RCPedia: Rtcs

Summary

Retrocopy Name	SCP2P1	Plot displaying the genomic locations of a retrocopy (in chr5) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr5:71475803-71476310 UCSC
Coordinates (T2T)	chr5:71957119-71957626 UCSC
Coordinates (hg19)	chr5:70771630-70772137 UCSC
Strand	-
Parental Sequence	NM_002979.5
Parental seq. overlap	423 bp
Parental seq. overlap (%)	15.2%
Genomic Region	Intragenic (PTPN18) Intragenic (BDP1)
Retrocopy Summary	SCP2P1, located on chr5:71475803-71476310, is a retrocopy of the parental gene SCP2. 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	SCP2
Full Name	sterol carrier protein 2
Also known as	NLTP\|NSL-TP\|SCOX\|SCP-2\|SCP-CHI\|SCP-X\|SCPX
Coordinate	chr1:52927276-53051698
Strand	+
Gene summary	This gene encodes two proteins: sterol carrier protein X (SCPx) and sterol carrier protein 2 (SCP2), as a result of transcription initiation from 2 independently regulated promoters. The transcript initiated from the proximal promoter encodes the longer SCPx protein, and the transcript initiated from the distal promoter encodes the shorter SCP2 protein, with the 2 proteins sharing a common C-terminus. Evidence suggests that the SCPx protein is a peroxisome-associated thiolase that is involved in the oxidation of branched chain fatty acids, while the SCP2 protein is thought to be an intracellular lipid transfer protein. This gene is highly expressed in organs involved in lipid metabolism, and may play a role in Zellweger syndrome, in which cells are deficient in peroxisomes and have impaired bile acid synthesis. Alternative splicing of this gene produces multiple transcript variants, some encoding different isoforms.[provided by RefSeq, Aug 2010]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	SCP2P1
Bonobo	Pan paniscus	SCP2P1
Orangutan	Pongo abelii	SCP2P1
Gibbon	Nomascus leucogenys	SCP2P1
Green monkey	Chlorocebus sabaeus	SCP2P1
Crab-eating macaque	Macaca fascicularis	SCP2P1
Rhesus	Macaca mulatta	SCP2P1
Golden snub-nosed monkey	Rhinopithecus roxellana	SCP2P1
Marmoset	Callithrix jacchus	SCP2P1
Gorilla	Gorilla gorilla	Without Homology
Baboon	Papio anubis	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

>SCP2P1
TCAGTGTGCTGAACTTTGCTAGCAGCTGAGAAAGGAAGCTAGAAAGAGGCAAGCTCCTGATGCAAAGGTTGGCGTGCAGCATAATTTAGGCCTTAGAGAAGCTGGGGTTTTAACACTTCACAAGATGTGTTTTCTCAAAGCTGCCAGTTCTTTTAGAACTCATCAAATTAGGCTGCTCCAACCAGCTTTACAGGGAATGGATTTAAGGCAAATCTTGTGTTTAAAGAGATTTAGAGGAAGCCTGAAGAGGAAAGTGGACAGATTGTGAAGAAAATCCGTGGTATTTTTGCCTTTAAGGTGAAGAATGAATGGCCTAGGGGGTAAAGAAGCCACCTAGTGGTGGAGGTAAAGAACACAAAGGATCAGTGCTTTCTAACTCTAACTCAGATGAGAAAGCTGACCACACAATCACAAAGACTGACTAGGATTTACTGGCTTTAGTGATTGAAGTGGTAAAATGAATCCTCAGTTCTCCTTCTTTCAAGGCAAAGGGAAAATCACTGGCAAT

>NM_002979.5
ACGCGCCTGTGTTGCCGCCCGCGGCCCTGGCTTCGGGCTTCAGGGAGCTCTGGTGCAGTCTCCGCCTGTCAGTGCCGGCAGTCGTCCGCGGCGCCCGCCCCGGTCCCGCACTGGTGCAGCCATGTCCTCTTCCCCGTGGGAGCCTGCGACCCTGCGCCGGGTGTTCGTGGTGGGGGTTGGCATGACCAAGTTTGTGAAGCCTGGAGCTGAGAATTCAAGAGACTACCCTGACTTGGCAGAAGAAGCAGGCAAGAAGGCTTTAGCTGATGCACAGATCCCTTATTCAGCAGTGGACCAGGCATGTGTTGGCTATGTTTTTGGTGACTCTACCTGTGGGCAGAGGGCTATCTATCACAGTTTGGGAATGACTGGAATTCCTATAATCAATGTCAACAATAACTGTGCTACTGGTTCTACTGCTTTGTTTATGGCCCGCCAGCTGATTCAGGGTGGTGTGGCAGAATGTGTCTTGGCTCTTGGGTTTGAGAAGATGAGTAAGGGAAGCCTTGGAATAAAATTTTCAGATAGAACCATTCCCACTGATAAGCATGTTGACCTCCTGATCAATAAGTATGGATTGTCTGCTCACCCAGTTGCTCCTCAGATGTTTGGGTATGCTGGAAAAGAACATATGGAAAAATATGGAACAAAAATTGAACACTTTGCAAAAATTGGATGGAAAAATCATAAACATTCAGTTAATAACCCGTATTCCCAGTTCCAAGATGAATACAGTTTAGATGAAGTGATGGCATCTAAAGAAGTTTTTGATTTTTTGACTATCTTACAATGTTGTCCCACTTCAGATGGTGCTGCAGCAGCAATTTTGGCCAGTGAAGCATTTGTACAGAAGTATGGCCTGCAATCCAAAGCTGTGGAAATTTTGGCACAAGAAATGATGACTGATTTGCCAAGCTCGTTTGAAGAAAAAAGCATTATTAAAATGGTTGGCTTTGATATGAGTAAAGAAGCTGCAAGAAAATGCTATGAGAAATCTGGCCTGACACCAAATGATATTGACGTAATAGAACTTCACGATTGCTTTTCTACCAACGAACTCCTTACTTATGAAGCACTGGGACTCTGTCCAGAAGGACAAGGTGCAACGCTGGTTGATAGAGGAGATAATACATATGGAGGAAAGTGGGTCATAAATCCTAGTGGTGGACTGATTTCAAAGGGACACCCACTAGGCGCTACAGGTCTTGCTCAGTGTGCAGAACTCTGCTGGCAGCTGAGAGGGGAAGCCGGAAAGAGGCAAGTTCCTGGTGCAAAGGTGGCTCTGCAGCATAATTTAGGCATTGGAGGAGCTGTGGTTGTAACACTCTACAAGATGGGTTTTCCGGAAGCCGCCAGTTCTTTTAGAACTCATCAAATTGAAGCTGTTCCAACCAGCTCTGCAAGTGATGGATTTAAGGCAAATCTTGTTTTTAAGGAGATTGAGAAGAAACTTGAAGAGGAAGGGGAACAGTTTGTGAAGAAAATCGGTGGTATTTTTGCCTTCAAGGTGAAAGATGGCCCTGGGGGTAAAGAGGCCACCTGGGTGGTGGATGTGAAGAATGGCAAAGGATCAGTGCTTCCTAACTCAGATAAGAAGGCTGACTGCACAATCACAATGGCTGACTCAGACTTCCTGGCTTTAATGACTGGTAAAATGAATCCTCAGTCGGCCTTCTTTCAAGGCAAATTGAAAATCACTGGCAACATGGGTCTCGCTATGAAGTTACAAAATCTTCAGCTTCAGCCAGGCAACGCTAAGCTCTGAAGAACTCCCTTTGGCTACTTTTGAAAATCAAGATGAGATATATAGATATATATCCATACATTTTATTGTCAGAATTTAGACTGAAACTACACATTGGCAAATAGCGTGGGATAGATTTGTTTCTTAATGGGTGTGACCAATCCTGTTTTTCCTATGCTCTGGGTGAATAGAGCCTGATGGTATACTACTGCTTTGCGGAATTGCATACAACTGTGCATTACAAAGTTAATATGGTAATTATGGTCTGGGGTAAAATTGAGTTTCAGAATAAAATTAGGAACAGTAAAATCCAAAGAACTATGTAAACAAAAAAGCTTTTGTTTTGCTTACAAAGTATATTTAAGGATTATTCTGCTGAAGATTCAGTTTAAGAGTTTTCCTTGGGAGAACTAAGTAAGAAACACAATGCCAACAGCTGGCCAGTAATTAGTGTTGTGCACTTCATGTCATTAATCAATTTCTCAATAGTTCTTAAAATTAGTGAGATTAAAAATCTAAAAATTTTGCATTTCATGCTATCAGAAACAGTATTTTCTTCCCAAATCAAAATAAAAGAAATATGATCAGAGCTTGAACACAGGCTTATTTTTAAAATAAAAATATTTTTAACATGGGTTTCCTTATTGAAAAATCAGTGTATTAGTCATAAAACACCATCATTAAGAATAATTGAACAATAAAGTTTGCTTTCAGATGCAGTTTTCAAATTATAATCTCATTTCAATTTATAACGTTCTCAGTCCTTTGTTATAATTTTCCTTTTTCATGTAAGTTTAATTATCTGCATTTATCTTTTTTCCTAGTTTTTCTAATACTAATGTTATTTCTTAAAATTCAGTGAGATATAGGATAAAATAATGCTTTGAGAAGAATGTTTAATAGAAAATTAAAATAACTTTTTCTGGCCTCTCTTGTTTTTACTGTGTATGTTCTTGCTCAGGGCTCTCTAGATAATGCAGAATAAAGAGAAACGTTGGGGGATTTATAAACTGAA

>NM_002979.5 

ACGCGCCTGTGTTGCCGCCCGCGGCCCTGGCTTCGGGCTTCAGGGAGCTCTGGTGCAGTCTCCGCCTGTCAGTGCCGGCAGTCGTCCGCGGCGCCCGCCCCGGTCCCGCACTGGTGCAGCCATGTCCTCTTCCCCGTGGGAGCCTGCGACCCTGCGCCGGGTGTTCGTGGTGGGGGTTGGCATGACCAAGTTTGTGAAGCCTGGAGCTGAGAATTCAAGAGACTACCCTGACTTGGCAGAAGAAGCAGGCAAGAAGGCTTTAGCTGATGCACAGATCCCTTATTCAGCAGTGGACCAGGCATGTGTTGGCTATGTTTTTGGTGACTCTACCTGTGGGCAGAGGGCTATCTATCACAGTTTGGGAATGACTGGAATTCCTATAATCAATGTCAACAATAACTGTGCTACTGGTTCTACTGCTTTGTTTATGGCCCGCCAGCTGATTCAGGGTGGTGTGGCAGAATGTGTCTTGGCTCTTGGGTTTGAGAAGATGAGTAAGGGAAGCCTTGGAATAAAATTTTCAGATAGAACCATTCCCACTGATAAGCATGTTGACCTCCTGATCAATAAGTATGGATTGTCTGCTCACCCAGTTGCTCCTCAGATGTTTGGGTATGCTGGAAAAGAACATATGGAAAAATATGGAACAAAAATTGAACACTTTGCAAAAATTGGATGGAAAAATCATAAACATTCAGTTAATAACCCGTATTCCCAGTTCCAAGATGAATACAGTTTAGATGAAGTGATGGCATCTAAAGAAGTTTTTGATTTTTTGACTATCTTACAATGTTGTCCCACTTCAGATGGTGCTGCAGCAGCAATTTTGGCCAGTGAAGCATTTGTACAGAAGTATGGCCTGCAATCCAAAGCTGTGGAAATTTTGGCACAAGAAATGATGACTGATTTGCCAAGCTCGTTTGAAGAAAAAAGCATTATTAAAATGGTTGGCTTTGATATGAGTAAAGAAGCTGCAAGAAAATGCTATGAGAAATCTGGCCTGACACCAAATGATATTGACGTAATAGAACTTCACGATTGCTTTTCTACCAACGAACTCCTTACTTATGAAGCACTGGGACTCTGTCCAGAAGGACAAGGTGCAACGCTGGTTGATAGAGGAGATAATACATATGGAGGAAAGTGGGTCATAAATCCTAGTGGTGGACTGATTTCAAAGGGACACCCACTAGGCGCTACAGGTCTTGCTCAGTGTGCAGAACTCTGCTGGCAGCTGAGAGGGGAAGCCGGAAAGAGGCAAGTTCCTGGTGCAAAGGTGGCTCTGCAGCATAATTTAGGCATTGGAGGAGCTGTGGTTGTAACACTCTACAAGATGGGTTTTCCGGAAGCCGCCAGTTCTTTTAGAACTCATCAAATTGAAGCTGTTCCAACCAGCTCTGCAAGTGATGGATTTAAGGCAAATCTTGTTTTTAAGGAGATTGAGAAGAAACTTGAAGAGGAAGGGGAACAGTTTGTGAAGAAAATCGGTGGTATTTTTGCCTTCAAGGTGAAAGATGGCCCTGGGGGTAAAGAGGCCACCTGGGTGGTGGATGTGAAGAATGGCAAAGGATCAGTGCTTCCTAACTCAGATAAGAAGGCTGACTGCACAATCACAATGGCTGACTCAGACTTCCTGGCTTTAATGACTGGTAAAATGAATCCTCAGTCGGCCTTCTTTCAAGGCAAATTGAAAATCACTGGCAACATGGGTCTCGCTATGAAGTTACAAAATCTTCAGCTTCAGCCAGGCAACGCTAAGCTCTGAAGAACTCCCTTTGGCTACTTTTGAAAATCAAGATGAGATATATAGATATATATCCATACATTTTATTGTCAGAATTTAGACTGAAACTACACATTGGCAAATAGCGTGGGATAGATTTGTTTCTTAATGGGTGTGACCAATCCTGTTTTTCCTATGCTCTGGGTGAATAGAGCCTGATGGTATACTACTGCTTTGCGGAATTGCATACAACTGTGCATTACAAAGTTAATATGGTAATTATGGTCTGGGGTAAAATTGAGTTTCAGAATAAAATTAGGAACAGTAAAATCCAAAGAACTATGTAAACAAAAAAGCTTTTGTTTTGCTTACAAAGTATATTTAAGGATTATTCTGCTGAAGATTCAGTTTAAGAGTTTTCCTTGGGAGAACTAAGTAAGAAACACAATGCCAACAGCTGGCCAGTAATTAGTGTTGTGCACTTCATGTCATTAATCAATTTCTCAATAGTTCTTAAAATTAGTGAGATTAAAAATCTAAAAATTTTGCATTTCATGCTATCAGAAACAGTATTTTCTTCCCAAATCAAAATAAAAGAAATATGATCAGAGCTTGAACACAGGCTTATTTTTAAAATAAAAATATTTTTAACATGGGTTTCCTTATTGAAAAATCAGTGTATTAGTCATAAAACACCATCATTAAGAATAATTGAACAATAAAGTTTGCTTTCAGATGCAGTTTTCAAATTATAATCTCATTTCAATTTATAACGTTCTCAGTCCTTTGTTATAATTTTCCTTTTTCATGTAAGTTTAATTATCTGCATTTATCTTTTTTCCTAGTTTTTCTAATACTAATGTTATTTCTTAAAATTCAGTGAGATATAGGATAAAATAATGCTTTGAGAAGAATGTTTAATAGAAAATTAAAATAACTTTTTCTGGCCTCTCTTGTTTTTACTGTGTATGTTCTTGCTCAGGGCTCTCTAGATAATGCAGAATAAAGAGAAACGTTGGGGGATTTATAAACTGAA

Publications

PMID - Link	Title