RetrogeneDB ID: retro_mdom_81

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:23636054..23636660(-)
• Located in intron of: ENSMODG00000009164

Retrocopy information

• Ensembl ID: ENSMODG00000025215
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000019430
• Aliases: None
• Description: None

Sequence

>retro_mdom_81
ATGGCGGCTGCAGCAGCTGTAAACGGAGCAAAGCGTAATTTGCGGACTGAGATAAAGCAGCGGCTACGGACGCTAAGCGC
CGAGGAACGGCTCCGCCAGTCCCGGCTGCTGACCGAGAAGGTGATTGCTCACAGTAAATATCAAGAGTCTCAGAGAATTT
CCATCTTTCTGAGCATGCAAGATGAAATTGAAACAGAAGAAATTATCAAGGATATTTTTCAGCGTGGCAAAACATGTTTT
ATCCCTCGATACAAATTCAAGAGCAACTATATGGATATGGTCAAGTTATTTTCAGCAGAGGAAATTATTTCACTTCCCAA
AACTTCTTGGAACATTCATCAACCCAGTGATGATGAAGTGAGGGAGGAAGCTTTGTCAACAGGAGGTTTGGATCTCATCT
TCATGCCAGGTCTTGGATTTGACAAACAGGGCAATCGCCTGGGAAGGGGCAAGGGATACTATGACACCTACCTGAAGCGG
TGCCTGCAACACCAAGAAAGAAAACCTTATACAATTGCTTTGGCTTTCAAAGAACAGATCTGTGGTGAGGTGCCAGTCGG
AGAAAACGATATGAGAATAGACGAAGTGCTTTATGAAGACAAATAA

Alignment

ORF - retro_mdom_81 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

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

Retrocopy - Parental Gene Alignment:

Parental  MAAAAAVNGAKRNLRTEIKQRLRTLSAEERLRQSRLLTEKVIAHSKYQESQRISIFLSMQDEIETEEIIK
          MAAAAAVNGAKRNLRTEIKQRLRTLSAEERLRQSRLLTEKVIAHSKYQESQRISIFLSMQDEIETEEIIK
Retrocopy MAAAAAVNGAKRNLRTEIKQRLRTLSAEERLRQSRLLTEKVIAHSKYQESQRISIFLSMQDEIETEEIIK

Parental  DIFQRGKTCFIPRYKFKSNYMDMVKLFSAEEIISLPKTSWNIHQPSDDEVREEALSTGGLDLIFMPGLGF
          DIFQRGKTCFIPRYKFKSNYMDMVKLFSAEEIISLPKTSWNIHQPSDDEVREEALSTGGLDLIFMPGLGF
Retrocopy DIFQRGKTCFIPRYKFKSNYMDMVKLFSAEEIISLPKTSWNIHQPSDDEVREEALSTGGLDLIFMPGLGF

Parental  DKQGNRLGRGKGYYDTYLKRCLQHQERKPYTIALAFKEQICGEVPVGENDMRIDEVLYEDK
          DKQGNRLGRGKGYYDTYLKRCLQHQERKPYTIALAFKEQICGEVPVGENDMRIDEVLYEDK
Retrocopy DKQGNRLGRGKGYYDTYLKRCLQHQERKPYTIALAFKEQICGEVPVGENDMRIDEVLYEDK

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	0.12 RPM	1.07 RPM
SRP007412_cerebellum	0.00 RPM	0.98 RPM
SRP007412_heart	0.00 RPM	2.19 RPM
SRP007412_kidney	0.00 RPM	11.85 RPM
SRP007412_liver	2.01 RPM	30.71 RPM
SRP007412_testis	0.20 RPM	0.98 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_81 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_81 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020023	1 retrocopy	retro_btau_968,
Monodelphis domestica	ENSMODG00000019430	1 retrocopy	retro_mdom_81 ,