RetrogeneDB ID: retro_mdom_188

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 5:198636634..198636955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000006904
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000025628
• Aliases: None
• Description: None

Sequence

>retro_mdom_188
GAGCGGCGGCGGCAGCGGCAGCAGCAGCAGAGTCCAGATGAGCCGCCGCCGCCCCCGGGGGCCGCCGCCGCCCCTACATC
CGCCGGCGGCGGCGAGCGGAAGAAGAGGAGCGGGCCCGGCCCTGCGGCACTCAGCTTCGTGGGCAAGCGGAGAGGCGGGA
ACAAGCTAGCCCTCAAGACAGGAATAGTAGCCAAGAAGCAGAAGACCGAGGATGAGGTTATGACAAGTAAAGGAGATGCT
TGGGCCAAGTACATGGCGGAAGTGAAAAAATACAAGGCACATCAGTGCAGTGATGATGACAAAACCCGGCCCCTGGTGAA
A

Alignment

ORF - retro_mdom_188 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.13 %
• Parental protein coverage: 55.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERRRQRQQQQSPDEPPPPPGAAAAPTPAGGGEPKKRSGPGPAALSFVGKRRGGNKLALKTGIVAKKQKTE
          ERRRQRQQQQSPDEPPPPPGAAAAPT.AGGGE.KKRSGPGPAALSFVGKRRGGNKLALKTGIVAKKQKTE
Retrocopy ERRRQRQQQQSPDEPPPPPGAAAAPTSAGGGERKKRSGPGPAALSFVGKRRGGNKLALKTGIVAKKQKTE

Parental  DEVMTSKGDAWAKYMAEVKKYKAHQCSDDDKTRPLVK
          DEVMTSKGDAWAKYMAEVKKYKAHQCSDDDKTRPLVK
Retrocopy DEVMTSKGDAWAKYMAEVKKYKAHQCSDDDKTRPLVK

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_188 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_188 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000025628	1 retrocopy	retro_mdom_188 ,
Rattus norvegicus	ENSRNOG00000003863	3 retrocopies	retro_rnor_1080, retro_rnor_2556, retro_rnor_2675,
Tursiops truncatus	ENSTTRG00000005460	1 retrocopy	retro_ttru_922,