RCPedia: Rtcs

Summary

Retrocopy Name	SNRPD2P1	Plot displaying the genomic locations of a retrocopy (in chr10) and its respective parental gene (in chr19). Each line represents a retrocopy.
Species	Homo sapiens
Coordinates (hg38)	chr10:89978661-89979168 UCSC
Coordinates (T2T)	chr10:90862172-90862679 UCSC
Coordinates (hg19)	chr10:91738418-91738925 UCSC
Strand	+
Parental Sequence	NM_004597.6
Parental seq. overlap	475 bp
Parental seq. overlap (%)	66.7%
Genomic Region	Intergenic
Retrocopy Summary	SNRPD2P1, located on chr10:89978661-89979168, is a retrocopy of the parental gene SNRPD2. 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	SNRPD2
Full Name	small nuclear ribonucleoprotein D2 polypeptide
Also known as	SMD2\|SNRPD1\|Sm-D2
Coordinate	chr19:45687454-45692316
Strand	-
Gene summary	The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

Homology

Species	Scientific Name	Retrocopy
Chimpanzee	Pan troglodytes	SNRPD2P2
Gorilla	Gorilla gorilla	SNRPD2P2
Orangutan	Pongo abelii	SNRPD2P2
Gibbon	Nomascus leucogenys	SNRPD2P1
Green monkey	Chlorocebus sabaeus	SNRPD2P2
Crab-eating macaque	Macaca fascicularis	SNRPD2P2
Rhesus	Macaca mulatta	SNRPD2P2
Baboon	Papio anubis	SNRPD2P1
Golden snub-nosed monkey	Rhinopithecus roxellana	SNRPD2P1
Bonobo	Pan paniscus	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

Related Sequence

>SNRPD2P1
TTCAGGCAGCAGCAACGCGGAGGAAACGGGAATGAACCGAGAGCGTAGTGACCATCATGAGCCTCCTTAACAAGTCCAAGAGTGAGATGACCCCAGAGGAGCTGCAGAAGCGAGAGGAGGAGGAATTTAACACGGGTCCACTTTCTGTGCTCACACAGTCAGTCAAGAACAACACGCAAGTGCTCATCAACTGTCGCCACAACACGAAACTCCTGGGCCACGTGAAGGCCTTCCACAGGCACTGCAACATGGTGCTGGAGAACGTGAAGGAGACGTGGACTGAGGTACCCAAGAGCGGCAAGGGCAAGAAGTCCAAGCCAGTCAACAAAGACTGCTATATCTCCAGGATGTTCCTGCACGGGGACTTGGTCATCGTGGTCCTGCGGAACCCACTCATCGCCAGCAAGTAGGGGCCACCTATCTGTCGACAGAACTCACTCCGCTGGCCTATGAAGACCGCTGCCATTGGTGTTGAGAATAATAGAGCTCTGTGTTTTTTTTCTAGTGG

>NM_004597.6
CGCGTCCCAGAGGGAAGAGGGGCGGTGCCTGTCTCCGAAGCGAGGAGCGGATTGGCTTCACGGAGGCCGCGCCCCCGAAGTCACGGCCGGCGGGCATTTGGAAATAGCTTGTCATTTCCCTCCTTCAACCTGTACCATTCTTCAAGAAACGGCGCCAACGGAAGTGGGTCGCAGGAAGAGGAAGTCCCGCCTCTCTCTCCTCAGGCAGCAGCAACGCGGAGGAAACGGGAGTGAACGGAGAGCGTAGTGACCATCATGAGCCTCCTCAACAAGCCCAAGAGTGAGATGACCCCAGAGGAGCTGCAGAAGCGAGAGGAGGAGGAATTTAACACCGGTCCACTCTCTGTGCTCACACAGTCAGTCAAGAACAATACCCAAGTGCTCATCAACTGCCGCAACAATAAGAAACTCCTGGGCCGCGTGAAGGCCTTCGATAGGCACTGCAACATGGTGCTGGAGAACGTGAAGGAGATGTGGACTGAGGTACCCAAGAGTGGCAAGGGCAAGAAGAAGTCCAAGCCAGTCAACAAAGACCGCTACATCTCCAAGATGTTCCTGCGCGGGGACTCAGTCATCGTGGTCCTGCGGAACCCGCTCATCGCCGGCAAGTAGGGGCCGCCTGTCTGTTGACAGAACTCACTCCTCTGTCCTATGAAGACCGCTGCCATTGGTGTTGAGAATAATAAAGCTCTGTGTTTTTTTCTAGTGGTA

>NM_004597.6 

CGCGTCCCAGAGGGAAGAGGGGCGGTGCCTGTCTCCGAAGCGAGGAGCGGATTGGCTTCACGGAGGCCGCGCCCCCGAAGTCACGGCCGGCGGGCATTTGGAAATAGCTTGTCATTTCCCTCCTTCAACCTGTACCATTCTTCAAGAAACGGCGCCAACGGAAGTGGGTCGCAGGAAGAGGAAGTCCCGCCTCTCTCTCCTCAGGCAGCAGCAACGCGGAGGAAACGGGAGTGAACGGAGAGCGTAGTGACCATCATGAGCCTCCTCAACAAGCCCAAGAGTGAGATGACCCCAGAGGAGCTGCAGAAGCGAGAGGAGGAGGAATTTAACACCGGTCCACTCTCTGTGCTCACACAGTCAGTCAAGAACAATACCCAAGTGCTCATCAACTGCCGCAACAATAAGAAACTCCTGGGCCGCGTGAAGGCCTTCGATAGGCACTGCAACATGGTGCTGGAGAACGTGAAGGAGATGTGGACTGAGGTACCCAAGAGTGGCAAGGGCAAGAAGAAGTCCAAGCCAGTCAACAAAGACCGCTACATCTCCAAGATGTTCCTGCGCGGGGACTCAGTCATCGTGGTCCTGCGGAACCCGCTCATCGCCGGCAAGTAGGGGCCGCCTGTCTGTTGACAGAACTCACTCCTCTGTCCTATGAAGACCGCTGCCATTGGTGTTGAGAATAATAAAGCTCTGTGTTTTTTTCTAGTGGTA

Publications

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