RetrogeneDB ID: retro_mdom_1363

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:147285901..147286075(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPX4
• Ensembl ID: ENSMODG00000005486
• Aliases: None
• Description: glutathione peroxidase 4 [Source:HGNC Symbol;Acc:4556]

Sequence

>retro_mdom_1363
GTAAATGGCTACAATGTCCACCCTCTGTGGAAGTGGATAAAAATTCAACCCAAAAGAAAGGGTATTTTGGGCAATGTGCT
AAAGTGGAACTTCATCAATTTCCTTATTGACAAAGATGACTTTATGGTGAAGTTATAAGGTCCAGTGGAATAGCCCTTGG
TGATTGAGAAGAAC

Alignment

ORF - retro_mdom_1363 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.24 %
• Parental protein coverage: 84.06 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNGDDAHPLWKWMKIQPRGKGILGNAIKWNFTKFLIDKDGCVVKRYGPMEEPQVIEKD
          VNG...HPLWKW.KIQP..KGILGN..KWNF..FLIDKD...VK..GP.E.P.VIEK.
Retrocopy VNGYNVHPLWKWIKIQPKRKGILGNVLKWNFINFLIDKDDFMVKL*GPVE*PLVIEKN

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_1363 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1363 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Felis catus	ENSFCAG00000022744	1 retrocopy	retro_fcat_1113,
Monodelphis domestica	ENSMODG00000005486	1 retrocopy	retro_mdom_1363 ,
Mus musculus	ENSMUSG00000075706	2 retrocopies	retro_mmus_1595, retro_mmus_560,
Ochotona princeps	ENSOPRG00000008347	4 retrocopies	retro_opri_1144, retro_opri_63, retro_opri_705, retro_opri_929,