAGAGTCTTTTTTTTTTAATGTGGAAGAATGTCTTATAAAACCTGAATCCTGAGGCTGATGAATTGTGAAAATTCCTCAAAAGGAAATTATGCTGGTCATCACAGGAACATCTCAACGTTCGAGTAAACTGGAGGACTGTGGCTATTCCTGAACCTTCTTTGAGACAGAATCCCTCAGAATCTCACACTTATAACTTCCTACCTTTTACTTGAATGCTTTGCCATATTCAGGACAGAGACTCTCACAAAGTTCAGAAAACAGCTGGACTTACCAGTAAAATCAAATGAGAGGACCTATTTTCTCTGGTAGTGGTTGATTACTACATTATTTTCTTAAGTGGCTGGTTTTTTAGTTACTATGTAAATGGTCGTTTTTCTGTTAATGATGCTAATGTGTTGTAAACAAGATTCTAAATTTAAAAAGGAAAACAAAACAAACTTGTTCTTTGCAGCTTATCACCTTGTGAATGTCGGTAACTTACTTTTCCATAATATTGCAAATAACATAAAATCTTAAAATAATTCCAAGCTGAGTCTTCTAGATTGAGCAGAAATGGTGAAAGGAGTATTGATAACTTGGCGTATGTGATGGGCCCCTCTTGTTTATTTTCTATGTGAGTCACATTGACATGCGATCAGTTTGGGAAATGTGATGAAAACAAAGACTAGATGGGTATGTGTGTTTATGTGTTGGGTAGGGAGGTGACGATTGCCACTCATAAAATAAAGGATTTTATAAAATACCTTCCTACTGTGTATGTAGGATTTGGGGGGATCTTAGGGACCTAATCGACTTCTTTGCACACTAAAAACATCAGACAATGGGACATACTGACTGACCAGTCTAGGTTGAAAGATAGGCAGCCTTACCCAGAACACAACATTAGCAGCTGGGAAGGTGTCTGAGGTCCCCAATTACATATCCCAAAGAGTttcttacttctgtttctgtcatttcccctctgttccagacagtcatcatttatcctctgttcttcctggactgttgctgtggtctcttctcatcttaactgtcccttccaaccaccctccacactgctgccagagcaatcttaaaaatgtaaactggccctattactcctgcttagaaccctgtagtgacttatcatggcctctgaaaaatctagactttcattatgcatacaagtccctTGTGtttttttgtttgtttatagacagggtctctattgtcacccaggctggagtgtggtggtgtgataatagctcaccttgacctcctaggctcaactgatcttcccacctcagcctcctgaatagctgggactaccagcacgctccaccatgccttgctaattattttttatacagatggagtctcactatgttgtccaggctggtcttgaactggcctcaagtgattctcttaccacagcctgccagagtgctgagattgtaggcatgaaccaccgtgccTAACATAAGGCCCCTATTTAAACATTTTTCTTAAATAAAAAACAAAAGAATTAAACTGTAACTCTACTATCTTAACATAGAATCAGTCTTACCCCTTCTTCCAACCCTTTTCCTTTTCCGTGCATGTATTGATCTAttttttttttttttttgagatgaagtcttgctctgtcgcctgggctggagtgcagtggtgcgatcttagctcactgcaacctctgtttcctgggttcaagcgattctcctgcctcagcctcccgagtagttgagatttacaggtgcccaccaccatgccaggctaatttttgtatttttagtagagacggggtttcaccatgttggccaggctggtctcgaactcctgaccccaaatgatccacccacctcggcctcccaaagtgctgggattacaggtgtgagccaccgcacccagccATGTTGATCTATTTTTAAAAAGTTTTTATTTCCTGTTACACTGTGTTCAGCTATCTTCAGCCACCTTAAATTCCCATGGATGAGTTTTCataaactttttgaaaatagatttagatttacgggaaagttgcaaagataatacagaATTTAATGGATGAGtttttttattgatgtgtaatagatgtatgtattttcagagtacaagtgataatttaatacatgtatataatgtgtaaatattaaatcaagagttattggga

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