RetrogeneDB ID: retro_mdom_1461

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:174336652..174336958(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED11
• Ensembl ID: ENSMODG00000028979
• Aliases: None
• Description: mediator complex subunit 11 [Source:HGNC Symbol;Acc:32687]

Sequence

>retro_mdom_1461
GCAAGGGTTCTTCTTACATTCATGTTGAAGTATACTTTGGCCAACCAGAAAGGTGCAGACCTTGGAGAAAATTGATGGAG
AAATCAGAACTATCCTGCAGAATGCTGGGAACATAATTCTTGATCTGTCCAAAAAGAAGATAAATAAAAGGTGGCTGAAC
CTGCAGATGACAGCCTTCATTGCCTCTTACAATATGTAGAGACTGAGTTGTCTGCTCAGATTGACCATCTCACTCAGGTA
GTAGTTGACTAGGCTCACGAGGGTTCGAGCTGTGCATCAGAAATGGATTGCCAGGTGGCAATGAAA

Alignment

ORF - retro_mdom_1461 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.81 %
• Parental protein coverage: 95.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ARILVSFMATYSLANER-LRALEDIEREIGTILQSAGNVILELSKEKANERLLDRQAAAFTSS-VQHVEA
          AR.L..FM..Y.LAN......LE.I..EI.TILQ.AGN.IL.LSK.K.N.R.L..Q..AF..S..Q.VE.
Retrocopy ARVLLTFMLKYTLANQK>VQTLEKIDGEIRTILQNAGNIILDLSKKKINKRWLNLQMTAFIAS<LQYVET

Parental  ELSAQIRYLTQVATGQPHESSSYSSRKDCQMALK
          ELSAQI..LTQV.....HE.SS..S..DCQ.A.K
Retrocopy ELSAQIDHLTQVVVD*AHEGSSCASEMDCQVAMK

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_1461 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1461 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000004247	2 retrocopies	retro_meug_1797, retro_meug_2072,
Myotis lucifugus	ENSMLUG00000002540	2 retrocopies	retro_mluc_376, retro_mluc_38,
Monodelphis domestica	ENSMODG00000028979	1 retrocopy	retro_mdom_1461 ,
Tarsius syrichta	ENSTSYG00000014148	1 retrocopy	retro_tsyr_1797,