RetrogeneDB ID: retro_mdom_885

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 2:295875237..295875979(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000018856
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCGF3
• Ensembl ID: ENSMODG00000005677
• Aliases: None
• Description: polycomb group ring finger 3 [Source:HGNC Symbol;Acc:10066]

Sequence

>retro_mdom_885
CTTGTGACAGCAAAGATGTTGACCAGAAAGATTAAGCTTTGGGACATAAATGCCCATATCACATGCCATCTGTGCAATGG
ATACCTAATTGATGCTACCACTGTAAAGGAGTGTTTGCATAACTTCTGTAGAAGTTGCCTGGTAAAGTATTTGGAAGAAA
ATAACACTTGCCCTACGTGTAGAATTGTTATTCATCAGAGTCATCCACTGCAATACATTGGTCATGACAGGACAATGCAA
GATATTGTTTACAAATTGGTACCAGGCCTCCAAGAAGCGGAAATGAGGAAACAGAGGGAATTCTATCACAAATTAGGCAT
GGAAGTGCCTGGAGACATCAAAGGGGAGACTTCCTCTGCAAAGCAGCACTTAGACTCACATCGGAATGGTGAAACAAAAG
CTGATGACAGTTCCAACAAAGAAACATCAGAAGAAAAACAAGAAGAGGATAATGACTATCACAGAAGTGATGAACAGGTA
AGCATCTGCCTGGAATGCAATAGCAGCAAATTACGTGGATTGAAACAAAAATGGATCCGCTGCTCAGCACAGGCAACAGT
CTTGCATCTAAAGAAGTTCATTGCCAAAAAAACTTAATCTTTCATCTTTCAATGAGCTGGATATATTATGCAATGAAGAA
ATTCTTGGCAAGGACCACACACTCAAGTTTGTAGTTGTTACTAGATGGAGATTTAAGAAAGCACCTCTACTGCTACATTA
CAGACCCAAAATGGACTTGCTG

Alignment

ORF - retro_mdom_885 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LQTPKMLTRKIKLWDINAHITCRLCNGYLIDATTVTECLHTFCRSCLVKYLEENNTCPTCRIVIHQSHPL
          L.T.KMLTRKIKLWDINAHITC.LCNGYLIDATTV.ECLH.FCRSCLVKYLEENNTCPTCRIVIHQSHPL
Retrocopy LVTAKMLTRKIKLWDINAHITCHLCNGYLIDATTVKECLHNFCRSCLVKYLEENNTCPTCRIVIHQSHPL

Parental  QYIGHDRTMQDIVYKLVPGLQEAEMRKQREFYHKLGMEVPGDIKGETCSAKQHLDSHRNGETKADDSSNK
          QYIGHDRTMQDIVYKLVPGLQEAEMRKQREFYHKLGMEVPGDIKGET.SAKQHLDSHRNGETKADDSSNK
Retrocopy QYIGHDRTMQDIVYKLVPGLQEAEMRKQREFYHKLGMEVPGDIKGETSSAKQHLDSHRNGETKADDSSNK

Parental  ETSEEKQEEDNDYHRSDEQVVSICLECNSSKLRGLKRKWIRCSAQATVLHLKKFIA-KKLNLSSFNELDI
          ETSEEKQEEDNDYHRSDEQ.VSICLECNSSKLRGLK.KWIRCSAQATVLHLKKFIA.KKLNLSSFNELDI
Retrocopy ETSEEKQEEDNDYHRSDEQ-VSICLECNSSKLRGLKQKWIRCSAQATVLHLKKFIA>KKLNLSSFNELDI

Parental  LCNEEILGKDHTLKFVVVTRWRFKKAPLLLHYRPKMDLL
          LCNEEILGKDHTLKFVVVTRWRFKKAPLLLHYRPKMDLL
Retrocopy LCNEEILGKDHTLKFVVVTRWRFKKAPLLLHYRPKMDLL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_885 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_885 was not experimentally validated.

Homology

Retrocopy orthology:

Monodelphis domestica does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001960	1 retrocopy	retro_cjac_707,
Macaca mulatta	ENSMMUG00000012624	1 retrocopy	retro_mmul_2182,
Monodelphis domestica	ENSMODG00000005677	3 retrocopies	retro_mdom_1481, retro_mdom_885 , retro_mdom_985,
Nomascus leucogenys	ENSNLEG00000000926	1 retrocopy	retro_nleu_1826,
Otolemur garnettii	ENSOGAG00000015569	1 retrocopy	retro_ogar_2846,