RetrogeneDB ID: retro_mdom_1116

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:146022384..146022784(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006029
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FOPNL
• Ensembl ID: ENSMODG00000004204
• Aliases: None
• Description: FGFR1OP N-terminal like [Source:HGNC Symbol;Acc:26435]

Sequence

>retro_mdom_1116
ATGGCGACTGTTGCGGAGCTCAAAGCAGTTTTAAAGGATACACTGGAAAAAAGAGGTGTATTGGGCCACTTAAAAGCAAA
GATCCAAGCTGAAGTTTTTAATGCACTAGATGATCAAGGTGAAAAACCTCCACCACTGTCTCATGAAAACCTTCTAATTA
ATGAATTAATTAGGGAGTATTTGGAATTCAACAAATATAAGTATTCAGCATCTGTCCTTGCAGCTGAATCTGGTCAACCG
GCTATGCCATTGGAAAGACAATTTCTCATTAAGGAATTAAATATATTTGAAGATTCGAATGCAAAAACAACCTCTTTTAT
ATGGAATTATATCTCATTTCTTACATGCAAGTAAAGATGGCATCCGAACCACTTTCATGAAAGGATCTTCACTTCAGCCT

Alignment

ORF - retro_mdom_1116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MATVAELKAVLKDTLEKRGVLGHLRAKIRAEVFNALDDQGEKPPPLSHENLLINELIREYLEFNKYKYSA
          MATVAELKAVLKDTLEKRGVLGHL.AKI.AEVFNALDDQGEKPPPLSHENLLINELIREYLEFNKYKYSA
Retrocopy MATVAELKAVLKDTLEKRGVLGHLKAKIQAEVFNALDDQGEKPPPLSHENLLINELIREYLEFNKYKYSA

Parental  SVLAAESGQPAMPLERQFLIKELNIFEDSNAKTVPLLYGIISHFL-HASEDGIQTTFMKGSSLQP
          SVLAAESGQPAMPLERQFLIKELNIFEDSNAKT.......IS.FL.HAS.DGI.TTFMKGSSLQP
Retrocopy SVLAAESGQPAMPLERQFLIKELNIFEDSNAKTTSFIWNYIS-FL>HASKDGIRTTFMKGSSLQP

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_1116 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1116 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000004411	1 retrocopy	retro_mluc_837,
Monodelphis domestica	ENSMODG00000004204	6 retrocopies	retro_mdom_1116 , retro_mdom_1500, retro_mdom_1902, retro_mdom_383, retro_mdom_396, retro_mdom_715,