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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name CLCP1
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Plot displaying the genomic locations of a retrocopy (in chr22) and its respective parental gene (in chr19). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr22:17424268-17424522  UCSC
Coordinates (T2T) chr22:18091986-18092240  UCSC
Coordinates (hg19) chr22:17903316-17903570  UCSC
Strand -
Parental Sequence NM_020129.3
Parental seq. overlap 209 bp
Parental seq. overlap (%) 34.6%
Genomic Region Intragenic (CECR2)
Retrocopy Summary CLCP1, located on chr22:17424268-17424522, is a retrocopy of the parental gene LGALS14. 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 LGALS14
Full Name galectin 14
Also known as CLC2|PPL13
Coordinate chr19:39704481-39709444
Strand +
Gene summary This gene is predominantly expressed in placenta. The encoded protein belongs to the galectin (galaptin/S-lectin) family. The members of galectin family contain one or two carbohydrate recognition domains, which can bind beta-galactoside. Two alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

Homology

Species Scientific Name Retrocopy
Gibbon Nomascus leucogenys LOC100589518P1
Crab-eating macaque Macaca fascicularis LOC102120471P1
Baboon Papio anubis LOC103880095P1
Golden snub-nosed monkey Rhinopithecus roxellana LOC104676185P1
Chimpanzee Pan troglodytes Without Homology
Bonobo Pan paniscus Without Homology
Gorilla Gorilla gorilla Without Homology
Orangutan Pongo abelii Without Homology
Green monkey Chlorocebus sabaeus Without Homology
Rhesus Macaca mulatta 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

The Genotype-Tissue Expression project - (GTEx)

Adipose SubcutaneousMuscle SkeletalArtery TibialArtery CoronaryHeart Atrial AppendageAdipose VisceralUterusVaginaBreast Mammary TissueSkin Not Sun ExposedMinor Salivary GlandBrain CortexAdrenal GlandThyroidLungSpleenPancreasEsophagus MuscularisEsophagus MucosaEsophagus Gastroesophageal JunctionStomachColon SigmoidSmall Intestine Terminal IleumColon TransverseProstateTestisNerve TibialSkin Sun ExposedHeart Left VentricleBrain CerebellumWhole BloodArtery AortaPituitaryBrain Frontal CortexBrain CaudateBrain Nucleus AccumbensBrain PutamenBrain HypothalamusBrain Spinal CordBrain HippocampusBrain Anterior Cingulate CortexOvaryBrain Cerebellar HemisphereLiverBrain Substantia NigraKidney CortexBrain AmygdalaCervix EctocervixFallopian TubeCervix EndocervixBladderKidney Medulla00.20.40.6
log10(TPM+1)

Related Sequence

>CLCP1
ACAATGAATACCAGGCAATGGTAAACGGCCATCACTGTTACACAGCTTTGCCCATCGACTGCTGCCAGGGTCTGTGAAGATGGTCCAAGTGTGGAGAGATGTCTCCCTGAACTCAAGGTGTGTCTGCAATTGAGGGAGATGACCACACTCCCCATTGTGGAGGAATCCCTTTTTCTACATGACCATGAGATTCCCAGAGCCTGCTAACAGAGTAATCCCTACTCACTCCAACCCTTAGACTTGGTCATTAAAAc
>NM_020129.3
ACAGAAGACTGGACACAATTCCGAAGAGCTGCCCAGAAGGAGAGAACAATGTCATCACTACCCGTACCATACACACTGCCTGTTTCCTTGCCTGTTGGTTCGTGCGTGATAATCACAGGGACACCGATCCTCACTTTTGTCAAGGACCCACAGCTGGAGGTGAATTTCTACACTGGGATGGATGAGGACTCAGATATTGCTTTCCAATTCCGACTGCACTTTGGTCATCCTGCAATCATGAACAGTTGTGTGTTTGGCATATGGAGATATGAGGAGAAATGCTACTATTTACCCTTTGAAGATGGCAAACCATTTGAGCTGTGCATCTATGTGCGTCACAAGGAATACAAGGTAATGGTAAATGGCCAACGCATTTACAACTTTGCCCATCGATTCCCGCCAGCATCTGTGAAGATGCTGCAAGTCTTCAGAGATATCTCCCTGACCAGAGTGCTTATCAGCGATTGAGGGAGATGATCAGACTCCTCATTGTTGAGGAATCCCTCTTTCTACCTGACCATGGGATTCCCAGAGCCTACTAACAGAATAATCCCTCCTCACCCCTTCCCCTACACTTGATCATTAAAACAGCACCAAAC

Publications

PMID - Link Title
No publications available for this retrocopy