RetrogeneDB ID: retro_mdom_1545

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:193273658..193274002(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YEATS4
• Ensembl ID: ENSMODG00000020377
• Aliases: None
• Description: YEATS domain containing 4 [Source:HGNC Symbol;Acc:24859]

Sequence

>retro_mdom_1545
ATGTTCGAGAGAATGGGAGAATTTGGGCTTAACTCCTGGCAGGGGAGAGAAGGGGGTTACTATTGCTAAGCCTGTAGTTT
ATGGTAATGTTGCTCATTATTTTGGAAAGAAGAGAGAAGAAGATGATCATACTCATCAGTGGACAGTATATGTTAAAACC
ATATAGGAATGAAGATATGTCAGCATATGTGAAGGAAATCCAGTTTAAATTGCATGAAAGTTATGGTAATCCTTTAAGCG
TTGTTACAAAGCCACCATATGAGATTACAGAAACAGGGTGGGGTGAATTTGAAAGAATTATCAAAATATTATTCATTGAT
TCTAATGAAAGACCTGTAATACTT

Alignment

ORF - retro_mdom_1545 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.62 %
• Parental protein coverage: 50.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFKRMAEFGPDS-GGRVKGVTIVKPIVYGNVARYFGKKREEDGHTHQWTVYVK-PYRNEDMSAYVKKIQF
          MF.RM.EFG..S.G...KGVTI.KP.VYGNVA.YFGKKREED.HTHQWTVYVK.PYRNEDMSAYVK.IQF
Retrocopy MFERMGEFGLNS>GRGEKGVTIAKPVVYGNVAHYFGKKREEDDHTHQWTVYVK>PYRNEDMSAYVKEIQF

Parental  KLHESYGNPLRVVTKPPYEITETGWGEFEIIIKIFFIDPNERPVTL
          KLHESYGNPL.VVTKPPYEITETGWGEFE.IIKI.FID.NERPV.L
Retrocopy KLHESYGNPLSVVTKPPYEITETGWGEFERIIKILFIDSNERPVIL

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_1545 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1545 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000010793	1 retrocopy	retro_etel_836,
Microcebus murinus	ENSMICG00000002467	1 retrocopy	retro_mmur_1433,
Monodelphis domestica	ENSMODG00000020377	1 retrocopy	retro_mdom_1545 ,
Nomascus leucogenys	ENSNLEG00000003837	1 retrocopy	retro_nleu_816,
Oryctolagus cuniculus	ENSOCUG00000011552	1 retrocopy	retro_ocun_1414,
Tursiops truncatus	ENSTTRG00000013951	2 retrocopies	retro_ttru_226, retro_ttru_295,