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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name H3f3aP27
Plot displaying the genomic locations of a retrocopy (in chr12) and its respective parental gene (in chr1). Each line represents a retrocopy.
Species Mus musculus
Coordinates chr12:104993156-104994225  UCSC
Strand -
Parental Sequence NM_008210.5
Parental seq. overlap 775 bp
Parental seq. overlap (%) 69.2%
Genomic Region Intergenic
Retrocopy Summary H3f3aP27, located on chr12:104993156-104994225, is a retrocopy of the parental gene H3f3a. 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 H3f3a
Full Name H3.3 histone A
Also known as EyeLinc14|H3-3a|H3-3b|H3.3A
Coordinate chr1:180630125-180641170
Strand -
Gene summary Histones are basic nuclear proteins that are responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two molecules of each of the four core histones (H2A, H2B, H3, and H4) form an octamer, around which approximately 146 bp of DNA is wrapped in repeating units, called nucleosomes. The linker histone, H1, interacts with linker DNA between nucleosomes and functions in the compaction of chromatin into higher order structures. This gene contains introns and its mRNA is polyadenylated, unlike most histone genes. The protein encoded is a replication-independent member of the histone H3 family. [provided by RefSeq, Nov 2015]

Homology

Species Scientific Name Retrocopy
Rat Rattus norvegicus LOC100359421P6
Human Homo sapiens Without Homology
Chimpanzee Pan troglodytes Without Homology
Bonobo Pan paniscus Without Homology
Gorilla Gorilla gorilla Without Homology
Orangutan Pongo abelii Without Homology
Gibbon Nomascus leucogenys 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
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

>H3f3aP27
gTGGTAAAACACCCAGGAAACAACTGGCTTCAAAAGCCGCTCACACGCGTGCGCCCTCTACTGGACGGTGAAGAAACCTCGTCGTCACAGGCCCAGTACTGTGGCACTCTGAAATCAGCCGCTATCAGAAGTCAACAGAACTGAACTGCTGACTCGCAAGCTCCCCTTTCAGCGTCTGGTGCAAGAAATTGCTCAGGATTTCAAAACAGATCTGCGCTTCCAGAGTGCAGATACTGGTGCTGAGCAGGAGGCAAGTGAGGCCTATCGGGTTGGCCTTTGGGAAGATACCAATCTGTGTGCTATCCATGCCAAACATGTAAATCTCCAAAAGATATCCAGCTACACACGCAGAGAACATGCTTAAGAGTCcactattaggtTAAAAAAAGTACTCTATGAGAGGAAAAATTtcattctcaaaataaaaaatttttttcctcttcttcctgttatcAGTAGTTCTGAATGTTAGATAATTTTTCCATGGGATCAAAGGTACCCAAGTATATGATTGGGGGGTGGAAACATAGGGGACAGAATCAGGTATTGGTAGCTTCTCCACATTCATGTGTGAGCTTTTAATATAAATTCAAGATGTAAAGCATTAATGCAAGCAAAATGTTTCAGTGAACACGTTTTCAACAGTTCAACTTtataacaattttaaataaaCCTGTTAGATTTTTCTGAACAATGCCAGCATTCGGATTTTTAAAACATAAGTAAATTTATATTGACAGAAACTAAATGGTGTTTGTGACATTTTTATCATCCAGTAGAGTTCATCCATTCACTATACCTTCTGAGTTGCCCTGTGTACAAGTTTTTAATATTGTCTGTCCTCTGCTTTTCCTATAAGTTTGCTattaaaacacattaaactc
>NM_008210.5
GGGGCGGCGtgtgtaggggaaagcctcggTGTCAGCCATCTTTCAATTGTGTTCGCAGCCTTCGCCGCGCCGCTGCCGCTCTCCAACGCCAGCGCCGCCTCTCGCTTGCCGAGCTCCAGCCGAAGGAGAAGGGGGGTAAGTAAGGAGGTGTCCTTACCATGGCTCGTACAAAGCAGACTGCCCGCAAATCCACCGGTGGTAAAGCACCCAGGAAACAACTGGCTACAAAAGCCGCTCGCAAGAGTGCGCCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACAGGCCTGGTACTGTGGCCCTCCGTGAAATCAGACGCTATCAGAAGtccactgaacttctgatccgCAAGCTCCCCTTTCAGCGTCTGGTGCGAGAAATTGCTCAGGACTTCAAAACAGATCTGCGCTTCCAGAGTGCAGCTATTGGTGCTTTGCAGGAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGATACCAATCTGTGTGCTATCCATGCCAAACGTGTAACAATTATGCCAAAAGATATCCAGCTAGCACGCCGCATACGCGGAGAACGTGCTTAAGAGTCCACTATGAGGGGAAACATTtcattctcaaaaaaattttttttcctcttcttcctgttatcAGTAGTTCTGAATGTTAGATATTTTTTCCATGGGGTCAAAGGTACCTAAGTATATGATTGCGAGTGGAAACATAGGGGACAGAATCAGGTATTGGCGTTTCTCCacgttcatttgtgtgtgaatttttaatataaatgcaagATGGAAAGCATTAATGCAAGCAAAATGTTTCAGTGAACACATTTCAACAGTTCAActttataacaattataaataaacctgttaaaattttctggacaatgccagcatttggatttttttaaaataagtaaatttcttaTTGACGGCAACTAAATGGTGTTTGTAGCATTTTTATCACACAGTAGATTCCATCCATTCACTATACTTTTCTAACTGAGTTGTCCTACATACAAGTACATGTTTTTAATGTTGTCAGTCTTCTGTGCTGTTCCTGTAAGTTTgctattaaaatacattaaactaTACCTGC

Publications

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