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Example: RPL12P6, GAPDH, ENSG00000237984

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Summary

Retrocopy Name TAF9P3
Plot displaying the genomic locations of a retrocopy (in chr19) and its respective parental gene (in chr5). Each line represents a retrocopy.
Species Homo sapiens
Coordinates (hg38) chr19:30037265-30038386  UCSC
Coordinates (T2T) chr19:32557675-32558799  UCSC
Coordinates (hg19) chr19:30528172-30529293  UCSC
Strand +
Parental Sequence NM_003187.5_2
Parental seq. overlap 1058 bp
Parental seq. overlap (%) 90.7%
Genomic Region Intergenic
Retrocopy Summary TAF9P3, located on chr19:30037265-30038386, is a retrocopy of the parental gene TAF9. 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 TAF9
Full Name TATA-box binding protein associated factor 9
Also known as MGC:5067|STAF31/32|TAF2G|TAFII-31|TAFII-32|TAFII31|TAFII32|TAFIID32
Coordinate chr5:69364743-69369824
Strand -
Gene summary Initiation of transcription by RNA polymerase II requires the activities of more than 70 polypeptides. The protein that coordinates these activities is transcription factor IID (TFIID), which binds to the core promoter to position the polymerase properly, serves as the scaffold for assembly of the remainder of the transcription complex, and acts as a channel for regulatory signals. TFIID is composed of the TATA-binding protein (TBP) and a group of evolutionarily conserved proteins known as TBP-associated factors or TAFs. TAFs may participate in basal transcription, serve as coactivators, function in promoter recognition or modify general transcription factors (GTFs) to facilitate complex assembly and transcription initiation. This gene encodes one of the smaller subunits of TFIID that binds to the basal transcription factor GTF2B as well as to several transcriptional activators such as p53 and VP16. In human, TAF9 and AK6 (GeneID: 102157402) are two distinct genes that share 5' exons. A similar but distinct gene (TAF9L) has been found on the X chromosome and a pseudogene has been identified on chromosome 19. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

Homology

Species Scientific Name Retrocopy
Chimpanzee Pan troglodytes TAF9P2
Bonobo Pan paniscus TAF9P2
Gorilla Gorilla gorilla TAF9P1
Orangutan Pongo abelii TAF9P2
Gibbon Nomascus leucogenys TAF9P2
Green monkey Chlorocebus sabaeus TAF9P1
Crab-eating macaque Macaca fascicularis TAF9P3
Rhesus Macaca mulatta TAF9P3
Baboon Papio anubis TAF9P3
Golden snub-nosed monkey Rhinopithecus roxellana TAF9P2
Marmoset Callithrix jacchus TAF9P5
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

>TAF9P3
GAGCCGTCGTGGGGAGGACCATGTTGCTTCCAAGCATCCTGCTCACCAGTACACCAGGGGTTGGAAAAACCACACTAGGCAAAGGACTTGTGTCAAAATCAGGACTGAAATACATTAATGTGGGTGATTTAGCTCAAGAAGTCTGATCATCGTATATCATGGAGTCTGGCAAGATGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAAATCCTGAAGGATCTGGGAATTACAGAATATGAGCCAAGACTTATAAATCAGATGTTAGAGTTTGCCTTCCGTTATGTGACCACAATTCTAGATGATGCAAAAATTTACTCCAGCCATGCTAAGAAAGCTACCGTTGATGCAGATGATGTGCAGTTGGCAATCCAGTTCCACGCTGACCAGTCTTTTACCTCTCTTCCCCCAAGAGATTTTTTTATTAGATATCGCAAGGCAAAGAAATCAAACCCCTTTTCCATTAATCAAGCCATATTCAGGTCCTAGATTGCCACCTGATAGATATTGCTTAACAGCTCCAAATTATAGGCTGAAATCTTTACAGAAAAAGGCATCAACTTCCACGGGAAGAGTAACAGTCCCGCAGTTAAGTGTTGGTTCAGTTGCTAGCAGACCAAGTACTCCCACACTAGGCACACCAACCCCACAGACCATGTCTGTTTCAACTAAAGTAGGGACTCCCGTGTCCCTCACAGGGCAAAGGTTTACAGTACAGATGCCTACTTCACAGTCTCCAGCTGTAAAATCTTCAATTCCTGCAACATCAGCAGTTCAGAATGTTCTGATTAATCCATCATTAATTGGGTCCAAAAGCTTCTTATTACCACTAATACGGTGTTATCACAAAATACTGCCAATGAATCATCAAATGCATTGAAAAAGCGTGAAGAAGATGATTATGATAATTTGTAATTTAGCCTTGCTGCATGTAACATGTATACTTGGTCTTGAATTCATTGTACTGATACTAAACATGCGTGCTGGATGTTTTCAAGTTGTATTTTAGAAAACTTTCATATTTAATGAGTAAATACAATTACCATACTTTTCAATTGAAATGAAGGTTTTTCATCAGCCTTAAAAGTGTAAGAAAAATCAAGTTGTCATT
>NM_003187.5_2
GAGGCGCCCGAAGCCGTCGCGGCGGGGACCATGTTGCTTCCGAACATCCTGCTCACCGGTACACCAGGGGTTGGAAAAACCACACTAGGCAAAGAACTTGCGTCAAAATCAGGACTGAAATACATTAATGTGGGTGATTTAGCTCGAGAAGTCTGATCATCGGATATCATGGAGTCTGGCAAGACGGCTTCTCCCAAGAGCATGCCGAAAGATGCACAGATGATGGCACAAATCCTGAAGGATATGGGGATTACAGAATATGAGCCAAGAGTTATAAATCAGATGTTGGAGTTTGCCTTCCGATATGTGACCACAATTCTAGATGATGCAAAAATTTATTCAAGCCATGCTAAGAAAGCTACTGTTGATGCAGATGATGTGCGATTGGCAATCCAGTGCCGCGCTGATCAGTCTTTTACCTCTCCTCCCCCAAGAGATTTTTTATTAGATATTGCAAGGCAAAGAAATCAAACCCCTTTGCCATTGATCAAGCCATATTCAGGTCCTAGGTTGCCACCTGATAGATACTGCTTAACAGCTCCAAACTATAGGCTGAAATCTTTACAGAAAAAGGCATCAACTTCTGCGGGAAGAATAACAGTCCCGCGGTTAAGTGTTGGTTCAGTTACTAGCAGACCAAGTACTCCCACACTAGGCACACCAACCCCACAGACCATGTCTGTTTCAACTAAAGTAGGGACTCCCATGTCCCTCACAGGTCAAAGGTTTACAGTACAGATGCCTACTTCTCAGTCTCCAGCTGTAAAAGCTTCAATTCCTGCAACCTCAGCAGTTCAGAATGTTCTGATTAATCCATCATTAATCGGGTCCAAAAACATTCTTATTACCACTAATATGATGTCATCACAAAATACTGCCAATGAATCATCAAATGCATTGAAAAGAAAACGTGAAgatgatgatgatgacgatgatgatgatgatgaCTATGATAATCTGTAATCTAGCCTTGCTGAATGTAACATGTATACTTGGTCTTGAATTCATTGTACTGATATTAAACATGCATGCTGGATGTTTTCAAGTTGTGTTTTAGAAAACTAATAATAATGAGTAAACACAGTTACCATACTTTTCAATTGAAATGAAGGTTTTTCATCAGCCTTAAAAGTGTAAGAAAAATAAAGTTGTCATTCATTCGA

Publications

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