RCPedia: Rtcs

Summary

Retrocopy Name	GTF2A2P3	Plot displaying the genomic locations of a retrocopy (in chr9) and its respective parental gene (in chr15). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr9:1328811-1328991 UCSC
Coordinates (T2T)	chr9:1330506-1330686 UCSC
Coordinates (hg19)	chr9:1328811-1328991 UCSC
Strand	+
Parental Sequence	NM_001320930.2
Parental seq. overlap	157 bp
Parental seq. overlap (%)	8.8%
Genomic Region	Intergenic
Retrocopy Summary	GTF2A2P3, located on chr9:1328811-1328991, is a retrocopy of the parental gene GTF2A2. 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	GTF2A2
Full Name	general transcription factor IIA subunit 2
Also known as	HsT18745\|T18745\|TF2A2\|TFIIA\|TFIIA-12\|TFIIA-gamma\|TFIIAS
Coordinate	chr15:59638062-59657515
Strand	-
Gene summary	Accurate transcription initiation on TATA-containing class II genes involves the ordered assembly of RNA polymerase II (POLR2A; MIM 180660) and the general initiation factors TFIIA, TFIIB (MIM 189963), TFIID (MIM 313650), TFIIE (MIM 189962), TFIIF (MIM 189968), TFIIG/TFIIJ, and TFIIH (MIM 189972). The first step involves recognition of the TATA element by the TATA-binding subunit (TBP; MIM 600075) and may be regulated by TFIIA, a factor that interacts with both TBP and a TBP-associated factor (TAF; MIM 600475) in TFIID. TFIIA has 2 subunits (43 and 12 kD) in yeast and 3 subunits in higher eukaryotes. In HeLa extracts, it consists of a 35-kD alpha subunit and a 19-kD beta subunit encoded by the N- and C-terminal regions of GTF2A1 (MIM 600520), respectively, and a 12-kD gamma subunit encoded by GTF2A2 (DeJong et al., 1995 [PubMed 7724559]).[supplied by OMIM, Mar 2008]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	GTF2A2P3
Bonobo	Pan paniscus	GTF2A2P3
Horse	Equus caballus	GTF2A2P1
Egyptian rousette	Rousettus aegyptiacus	GTF2A2P2
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
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
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
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)

Related Sequence

>GTF2A2P3
ACAGGAACAGGATCAGTTTCAGAGGATTTCTAAATACATACAGATTCTGTGATCATGTCTGGACTTTTGTATTGAATGATGTTAAACTCAGAGAGATGGCAGAGGTTATCAAAGTGAATAAAGTGAAAATTGTAGCCTGTGATGGTAAAAATATAGGCTCCAAATATTACAGAATGAATAG

>NM_001320930.2
AGTTCTGCGGTTTCTGCGGCGGCTGGAGAGGTGGTCGGAGAAGTAGGAACCTCCTGCCGGGCTCGTGGCGGCTTCTGTCCGCTCCGCGGAGGGAAGCGCCTTCCCCACAGCTTGTTGTTTGAAGTCTGCCTTCCAACTTTCTTCGTGCGAACTCCGACAAAAGGAACGAATTTTAAACTTGGTGGTTTAATCAAAAAATGCTAGGACGAGTTACTTCCGAATTTGACTTCTAATTTTCTGAACTGCAAAACAAGAAGGGAACAATAAATTTCTGTGGCTGATACCACATCTAAAAGATTAGAACACTTAACAAGGAATTTTTAAAGAATGACATCAATGCAAGCTTGAATAAGAAAAACAAATTCTTCCTCCTAAGCCATGGCATATCAGTTATACAGAAATACTACTTTGGGAAACAGTCTTCAGGAGAGCCTAGATGAGCTCATACAGTCTCAACAGATCACCCCCCAACTTGCCCTTCAAGTTCTACTTCAGTTTGATAAGGCTATAAATGCAGCACTGGCTCAGAGGGTCAGGAACAGAGTCAATTTCAGGGGCTCTCTAAATACGTACAGATTCTGCGATAATGTGTGGACTTTTGTACTGAATGATGTTGAATTCAGAGAGGTGACAGAACTTATTAAAGTGGATAAAGTGAAAATTGTAGCCTGTGATGGTAAAAATACTGGCTCCAATACTACAGAATGAATAGAAAAAATATGACTTTTTTACACCATCTTCTGTTATTCATTGCTTTTGAAGAGAAGCATAGAAGAGACTTTTTATTTATTCTAGAATTGCAGAAATGACTACACTGTGCTATACCAGAGAATTCCAGTAGAAAGAAACTTGTAACTCTGTAGCCTCTTACATCACCTTTATTATACAGCATGAAAAACCATAACTTTTTTTTAAGGACAAAAGTTGTTGCCTTCCTAAGAACCTTCTTTAATAAACTCATTTTAAAACTCTGAGTAATAACTGGTGAAGCTATTAAGGTAGCAATATGAAGATATTAGATAATGCATTTTCCCATTTCCTTTGCAAGGAACATGATGCCCTTTCAGAATGCTTATTTCAATAAAGTCATGTTTTGTCAGTTGTAACTTTACCTGATGAAAGCATCAGCAGGGGCAAAACCAAACTCTGGATGGAATTTTTTAAGAAAATCCCTTGCTTTTTAAAATACAAAACCAAAGTTAATCATTGGTATAAAAAAACCCAAGTACAACTTGATTAGGAAAAGTTAGACAATCATAGCAAAAACAAAACCAAAAAACTTTCCTTCTTAGACCAGGTAACATGAGGAAGGGGGAAAAAAACCCAAACAAAATAGTCCCCCCACATGACAGGTGTCTTCAGCTTGCCATATTGATCCAAAGTTCATACATTTTATCATGTACAAGATACATTAGACTTACAATAAAGTCTAATTATTAGACTTTTATGTCAGTGGATTGTGCTTGCAGAAATACAGAAGTAACATACTGACCCTAGGTGAGGAGTTTCTTACATGGTTAACTGGATTGACCCAATTGGAGTAAAAGATTTTTGCTGTTACCTCGATGCTCCTGCAGTTGTTACCTCAGCATGCCACTGTAGTCCTTGACTCTCACATTAAAACTAACTTTggctaggtactggtggctcacacctgtaagtaatcccagtactttaggaggctgagactggaggattacttgagtccaggagttggagaccagcctggccaatatagactgtccctacaaagaaaataaaaTTGTTTCATCTTCCAA

>NM_001320930.2 

AGTTCTGCGGTTTCTGCGGCGGCTGGAGAGGTGGTCGGAGAAGTAGGAACCTCCTGCCGGGCTCGTGGCGGCTTCTGTCCGCTCCGCGGAGGGAAGCGCCTTCCCCACAGCTTGTTGTTTGAAGTCTGCCTTCCAACTTTCTTCGTGCGAACTCCGACAAAAGGAACGAATTTTAAACTTGGTGGTTTAATCAAAAAATGCTAGGACGAGTTACTTCCGAATTTGACTTCTAATTTTCTGAACTGCAAAACAAGAAGGGAACAATAAATTTCTGTGGCTGATACCACATCTAAAAGATTAGAACACTTAACAAGGAATTTTTAAAGAATGACATCAATGCAAGCTTGAATAAGAAAAACAAATTCTTCCTCCTAAGCCATGGCATATCAGTTATACAGAAATACTACTTTGGGAAACAGTCTTCAGGAGAGCCTAGATGAGCTCATACAGTCTCAACAGATCACCCCCCAACTTGCCCTTCAAGTTCTACTTCAGTTTGATAAGGCTATAAATGCAGCACTGGCTCAGAGGGTCAGGAACAGAGTCAATTTCAGGGGCTCTCTAAATACGTACAGATTCTGCGATAATGTGTGGACTTTTGTACTGAATGATGTTGAATTCAGAGAGGTGACAGAACTTATTAAAGTGGATAAAGTGAAAATTGTAGCCTGTGATGGTAAAAATACTGGCTCCAATACTACAGAATGAATAGAAAAAATATGACTTTTTTACACCATCTTCTGTTATTCATTGCTTTTGAAGAGAAGCATAGAAGAGACTTTTTATTTATTCTAGAATTGCAGAAATGACTACACTGTGCTATACCAGAGAATTCCAGTAGAAAGAAACTTGTAACTCTGTAGCCTCTTACATCACCTTTATTATACAGCATGAAAAACCATAACTTTTTTTTAAGGACAAAAGTTGTTGCCTTCCTAAGAACCTTCTTTAATAAACTCATTTTAAAACTCTGAGTAATAACTGGTGAAGCTATTAAGGTAGCAATATGAAGATATTAGATAATGCATTTTCCCATTTCCTTTGCAAGGAACATGATGCCCTTTCAGAATGCTTATTTCAATAAAGTCATGTTTTGTCAGTTGTAACTTTACCTGATGAAAGCATCAGCAGGGGCAAAACCAAACTCTGGATGGAATTTTTTAAGAAAATCCCTTGCTTTTTAAAATACAAAACCAAAGTTAATCATTGGTATAAAAAAACCCAAGTACAACTTGATTAGGAAAAGTTAGACAATCATAGCAAAAACAAAACCAAAAAACTTTCCTTCTTAGACCAGGTAACATGAGGAAGGGGGAAAAAAACCCAAACAAAATAGTCCCCCCACATGACAGGTGTCTTCAGCTTGCCATATTGATCCAAAGTTCATACATTTTATCATGTACAAGATACATTAGACTTACAATAAAGTCTAATTATTAGACTTTTATGTCAGTGGATTGTGCTTGCAGAAATACAGAAGTAACATACTGACCCTAGGTGAGGAGTTTCTTACATGGTTAACTGGATTGACCCAATTGGAGTAAAAGATTTTTGCTGTTACCTCGATGCTCCTGCAGTTGTTACCTCAGCATGCCACTGTAGTCCTTGACTCTCACATTAAAACTAACTTTggctaggtactggtggctcacacctgtaagtaatcccagtactttaggaggctgagactggaggattacttgagtccaggagttggagaccagcctggccaatatagactgtccctacaaagaaaataaaaTTGTTTCATCTTCCAA

Publications

PMID - Link	Title
No publications available for this retrocopy