RetrogeneDB ID: retro_mdom_1816

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 7:214572735..214573249(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000011135
• Aliases: None
• Description: None

Sequence

>retro_mdom_1816
GTCCAGCTGGTTGATGAGGAGTTGGACCATGCTCAGGAGCGAATGGCAACAGCTCTGTGGAACCTAGAAGTGGTAGAGAA
GGCAGCTGATGAGACAGAGAGCAATGAAAGCCATTGAAAATCAGGCCTGAAGAATGGAGAGAAAAGTGAGCTGCAAGAAA
CCCAGCTGAAAGTGATGAGTGTGCAGGGGAGGAAGGAGACAGGAAGGAAGAGGAGATGGCCAGCCAGTTGGTGATTATGG
AAACCTTCGAGTGTACAGGGGGGCCAGCCCAGCTGGCTGATCCCATTGCTGAGAGATGGGGGAGCAGAATAAATTGATGG
ACTAGAATGTTAAATTTCTGAATGCTAATGAAGAAAAGTATTCTCGAAAAGAAGACAAATATGAAGAGGAGATAAAGATT
CTTACTGAGAAACTCAAGGAGGCAGAGAAACACACCAAGTTTGCTGAGGGATTAGTGAAGCTGGAAAAGACAACTGAAGA
TTTGAAGGATGAGCTCTATGCCCCAAAACTGAAG

Alignment

ORF - retro_mdom_1816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.11 %
• Parental protein coverage: 61.62 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLK-EAKHIAEDADR
          .QLV.EELD.AQER.ATAL..LE..EKAADE.E.......S...K..EK.E.QE.QLK.......E..DR
Retrocopy VQLVDEELDHAQERMATALWNLEVVEKAADETESNESH*KS-GLKNGEKSELQETQLK<SDECAGEEGDR

Parental  KYEEVARKLVIIESDLERAEERAELSE-GKCAELEEELKTVTNNLKSLEAQAEKYSQKEDKYEEEIKVLS
          K.EE.A..LVI.E...E.....A.L.....C.E..E..K....N.K.L.A..EKYS.KEDKYEEEIK.L.
Retrocopy KEEEMASQLVIMET-FECTGGPAQLAD<SHC*EMGEQNKLMD*NVKFLNANEEKYSRKEDKYEEEIKILT

Parental  DKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLK
          .KLKEAE....FAE....KLEK...DL.DELYA.KLK
Retrocopy EKLKEAEKHTKFAE-GLVKLEKTTEDLKDELYAPKLK

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	165.09 RPM
SRP007412_cerebellum	0.00 RPM	117.52 RPM
SRP007412_heart	0.00 RPM	21805.30 RPM
SRP007412_kidney	0.00 RPM	235.71 RPM
SRP007412_liver	0.00 RPM	54.88 RPM
SRP007412_testis	0.00 RPM	106.66 RPM

ChIP-Seq

Monodelphis domestica was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mdom_1816 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1816 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000011135	1 retrocopy	retro_mdom_1816 ,
Monodelphis domestica	ENSMODG00000014882	1 retrocopy	retro_mdom_1354,