RetrogeneDB ID: retro_mdom_264

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 4:343184385..343184742(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000024030
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000012794
• Aliases: None
• Description: None

Sequence

>retro_mdom_264
ATGGCGAGTCAGTCTCAGAGAATCCAGCAGCTCTTGCAGGCAGAAAAACGAGTCAAAGACAAGTTAGAAGAAGCCAAGAA
GAGAAAAAATAAATGGTTAAGTCAAGTAAAAGAAGAAGTGATGACTGAAGTAGATCAGCATAGGATGCAGAAAGAAAAGG
AATTTCAGGAAAAGCAATCTTTGGTTTTGGGATCCCAAAGCAACTTCTTGGGCAAAATAGATGCACAGACAACAGGAAAA
ATTCAGAAACTCACTAGTAACTACAATGAGAGCTTGGAAAGTGTGATGAAAAAACTTTTGAGCATGGTTCGTAACTTGAA
ACCTGAAATGCATAAGAACTACAAAGGCACAGATTAA

Alignment

ORF - retro_mdom_264 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.29 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASQSQGIQQLLQAEKRAKDKLEEAKKRKNKRLRQAKEEAMAEVDQYRMQKEKEFREKQSLVLGSQSNLL
          MASQSQ.IQQLLQAEKR.KDKLEEAKKRKNK.L.Q.KEE.M.EVDQ.RMQKEKEF.EKQSLVLGSQSN.L
Retrocopy MASQSQRIQQLLQAEKRVKDKLEEAKKRKNKWLSQVKEEVMTEVDQHRMQKEKEFQEKQSLVLGSQSNFL

Parental  GEIDAQTTGKIQKLTSNYNESLESVMKKLLSMVCDLKPEIHKNYTGTD
          G.IDAQTTGKIQKLTSNYNESLESVMKKLLSMV..LKPE.HKNY.GTD
Retrocopy GKIDAQTTGKIQKLTSNYNESLESVMKKLLSMVRNLKPEMHKNYKGTD

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_264 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_264 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019890	1 retrocopy	retro_btau_787,
Loxodonta africana	ENSLAFG00000021963	1 retrocopy	retro_lafr_417,
Monodelphis domestica	ENSMODG00000012794	1 retrocopy	retro_mdom_264 ,
Monodelphis domestica	ENSMODG00000019574	1 retrocopy	retro_mdom_1675,