Imagem 1

Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name SFPQP1
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Plot displaying the genomic locations of a retrocopy (in chrY) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chrY:13094874-13095801  UCSC
Coordinates (T2T) chrY:14003146-14004073  UCSC
Coordinates (hg19) chrY:15206788-15207715  UCSC
Strand +
Parental Sequence NM_005066.3
Parental seq. overlap 773 bp
Parental seq. overlap (%) 20.6%
Genomic Region Intergenic
Retrocopy Summary SFPQP1, located on chrY:13094874-13095801, is a retrocopy of the parental gene SFPQ. 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 SFPQ
Full Name splicing factor proline and glutamine rich
Also known as POMP100|PPP1R140|PSF
Coordinate chr1:35176380-35193174
Strand -
Gene summary Enables DNA binding activity; histone deacetylase binding activity; and protein homodimerization activity. Involved in several processes, including alternative mRNA splicing, via spliceosome; positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway; and regulation of transcription by RNA polymerase II. Acts upstream of or within double-strand break repair via homologous recombination. Located in chromatin; nuclear matrix; and paraspeckles. [provided by Alliance of Genome Resources, Apr 2022]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes SFPQP1
Green monkey Chlorocebus sabaeus SFPQP2
Rhesus Macaca mulatta SFPQP2
Baboon Papio anubis SFPQP1
Bonobo Pan paniscus Without Homology
Gorilla Gorilla gorilla Without Homology
Orangutan Pongo abelii Without Homology
Gibbon Nomascus leucogenys Without Homology
Crab-eating macaque Macaca fascicularis 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

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 Medulla00.050.10.15
log10(TPM+1)

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

Related Sequence

>SFPQP1
ATTATGTTTCCAAAGAACTATTGGAAGAAACTTTTAACCAGCTTGGTGCTATTGAAAGGACCATTTAATAATGGATGAACATGGAATATCTATAGGAAAAAGCATTGTTGAATTTATTCTAGATTAGTAGTAGCAAGAAAGGCATTTGAATGATGCAGTAAAGATGTTTTCTTACTGACAACTCCTCATCTAGTCATTGTGAAACCACTCGAACAACTAAATGGTGATGACAGTATTCTTGAAAAAATTTCACAGAAGGGTCCAGTGTATCAAAAGAGAGATAAATCGCTCCTCATTTTGCCCTATATGACATTTAATTCTGAATATTCTTAGTGATGGAAGTCCTTGGATGAAACAAAACAGCAAAGGAATCATGTTGAAAAAACATGAATCATGTAAAATACTAATTTGGAAAGTGAAATAGGAGATGCACTCAAGGAACATCAAGGAAATCTTTTGCACCAAGATCTGATAAGGCAGGAGGAAGAATTATGATGCATGCAAAAACTTCACAATCAAGGAATGCAGAAACATAAAGAAATGCAATTGAGGCAAGAGGAGAAACGACAGAGGAGGAAAAGATGATGATTCATTGATATGGGATGGAAGAACAGATGAGGCACCAAATTACAGGAAAATTACAGTCAGATGGGCTACATGGATCCAAGAGAAAGAGATATGAGAATGGGTGGCACAGGAGATCCCTATGGTTCAGGAGGCCAGAAATGTCCACCTCTAGATGATAATGATGGCATAGGTTATGACACTAATTTTAGAATTCCATTAGAAACCACGAGTGGATCCATGAAGGAAAGTGTCATGTGTATGGAGTGATTTGGGCAAGAAGACACAGGACTTGTGGGGGGAAGGGTCCTAGATGAATGGAGCCCAGAATTCCACAGGGATATTGTAGAGGGAGAGAAGAGTA
>NM_005066.3
GCCTGTGTCATCCGCCATTTTGTGAGAAGCAAGGTGGCCTCCACGTTTCCTGAGCGTCTTCTTCGCTTTTGCCTCGACCGCCCCTTGACCACAGACATGTCTCGGGATcggttccggagtcgtggcggtggcggtggtggcttccacaggcgtggaggaggcggcggccgcggcggcCTCCACGACTTCCGTTCTCCGCCGCCCGGCATGGGCCTCAATCAGAATCGCGGCCCCATGGGTCCTGGCCCGGGCCAGAGCGGCCCTAAGCCTCCGATCccgccaccgcctccacaccaacagcagcaacagccaccaccgcagcagccaccgccgcagcagccgccaccgcatcagccgccgccgcatccacagccgcatcagcagcagcagccgccgccaccgccgcAGGACTCTTCCAAGCCCGTCGTTGCTCAGGGACCCGGCCCCGCTCCCGGAGTAGGCAGCGCACCACCAGCCTCCAGCTCGGCCCCGCCCGCCACTCCACCAACCTCGGGGGCCCCGCCAGGGTCCGGGCCAGGCCCGACTCCGACCCCGCCGCCTGCAGTCACCTCGGCCCCTCCCGGGGCGCCGCCACCCACCCCGCCAAGCAGCGGGGTCCCTACCACACCTCCTCAGGCCGGAGGCCCGCCGCCTCCGCCCGCGGCAGTCCCGGGCCCGGGTCCAGGGCCTAAGCAGGGCCCAGGTCCGGGTGGTCCCAAAGGCGGCAAAATGCCTGGCGGGCCGAAGCCAGGTGGCGGCCCGGGCCTAAGTACGCCTGGCGGCCACCCCAAGCCGCCGCATCGAGGCGGCGGGGAGCCCCGCGGGGGccgccagcaccacccgccctaccaccagcagcatcaccaGGGGCCCCCGCCCGGCGGGCCCGGCGGCCGCAGCGAGGAGAAGATCTCGGACTCGGAGGGGTTTAAAGCCAATTTGTCTCTCTTGAGGAGGCCTGGAGAGAAAACTTACACACAGCGATGTCGGTTGTTTGTTGGGAATCTACCTGCTGATATCACGGAGGATGAATTCAAAAGACTATTTGCTAAATATGGAGAACCAGGAGAAGTTTTTATCAACAAAGGCAAAGGATTCGGATTTATTAAGCTTGAATCTAGAGCTTTGGCTGAAATTGCCAAAGCCGAACTGGATGATACACCCATGAGAGGTAGACAGCTTCGAGTTCGCTTTGCCACACATGCTGCTGCCCTTTCTGTTCGTAATCTTTCACCTTATGTTTCCAATGAACTGTTGGAAGAAGCCTTTAGCCAATTTGGTCCTATTGAAAGGGCTGTTGTAATAGTGGATGATCGTGGAAGATCTACAGGGAAAGGCATTGTTGAATTTGCTTCTAAGCCAGCAGCAAGAAAGGCATTTGAACGATGCAGTGAAGGTGTTTTCTTACTGACGACAACTCCTCGTCCAGTCATTGTGGAACCACTTGAACAACTAGATGATGAAGATGGTCTTCCTGAAAAACTTGCCCAGAAGAATCCAATGTATCAAAAGGAGAGAGAAACCCCTCCTCGTTTTGCCCAGCATGGCACGTTTGAGTACGAATATTCTCAGCGATGGAAGTCTTTGGATGaaatggaaaaacagcaaagggaacaagttgaaaaaaacatgaaagatgcaaaagacaaattggaaagtgaaatggaagatgCCTATCATGAACATCAGGCAAATCTTTTGCGCCAAGATCTGATGAGACGACAGGAAGAATTAAGACGCATGGAAGAACTTCACAATCAAGAAATGCAGAAACGTAAAGAAATGCAATTGAGGCAAGAGGAGGAACGACGTAGAAGAGAGGAAGAGATGATGATTCGTCAACGTGAGATGGAAGAACAAATGAGGCGCCAAAGAGAGGAAAGTTACAGCCGAATGGGCTACATGGATCCACGGGAAAGAGACATGCGAATGGGTGGCGGAGGAGCAATGAACATGGGAGATCCCTATGGTTCAGGAGGCCAGAAATTTCCACCTCTAGGAGGTGGTGGTGGCATAGGTTATGAAGCTAATCCTGGCGTTCCACCAGCAACCATGAGTGGTTCCATGATGGGAAGTGACATGCGTACTGAGCGCTTTGGGCAGGGAGGTGCGGGGCCTGTGGGTGGACAGGGTCCTAGAGGAATGGGGCCTGGAACTCCAGCAGGATATGGTAGAGGGAGAGAAGAGTACGAAGGCCCAAACAAAAAACCCCGATTTTAGATGTGATATTTAGGCTTTCATTCCAGTTTGTTTTGTTTTTTTGTTTAGATACCAATCTTTTAAATTCTTGCATTTTAGTAAGAAAGCTATCTTTTTATGGATGTTAGCAGTTTATTGACCTAATATTTGTAAATGGTCTGTTTGGGCAGGTAAAATTATGTAATGCAGTGTTTGGAACAGGAGAAtttttttttcctttttatttctttattttttcttttttACTGTATAATGTCCCTCAAGTTTATGGCAGTGTACCTTGTGCCACTGAATTTCCAAAGTGTACCAATTTTTTTTTTTTTACTGTGCTTCAAATAAATAGAAAAATAGTTATAATATTGATCTTCAACTTTGCCATTCATGCTTCTATGCATATTAGGCTACGTATTCCACATTGAAAGCATGAGAGTGTCTAGGCCTTTGAATGGCATATGCCATTTCTGGGAAATGCATCTGGAGGCTAAGTATTGCTTTCTACAAATAATTGCCCCCTTTGTTTTAAAAAGAAGAAATGCATATTGAAGTAGTTTGATGATTTGTTTGGCATATAGGAAGCACGCTGGTGCTAAGTATTTTTTAAATGGTTATGTAAGCAAAGCTGAACTGTAAATCTTCAGGAATATGTATTAAGATTGTGGAATGGGTGTAAGACAATTGGTAGGGGGTGAAAGTGGGTTTGATTAAATGGATCTTTTATGGCCCTATGATCTATCCTTTACTTGAAAGCTTTTGAAAAGTGGAAAGGTCATTTTGTTGCATTTCCCCATTTCTTGTTTTTAAAAGACCAACAAATCTCAAGCCCTATAAATGGCTTGTATTGAACTTTTACATTTGAATTAAAGATGTTAAACATGAAGTCTTTTCATGTATTCAAGTGATTTATAAAGATGGGGTGTAGTCTAAAAAACAAAACTTGAAAGTAAGAAGGTTTAGTAACTGggccgggcgcggtggctcacgcctgtaatcccagcactttgggaggctgaggtgggcaaatcatgagatcaggagttcaagaccagcctggccaacatggtgaaaccccgtctctactaaaaatacaaaaaattagctgggcgtggtggcaggcgcctgtaatcccagctactcgggaggctgagccaggagaattgcttgaacctggagatggaggttgcagtgagctgagactgccactgcactccagcctggacaacagagcgagactctgtctcaaaaaaaaaaaaaGGTTTAGTACTGAAGTAGGTTTAGTTATATATACATTTGTACTCTGTAACTTTTACATCTCCTTGTGCTACTTCTGTTGGGCAAAATCTATAGGACTATAAAAATCTATTGGTTCTCTTCTAAGAGCTAGTGGTGATTGTTAACAAATAGGGTTGCAGATAATCATTCTTATTGTAAATTTAACTTGTTTTCACATAGTTTCGTTTTCATGTAGCACTAAATCTGGAGAAAGTTGCTCATGCTACACAGTACAAATATCCCTTCCTCCCACCATAAAGGCTTGGAATGTT

Publications

PMID - Link Title
No publications available for this retrocopy