RetrogeneDB ID: retro_mdom_165

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: Un:28382108..28382465(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000022786
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000013977
• Aliases: None
• Description: None

Sequence

>retro_mdom_165
ATGTGCGACAAGGAATTCATGTGGGCTTTGAAAAATGGAGACCTGGATGAGGTGAAAGACTATGTGGCCAAGGGTGAAGA
TGTCACCCGGACACTAGAAGGTGGTAGGAAGCCTCTTCCTTATGCAGCAGATTGTGGGCAGCTTGAAATCCTGGAATTTC
TGCTACTGAAAGGAGCTGATACTAATGCTCCAGATAAACATCATATCACCCCTCTTCTGTCTGCAGTATATGAAGGTCAC
GTTTCCTGTGTGAAACTGCTTCTATCAAAGGGTGCTGATAAAACTGTGAAAGGCCCAGATGGACCAACTGCCTTTGAAGC
CACTGACAACCAGGCAATCAAAGCTCTTCTTCAGTGA

Alignment

ORF - retro_mdom_165 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.61 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCDKEFMWALKNGDLDEVKDYVAKGEDVNRTLEGGRKPLHYAADCGQLEILEFLLLKGADINAPDKHHIT
          MCDKEFMWALKNGDLDEVKDYVAKGEDV.RTLEGGRKPL.YAADCGQLEILEFLLLKGAD.NAPDKHHIT
Retrocopy MCDKEFMWALKNGDLDEVKDYVAKGEDVTRTLEGGRKPLPYAADCGQLEILEFLLLKGADTNAPDKHHIT

Parental  PLLSAVYEGHVSCVKLLLSKGADKTVKGPDGLTAFEATDNQAIKALLQ
          PLLSAVYEGHVSCVKLLLSKGADKTVKGPDG.TAFEATDNQAIKALLQ
Retrocopy PLLSAVYEGHVSCVKLLLSKGADKTVKGPDGPTAFEATDNQAIKALLQ

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_165 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_165 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000029544	1 retrocopy	retro_lafr_924,
Monodelphis domestica	ENSMODG00000013977	4 retrocopies	retro_mdom_132, retro_mdom_165 , retro_mdom_1731, retro_mdom_247,
Oryctolagus cuniculus	ENSOCUG00000005642	4 retrocopies	retro_ocun_1746, retro_ocun_1830, retro_ocun_244, retro_ocun_993,
Drosophila melanogaster	FBgn0051715	1 retrocopy	retro_dmel_34,