RetrogeneDB ID: retro_mdom_498

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:62999335..62999806(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025562
• Aliases: None
• Description: None

Sequence

>retro_mdom_498
CAGGAACATGAGGCTCACACGATCCAGCCCATAGAAGCAGCTGCTGGGTACTACAGGAAAAAGCTCCAGGAGAATATGAA
ACTTGTACGTGAAACTTTAAAAGATGTTCAGAAGTTGATACTAGAGGAGAAGAAGGTACCTCGGACATGGGCTGTCCTGT
GGACAGAACAAGTAGAAATGCCAAGAAAAATGTTTCAGGAAAAATTTAAAGAAATAAGTGATTTCCTGAGTGATGAAGAG
GAAGAAGTCCACAGTCTAATGGAACTGGATGAGGAGGAGAATGAAATGTTTGAGCACTTGAAGGAGCATGAGGTCCAGCA
AGAAATCCAAAACAGAGAGAAAAAGATGATGAGCAACTTCCAACTGTCCCAACACAAGAATGACTTAAGGGAAATGGTCA
TAGCACTGGAAGAAAAGTCTCAGATGCCAGATAAGGAACTGCTGCAGGATGCAGGAAATACACTGAGCAAG

Alignment

ORF - retro_mdom_498 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.18 %
• Parental protein coverage: 55.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QEHEAHTIQPIEAAAGYYRKKLQENMKLVRETLKDVQKLILEEKKVPRT----WAEQVEMPRKTFQEKFK
          QEHEAHTIQPIEAAAGYYRKKLQENMKLVRETLKDVQKLILEEKKVPRT....W.EQVEMPRK.FQEKFK
Retrocopy QEHEAHTIQPIEAAAGYYRKKLQENMKLVRETLKDVQKLILEEKKVPRTWAVLWTEQVEMPRKMFQEKFK

Parental  EISDFLSDEEEEVHSLMELDEEENEMFEHLKEHEVQQEIQNREKKMMSNFQLSQHKNDLREMVIALEEKS
          EISDFLSDEEEEVHSLMELDEEENEMFEHLKEHEVQQEIQNREKKMMSNFQLSQHKNDLREMVIALEEKS
Retrocopy EISDFLSDEEEEVHSLMELDEEENEMFEHLKEHEVQQEIQNREKKMMSNFQLSQHKNDLREMVIALEEKS

Parental  QMPDKELLQDAGNTLSK
          QMPDKELLQDAGNTLSK
Retrocopy QMPDKELLQDAGNTLSK

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_498 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_498 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 1 parental gene, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025562	4 retrocopies	retro_mdom_1117, retro_mdom_1546, retro_mdom_1907, retro_mdom_498 ,