RetrogeneDB ID: retro_mdom_1575

Retrocopy location

• Organism: Opossum (Monodelphis domestica)
• Coordinates: 6:30470988..30471656(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMODG00000003007
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: REXO2
• Ensembl ID: ENSMODG00000013913
• Aliases: None
• Description: RNA exonuclease 2 [Source:HGNC Symbol;Acc:17851]

Sequence

>retro_mdom_1575
CTGAGGACTGTTGTGAAATCTGACTGGGAAGGATTTGGGGCTAGCTTGGGGATCAGATCCCTGGAGATTGAGTTGGTGGG
AAAGCACATGGTGCAGAGGATGTGAGTGGACCTGGAGATGATGGGATTCAATGTAGAGAAGGACCAGATCATGGAAAAGA
CCTGTCTCAGAATAGATTCTGACCTCCCCATTTTGGTTGAAGACCCTAACCTGATTCTAAATCATCCAGATGAGTTGCAG
GGCAGCCTGTCAGAGTGGCATAAGGAACATCCTGAGAAGTCTGATCTTACCAAGGCAGTGAAGGAGAGTTCAATTACACT
GAAGCAGGCAGAGGATGAATTTCTGTTCTTTGTACAGCAGCAGACTCCTCCAGGGCTCTGTCCAGTTGCAAGACATTCAG
TTCATGTAGATAAGAAGTTTCTTGACAAATACATGCCCCAGTTCATGAAACATCTTCATTATAGGGTAATTGATGTGAGC
ACTGGTAAAAGAACTGTGCAGATGCTGGTATTCAGAAAATATGAGTTTGAACCCAAGAAGGCTGCTTCTCACAGGGTACT
GGATGACAGCAAAAACATTGAGGAACTCCAGTTTATTGGAATAATATCTTTAAGAGCAAAACAGATGAAAAGAAGAGGAA
AACTATAGAAAATAAGGAAAATTAGAAG

Alignment

ORF - retro_mdom_1575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.97 %
• Parental protein coverage: 96.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LRSVLLRNLAGSGGRLGARGLRDGAAMAAGESMAQRMVWVDLEMTGLDIEKDQIIEMACLITDSDLNILA
          LR.V......G.G..L...G.R.......G..M.QRM..VDLEM.G...EKDQI.E..CL..DSDL.IL.
Retrocopy LRTVVKSDWEGFGASL---GIRSLEIELVGKHMVQRM*-VDLEMMGFNVEKDQIMEKTCLRIDSDLPILV

Parental  EGPNLIINQPDELLDSMSEWCKEHHGKSGLTKAVKESTITLQQAEYEFLSFVRQQTPPGLCPLAGNSVHA
          E.PNLI.N.PDEL..S.SEW.KEH..KS.LTKAVKES.ITL.QAE.EFL.FV.QQTPPGLCP.A..SVH.
Retrocopy EDPNLILNHPDELQGSLSEWHKEHPEKSDLTKAVKESSITLKQAEDEFLFFVQQQTPPGLCPVARHSVHV

Parental  DKKFLDKYMPQFMKHLHYRIIDVST-VKELCRRWYPE-EYEFVPKKAASHRALDDISESIKELQF-YRNN
          DKKFLDKYMPQFMKHLHYR.IDVST.VKELCR.WY.E..YEF.PKKAASHR.LDD.S..I.ELQF.Y.NN
Retrocopy DKKFLDKYMPQFMKHLHYRVIDVST>VKELCRCWYSE<KYEFEPKKAASHRVLDD-SKNIEELQF<YWNN

Parental  IFKRKTDEKKRKIIENGENEK
          IFK.KTDEKKRK.IEN.EN.K
Retrocopy IFKSKTDEKKRKTIENKEN*K

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_1575 retrocopy.

TSS

Monodelphis domestica was not studied using FANTOM5 data.

Lab

retro_mdom_1575 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013497	1 retrocopy	retro_chof_40,
Callithrix jacchus	ENSCJAG00000012434	1 retrocopy	retro_cjac_1493,
Dipodomys ordii	ENSDORG00000011255	1 retrocopy	retro_dord_374,
Equus caballus	ENSECAG00000005988	1 retrocopy	retro_ecab_572,
Myotis lucifugus	ENSMLUG00000009030	1 retrocopy	retro_mluc_1861,
Monodelphis domestica	ENSMODG00000013913	1 retrocopy	retro_mdom_1575 ,
Tarsius syrichta	ENSTSYG00000002237	1 retrocopy	retro_tsyr_1177,