RetrogeneDB ID: retro_mdom_1733

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:124409880..124410528(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CIDEA
• Ensembl ID: ENSMODG00000021430
• Aliases: None
• Description: cell death-inducing DFFA-like effector a [Source:HGNC Symbol;Acc:1976]

Sequence

>retro_mdom_1733
ATGGACACTGCCAGGGACTATGCCGGAGCCCTGATGAGGCTCTTGACTTTTGTGGGATCACAAACCAAATGAGTCCTATT
AACTCCCCTCATGTTTTCATCTCGGCCTTTCAGGGTCTCAAATCATGACAGAAGCAGCCGACGTGGGGTGACAGCCAACA
CACTGAAGGAACTCATTAACAAGACCTTGGATGCCCTAGCAATTACTACGGGCCTGGTTACTTTGGTGTTGGAATAAGAT
GGCACAGTCGTAGATACAGAAGAATTCTTTCAGACCCTAGGAGATAATACATATTTCGTGATCTTGGAAAAAGGGCAGAA
GTGGACACTGGGTCCTAAATATGCTACTCAGAAGCAGAAAAAATCTGGAATAGCAAGGGTCACTTTTGATTTGTATAAGA
CAAATCCCAAAGACTTCCTTGGATGCTTAAATGTGAAAGCCACCATGTATGAGATGTATTCTGTGTCCTATGACATCCGA
TGTACATCACCCAAAGCTGTGCTGAGGCAGTTGTTGCGGATTATGTCCTATGTTGCCCAAATCACCAGACAGTTTCTTGT
CTATGGCGGGACTTACATGTTGCATGTGCTTAACGACAGTGAAGATTCTGTCCCTCCTCCCAAACCAAGCACCAAGGGGT
GGCTCCTA

Alignment

ORF - retro_mdom_1733 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.37 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDTARDYAGVLMRPLTFVGSQTKRVLLTPLMFSSRPFRVSNHDRSSRRGVTANTLKELINKTLDALAITT
          MDTARDYAG.LMR.LTFVGSQTK.VLLTPLMFSSRPFRVSNHDRSSRRGVTANTLKELINKTLDALAITT
Retrocopy MDTARDYAGALMRLLTFVGSQTK*VLLTPLMFSSRPFRVSNHDRSSRRGVTANTLKELINKTLDALAITT

Parental  GLVTLVLEEDGTVVDTEEFFQTLGDNTHFMILEKGQKWTLGPKYATQKQKKSGIARVTFDLYKTNPKDFL
          GLVTLVLE.DGTVVDTEEFFQTLGDNT.F.ILEKGQKWTLGPKYATQKQKKSGIARVTFDLYKTNPKDFL
Retrocopy GLVTLVLE*DGTVVDTEEFFQTLGDNTYFVILEKGQKWTLGPKYATQKQKKSGIARVTFDLYKTNPKDFL

Parental  GCLNVKATMYEMYSVSYDIRCTSAKAVLRQLLRIMSYAAQITGQFLVYGGTYMLHVLNDSEDSIPPPKPS
          GCLNVKATMYEMYSVSYDIRCTS.KAVLRQLLRIMSY.AQIT.QFLVYGGTYMLHVLNDSEDS.PPPKPS
Retrocopy GCLNVKATMYEMYSVSYDIRCTSPKAVLRQLLRIMSYVAQITRQFLVYGGTYMLHVLNDSEDSVPPPKPS

Parental  TKGWLL
          TKGWLL
Retrocopy TKGWLL

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_1733 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1733 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000021430	2 retrocopies	retro_mdom_1700, retro_mdom_1733 ,