RetrogeneDB ID: retro_mdom_1246

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:85541060..85541337(+)
• Located in intron of: ENSMODG00000018252

Retrocopy information

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

Parental gene information

• Parental gene symbol: MYLPF
• Ensembl ID: ENSMODG00000001476
• Aliases: None
• Description: myosin light chain, phosphorylatable, fast skeletal muscle [Source:HGNC Symbol;Acc:29824]

Sequence

>retro_mdom_1246
AGACGGGCAGCTCCACTGTCTTCTCACCACCAAGATGGCACCATCGACAAGGAAGTCTGGGGAACATCTTTGCTGCTATG
GGTCAAATGAATGTGAAGTATGAGAAACAAGATGCCATGATGAAGGAGGCCAGTGACCTTTTCAGCTTCACTGTCTTCTT
GATCAAGTTTGAAGAGAAATTAAGGGGTGCTAATCAAGAGGATTAATCACTGGAGCCTTCAAAATTTTGGACCCTGAGGG
GAAGGGATCCATCAAGGATGAGGAGCTACTCACCACT

Alignment

ORF - retro_mdom_1246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.22 %
• Parental protein coverage: 56.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEAFTVIDQNRDGIIDKE-DLRDTFAAMGRLNVKNEELDAMMKEASGPINFTVFLTMFGEKLKGADPED-
          ..A........DG.IDKE..L...FAAMG..NVK.E..DAMMKEAS....FTVFL..F.EKL.GA..ED.
Retrocopy RRAAPLSSHHQDGTIDKE<SLGNIFAAMGQMNVKYEKQDAMMKEASDLFSFTVFLIKFEEKLRGANQED<

Parental  VITGAFKVLDPEGKGSIKKQFLEELLTT
          .ITGAFK.LDPEGKGSIK....EELLTT
Retrocopy LITGAFKILDPEGKGSIKD---EELLTT

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_1246 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1246 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000000482	1 retrocopy	retro_meug_1928,
Monodelphis domestica	ENSMODG00000001476	1 retrocopy	retro_mdom_1246 ,
Monodelphis domestica	ENSMODG00000021464	1 retrocopy	retro_mdom_987,