RetrogeneDB ID: retro_mdom_2018

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: X:38509002..38509333(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSMODG00000001314
• Aliases: None
• Description: None

Sequence

>retro_mdom_2018
CCCCAACTGGTATAGAATATCACAGCCCAAGTAGAGTCCTACCTATCCAATGAGAATTTGTCCCAGGATGACTTCTTCCT
GAAGCATATTCAGAAAAGCAAGCTGGGCTTCATCAGTTTTCAAGCTGCTGATGTCCTTCAAGAAAGTAAAGTGTTTGACA
TGTGAGTGCTGCTTGAATGCTCTGCATTCCTCAGCTGTGCTGGAGGTGAATGAGGTAGGCACTAAAATGTGTTGAAGGTT
TCTTGTCCCCAACTGGCTCTTGGATCTCTTGGGTACCAAATTGCTTCTGATATAGGAAGATCCAGAGCCTTAGCTCCCCA
AGAAGTCAACA

Alignment

ORF - retro_mdom_2018 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.72 %
• Parental protein coverage: 56. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PQLVRNIIAQVESYLSNENLAQDAFLLKHVQKSKLGFLSGDH-MSSLPQVKCLTRDWRLTCYALRSSAML
          PQLV.NI.AQVESYLSNENL.QD.F.LKH.QKSKLGF.S......S...VKCLT....L...AL.SSA.L
Retrocopy PQLV*NITAQVESYLSNENLSQDDFFLKHIQKSKLGFISFQA>LMSFKKVKCLTCECCLN--ALHSSAVL

Parental  EVNEEGTKVRRRIPVPDWLLVLSHTKLLLVWEDPEPGFPREST
          EVNE.GTK...R..VP.WLL.L..TKLLL..EDPEP..P..ST
Retrocopy EVNEVGTKMC*RFLVPNWLLDLLGTKLLLI*EDPEP*LPKKST

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_2018 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_2018 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018642	1 retrocopy	retro_cjac_3881,
Monodelphis domestica	ENSMODG00000001314	2 retrocopies	retro_mdom_1273, retro_mdom_2018 ,