RetrogeneDB ID: retro_mdom_1289

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:297280459..297280733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000008134
• Aliases: None
• Description: None

Sequence

>retro_mdom_1289
GCGGTGGCCAGTCAGCAGTGGTTTGCTCCGATGTTAGGGCTGCAGTTATTGCTTGTGTCAGTCCTGCAAGCGGTATCTGT
ACCAGGGATTTGAATTATCATCAGAAGCATGCAGAGATTTGGGTTTCTCCAGCAATTTGCTCTGTAGCTCTTGTGATCTT
CTTGGACAGTTTAGCTTAACTCAGCTGGATCCTGATTACAGAAAATGCTGCCAGGAAGAAGCACAGTTTGAAAACTGAAA
GCTGTATGCGGGTGCTATCCTGGAAGTATGTGGA

Alignment

ORF - retro_mdom_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 97.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AAAGRQWFAPMLGLRLLLVSVLQTISV-QGFELSSEACRDLGFSSNLLCSSCDLLGQFSLTQLDPGCRKC
          A.A..QWFAPMLGL.LLLVSVLQ..SV.QGFELSSEACRDLGFSSNLLCSSCDLLGQFSLTQLDP..RKC
Retrocopy AVASQQWFAPMLGLQLLLVSVLQAVSV>QGFELSSEACRDLGFSSNLLCSSCDLLGQFSLTQLDPDYRKC

Parental  CQEEAQFENRKLYAGAILEVCG
          CQEEAQFEN.KLYAGAILEVCG
Retrocopy CQEEAQFEN*KLYAGAILEVCG

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_1289 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1289 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004701	1 retrocopy	retro_dnov_2296,
Macropus eugenii	ENSMEUG00000005462	4 retrocopies	retro_meug_1005, retro_meug_2191, retro_meug_769, retro_meug_817,
Monodelphis domestica	ENSMODG00000008134	2 retrocopies	retro_mdom_1289 , retro_mdom_1504,
Ochotona princeps	ENSOPRG00000003411	2 retrocopies	retro_opri_157, retro_opri_897,
Vicugna pacos	ENSVPAG00000011775	1 retrocopy	retro_vpac_621,