RetrogeneDB ID: retro_mdom_325

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 1:141733401..141733799(+)
• Located in intron of: ENSMODG00000011845

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000018901
• Aliases: None
• Description: None

Sequence

>retro_mdom_325
ATGGCATCTAACTATCCACCAAGTACCAGACAACACAAAGGAGACTAATATAAAAGTAAAATTGAACAAAGAAAGAAAAC
AAGAAATCAAAGAGGCCTTTGACTTATTTTATATTGATGAGTATAGAAGCATTAATCTGTAGGAATTGAAGATTAGAAAG
CATGCCTTTGGATTTAAAGCAAGGAAAGAAGAAATGTTAAAAATGCTAGTAGAAATTGATAAAGAAGTATTTGGGCACCA
TTAACTTTGAAGACTTTTTCACCAGGATACATGTTAAAAGGAGTGAAAAGGATGAAAAAGAAGGAATTTTGAAGGTCTTC
AAATTATTTGATAACAATTGTTTAAGAAGTATTGACCTCAAAAATTTCAAGAGAGTAGGTAAGGGTCTTCATCCCAAC

Alignment

ORF - retro_mdom_325 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.19 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MASNYRPSTGLRK-KPNVKVELTEGQKQEIKEAFDLFDVDGSGSIDVKELKIAMRALGFEPKKEEIKKMI
          MASNY.PST...K...N.KV.L....KQEIKEAFDLF..D...SI...ELKI...A.GF...KEE..KM.
Retrocopy MASNYPPSTRQHK>ETNIKVKLNKERKQEIKEAFDLFYIDEYRSINL*ELKIRKHAFGFKARKEEMLKML

Parental  AEIDKEGF-GTINFEDFFAMMSVKMSEKDEKEEILKAFKLFDDDCTGGITLKNIKRVAKELGEN
          .EIDKE.F.GTINFEDFF....VK.SEKDEKE.ILK.FKLFD..C...I.LKN.KRV.K.L..N
Retrocopy VEIDKEVF>GTINFEDFFTRIHVKRSEKDEKEGILKVFKLFDNNCLRSIDLKNFKRVGKGLHPN

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	0.24 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_325 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_325 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000005932	1 retrocopy	retro_mdom_87,
Monodelphis domestica	ENSMODG00000018901	2 retrocopies	retro_mdom_182, retro_mdom_325 ,
Mus musculus	ENSMUSG00000045031	1 retrocopy	retro_mmus_246,