RetrogeneDB ID: retro_mdom_87

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 3:19315789..19316308(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000025382
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000005932
• Aliases: None
• Description: None

Sequence

>retro_mdom_87
ATGGCTAGTACCACCAAGAAGCCTAACATGGGTCCCTCCCTCCCAAGAAGGAAGCTAGAGCCCAAACCTGAACTCTCAGA
GGATCAGAAACAGGAAATTAGAGAGGCATTTGATCTCTTTGATACAGATGGAACCGGGACGATAGATGTGAAGGAGCTCA
AAGTGGCGGTGAGAGCTCTGGGCTTCGAGCCCAAGAAAGAAGAGATCAAAAAAATGATATCTGAGGTAGACAAGGAGGGG
ACAGGGAAGATCAGCTTCAACGACTTCTTGGCTGTGATGACTCAAAAAATGAACGAGAAGGACACCAAAGAAGAAATTCT
GAAGGCTTTCAAACTCTTCGATGATGATGACACTGGAAAGATTTCCTTCAAGAACTTGAAACGGGTGGCCAGAGAGCTCG
GGGAAAATCTCACTGATGAAGAACTACAAGAAATGATCGATGAAGCTGATCGAGATGGAGACGGAGAAGTCAACGAACAG
GAGTTCCTGCGGATCATGAAAAAGAGCAGTATCTACTGA

Alignment

ORF - retro_mdom_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.7 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASTIKKPNLGPAPPRKKMGPKPELTEDQKQEIREAFDLFDTDGTGTIDVKELKVAMRALGFEPKKEEIK
          MAST.KKPN.GP..PR.K..PKPEL.EDQKQEIREAFDLFDTDGTGTIDVKELKVA.RALGFEPKKEEIK
Retrocopy MASTTKKPNMGPSLPRRKLEPKPELSEDQKQEIREAFDLFDTDGTGTIDVKELKVAVRALGFEPKKEEIK

Parental  KMISDIDKEGTGKISFNDFLAVMTQKMAEKDTKEEILKAFRLFDDDETGKISFKNLKRVARELGENLTDE
          KMIS..DKEGTGKISFNDFLAVMTQKM.EKDTKEEILKAF.LFDDD.TGKISFKNLKRVARELGENLTDE
Retrocopy KMISEVDKEGTGKISFNDFLAVMTQKMNEKDTKEEILKAFKLFDDDDTGKISFKNLKRVARELGENLTDE

Parental  ELQEMIDEADRDGDGEVNEQEFLRIMKKTSLY
          ELQEMIDEADRDGDGEVNEQEFLRIMKK.S.Y
Retrocopy ELQEMIDEADRDGDGEVNEQEFLRIMKKSSIY

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_87 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_87 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000013823	2 retrocopies	retro_meug_1093, retro_meug_856,
Monodelphis domestica	ENSMODG00000005932	1 retrocopy	retro_mdom_87 ,
Monodelphis domestica	ENSMODG00000018901	2 retrocopies	retro_mdom_182, retro_mdom_325,
Sarcophilus harrisii	ENSSHAG00000015319	2 retrocopies	retro_shar_237, retro_shar_378,