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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name ISCA1P2
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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) chr1:229042244-229042680  UCSC
Coordinates (T2T) chr1:228420862-228421298  UCSC
Coordinates (hg19) chr1:229177991-229178427  UCSC
Strand +
Parental Sequence NM_030940.4
Parental seq. overlap 414 bp
Parental seq. overlap (%) 21%
Genomic Region Intergenic
Retrocopy Summary ISCA1P2, located on chr1:229042244-229042680, is a retrocopy of the parental gene ISCA1. 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 ISCA1
Full Name iron-sulfur cluster assembly 1
Also known as HBLD2|ISA1|MMDS5|hIscA
Coordinate chr9:86264546-86282538
Strand -
Gene summary ISCA1 is a mitochondrial protein involved in the biogenesis and assembly of iron-sulfur clusters, which play a role in electron-transfer reactions (Cozar-Castellano et al., 2004 [PubMed 15262227]).[supplied by OMIM, Mar 2008]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes ISCA1P1
Bonobo Pan paniscus ISCA1P1
Gorilla Gorilla gorilla ISCA1P1
Orangutan Pongo abelii ISCA1P1
Gibbon Nomascus leucogenys ISCA1P2
Green monkey Chlorocebus sabaeus ISCA1P7
Crab-eating macaque Macaca fascicularis ISCA1P1
Rhesus Macaca mulatta ISCA1P1
Baboon Papio anubis ISCA1P1
Golden snub-nosed monkey Rhinopithecus roxellana ISCA1P3
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 Medulla00.10.2
log10(TPM+1)

Massive Mining of Publicly Available RNA-seq Data from Human and Mouse - (ARCHS4)

Related Sequence

>ISCA1P2
AAAGAGGAAACTGCAGCCCAACGGGGCTGCCTTCACCCTGACACCCTCAGCAGTAAACAAGATAAAACAACTTCTTAAAGATAAGCCTGAGCATGTAGGTGTAAACGCTGGTGTCTGAATCAGGGGCTGTAATGGCCTTTCTTATACTGTAGAATATACAAAGACAAAAGGAGATTCTGATGAAGAAGTTATTCAAGATGGAGTCAGAGTATTCATCGAAAAGAAAGCCCAGCTAACACTTTTAGGAACAGAAATGGACTATGTTGAAGACAAATTATCCAGTGAGTTTTTGTTCAATAACCCAAACATCAAAGGAACTTGTGGCTGTCGAGAAACCTTTAATATTTGAAATCTCAGGACTCTTCTGGCCATAGGCTCCAGGAAAGCTCGTGGAAGCCTTGGGGCTCACTGAAGAAATCACGTGACTGTCACATGCT
>NM_030940.4
AATGCGCCCGCCGTGTCCATGGAGAGAAGCTGAGGCGGCCGACCTTCGGCCCGAGGCACCGGGGCGCCGGGACGGCGAAGATGTCGGCTTCCTTAGTCCGGGCAACTGTCCGGGCTGTGAGCAAGAGGAAGCTGCAGCCCACCCGGGCAGCCCTCACCCTGACACCTTCAGCAGTAAACAAGATAAAACAACTTCTTAAAGATAAGCCTGAGCATGTAGGTGTAAAAGTTGGTGTCCGAACCAGGGGCTGTAATGGCCTTTCTTATACTCTAGAATATACAAAGACAAAAGGAGATTCTGATGAAGAAGTTATTCAAGATGGAGTCAGAGTATTCATCGAAAAGAAAGCACAGCTAACACTTTTAGGAACAGAAATGGACTATGTTGAAGACAAATTATCCAGTGAGTTTGTGTTCAATAACCCAAACATCAAAGGGACTTGTGGCTGTGGAGAAAGCTTTAATATTTGAAATCTCAGGACTCTTCTGGCCGTAGGTTCCAGGAAAGCTCGTGGAAGCTTTGGGGCTCACTGCAGAAATCATGTGACTGTCACGTGCTGGAAAATAAAGTGATACATCTTGAAAATGAATCCAGTGTGTTGGATTCCAGAAGAAATGATATTTATATTCTCTATAGGGGACAGAAAATGAGAAGCCATCACTCTTTTTGGATCATTTAGGTCTCTTGTATCCTTTGTTTTAGAACCAGTTTCATTAAAGTTGCCTTCCTGGGCACCTGTTTATCCATTTCCTGAACTGTGTGCACTCCTTAGATCGCTATTGATGGCTTGATCATCCCTCAGCATTTCTCCCAACCAGATCGGTGACTCCTAAAATCTGAGACAGGACATCGTGACTGCTGGTAGTAATATGGTGGTGCATTGTTTTTTCCACCCAAACTTAACATAGCCTTTTTATACATTTTTATGAAAAATTTCATTGTCAGCTGCCTCACTGCATACTCTTTAATAGTACCAGGCAAAGATTTTCTTCAACTATAGTACAGATTAGTTCTGAGTGATGGTATCAAAAGGTGAGAAAGACGTCATCCGCCTTTTTTTAATCCATTTCTTTTGCCACCCTATATGTCTGTTCAGAGATGGGCTCTCAAGCTGACTTTGATTCTTTTAGTTGAGAAGTCTCTTAAAGCCATCTAGCCCACCTCCATCAATTCCCTATGTGAGGAAGCAAAACCCCAGGGAAGCCAAAGGGCTCCTGTCCACCCTGACACCACAGGCCGGGGGAGAGTAGGGACTCTACCCCCCTCTCCCCTTGTAGGTGACACATGCTCTGCCCTCTGAGGCAGTCAGCGAAGGCAAATGGTCTGACTTCTTTATGTGGTCAACATTTTGATAGAATTTCTTTATAATTTGATAGAGATTATATTATTTTTATTTTATTTTGAGTGGGAAGAATTTTAAAACCTTTTTATGTCAATTACCATCTTGTTTCTTTCACCTTTGAAACAATGGTTTGTAGCAGAGATGACATTGTAGCAACCCAGAATTATGCTTTTGGAATGTGGTCCTCACTGTACAGGAGAATGTGTAATCTTTTGTTAAAATTCCCAGTGTGCATACATTTTCTGGTTCCTCGGTCCAGTTGCTAAAGTTCTTAGTATTTTAGCCTAACATATTTATCACCAACTTTTCTTTAAAAGTGTTCCTTTTGTCACTTAGTTACTGATTTTCCTGGGTTTGACATAAGTATTCTATGAGATGATATATATGCTTTTTTTGAAAGCTGATTCTCATGAATTCAAGTAGCTGAGTTCCTTTATGTTTCGTTTATTCACTAAAGTAGCTGACACAAAACACACCAAAACCTAGAGCGGTAGTTTTATGTAAATGCTCATGAGTTTGTATCAATAATATAATTGTTGATCCACTTATAATTCGTGCAACACTGTATGTATGTAGAGATTGAGTTGTCAATTAAAAAAAATGTGGCCTCTTTGTGATCATAAAA

Publications

PMID - Link Title
No publications available for this retrocopy