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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name SPTLC1P1
Plot displaying the genomic locations of a retrocopy (in chr1) and its respective parental gene (in chr9). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr1:199407810-199407959  UCSC
Coordinates (T2T) chr1:198666568-198666717  UCSC
Coordinates (hg19) chr1:199376938-199377087  UCSC
Strand -
Parental Sequence XM_011518138.2
Parental seq. overlap 117 bp
Parental seq. overlap (%) 8.6%
Genomic Region Intergenic
Retrocopy Summary SPTLC1P1, located on chr1:199407810-199407959, is a retrocopy of the parental gene SPTLC1. 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 SPTLC1
Full Name serine palmitoyltransferase long chain base subunit 1
Also known as HSAN1|HSN1|LBC1|LCB1|SPT1|SPTI
Coordinate chr9:92031141-92115413
Strand -
Gene summary This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxosphinganine with pyridoxal 5'-phosphate and is the key enzyme in sphingolipid biosynthesis. Mutations in this gene were identified in patients with hereditary sensory neuropathy type 1. Alternatively spliced variants encoding different isoforms have been identified. Pseudogenes of this gene have been defined on chromosomes 1, 6, 10, and 13. [provided by RefSeq, Jul 2013]

Homology

Species Scientific Name Retrocopy
Orangutan Pongo abelii LOC100436909P1
Gibbon Nomascus leucogenys LOC101176191P1
Chimpanzee Pan troglodytes Without Homology
Bonobo Pan paniscus Without Homology
Gorilla Gorilla gorilla Without Homology
Green monkey Chlorocebus sabaeus Without Homology
Crab-eating macaque Macaca fascicularis Without Homology
Rhesus Macaca mulatta 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

>SPTLC1P1
TATTGAAGGCTTCTCCTGTGACAGATCTTTCATAATTGACCATCAGTGACTTTCCAGCCAGGATTACTGCTGTTCAGTTTTACTACTTCCCCTGTTAGCTTCTGCTGTAATTGAGGCTGTCAACATCATGGAAGAGAATT
>XM_011518138.2
GCTTGTGACCCGCCTTCCGGAAGGAAGCGGCTAACTATGGCGACCGCCACGGAGCAGTGGGTTCTGGTGGAGATGGTACAGGCGCTTTACGAGGCTCCTGCTTACCATCTTATTTTGGAAGGGATTCTGATCCTCTGGATAATCAGACTTCTTTTCTCTAAGACTTACAAATTACAAGAACGATCTGATCTTACAGTCAAGGAAAAAGAAGAACTGATTGAAGAGTGGCAACCAGAACCTCTTGTTCCTCCTGTCCCAAAAGACCATCCTGCTCTCAACTACAACATCGTTTCAGGCCCTCCAAGCCACAAAACTGTGGTGAATGGAAAAGAATGTATAAACTTCGCCTCATTTAATTTTCTTGGATTGTTGGATAACCCTAGGGTTAAGGCAGCAGCTTTAGCATCTCTAAAGAAGTATGGCGTGGGGACTTGTGGACCCAGAGGATTTTATGGCACATTTGATGTTCATTTGGATTTGGAAGACCGCCTGGCAAAATTTATGAAGACAGAAGAAGCCATTATATACTCATATGGATTTGCCACCATAGCCAGTGCTATTCCTGCTTACTCTAAAAGAGGGGACATTGTTTTTGTAGATAGAGCTGCCTGCTTTGCTATTCAGAAAGGATTACAGGCATCCCGTAGTGACATTAAGTTATTTAAGCATAATGACATGGCTGACCTCGAGCGACTACTAAAAGAACAAGAGATCGAAGATCAAAAGAATCCTCGCAAGGCTCGTGTAACTCGGCGTTTCATTGTAGTAGAAGGATTGTATATGAATACTGGAACTATTTGTCCTCTTCCAGAATTGGTTAAGTTAAAATACAAATACAAAGCAAGAATCTTCCTGGAGGAAAGCCTTTCATTTGGAGTCCTAGGAGAGCATGGCCGAGGAGTCACTGAACACTATGGAATCAATATTGATGATATTGATCTTATCAGTGCCAACATGGAGAATGCACTTGCTTCTATTGGAGGTTTCTGCTGTGGCAGGTCTTTTGTAATTGACCATCAGCGACTTTCCGGCCAGGGATACTGCTTTTCAGCTTCGTTACCTCCCCTGTTAGCTGCTGCAGCAATTGAGGCCCTCAACATCATGGAAGAGAATCCAGCCAGATTAGGATCTTGATGAGAACAAGAGGCATTGATTGTTCTTGAAAGCATCATTCCAGGTTTGTTGAAAGTGGGATACTGAGGTGAGAAGGGGCCAGTTAGCACGCACCAGAGACAAAGCTTGGGCCTTCAGGGGAGTATGGGTTCTTGGCTCTGTTAGTATGTAGAAGGATTTGTAGCATTTTAAATTGATGAACTTGATCTGGGTCTTCAAAAATATTTTTAGGTTAGTACTATC

Publications

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