RetrogeneDB ID: retro_dnov_500

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5363:67322..68333(-)
• Located in intron of: ENSDNOG00000018858

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDP2
• Ensembl ID: ENSDNOG00000010113
• Aliases: None
• Description: tyrosyl-DNA phosphodiesterase 2 [Source:HGNC Symbol;Acc:17768]

Sequence

>retro_dnov_500
CCAGAGCCGAGGCGGCGCGAGACGACGGGGAGCGGGGAGCCCCGGGTGAAGAAGCGGCGACTCTTGTGTGCGGAGTTTGC
CTCGGTCGCGAATTGCGACCCGGCCGTGGCCCAGTGCTTCCTGGCCGAGAACGACTGGGAGATGGAAAGAGCGCAGAACT
CCTACTTTGAGCCGTGCGTGGAGGAGAGCGCCCCGGAGAGCCGGCCTCGGACCCCCTGCCAGCCCGAGGCCTGTGTTGAC
CTAAGCAACGAAGATACGACTGATTCCAATTGTTCTAAAATCACCTCATCTGAAAATATTCAGCAAGAAGATGGCAGTAT
GTTCTCTTTAATTACCTGGAATATTGATGGATTGGATCTAAACAACCTGCAAGAGAGGGCTCGAGGGGTGTGTTCTTACT
TAACTTTGTACAGTCCAGATGTGATATTTCTACAGGAAGTTATTCCTCCGTACTACAGTTACCTAAAGAAGAGAGCAAGT
AATTACGAGATTATTACAGGTCGTGAAGAAGGATATTTCACAGCTATAATGTTGAAGAAATCAAGAGTGAAATTAAAAAG
CCAAGAGATTATTCCTTTTCCAAGTACCAAAATGATGAGAAACCTATTGTGTGTGCATGTGAGTGTGTCAGGAAATGAAC
TTTACCTTATGACTTCCCATTTAGAGAGCACCAGAGGACATGCTAAGGAACGAATCAATCAGTTAAAAGTGGTTTTAAAG
AAAATGCAAGAGGCTCCAGAGACAGCTACGGTTATATTTGCAGGAGATACGAATTTAAGGGATCAAGAAGTTACCAGATG
TGGTGGTTTGCCCAACAACATTTTGGATGTCTGGGAGTTTTTGGGTAAGCCTGAGCATTGCCAGTTTACATGGGATACGC
AAATGAACTTTAACCTTGGAATACCTGCTACTTGTAAGCTTCGTTTTGATTGAATCTTTTTCAGAGCAGCAGCAGAAGAG
GGCCATATCATTCCCCGAAGTATGGACCTTCTTGGGTTGGAAAAACTAGAG

Alignment

ORF - retro_dnov_500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.36 %
• Parental protein coverage: 93.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PEAGAEAARDDGEPRVKKRRLLCAEFASVANCDPAVAQCFLAENDWEMERALNSYFEPCVEESPPESRPR
          PE.........GEPRVKKRRLLCAEFASVANCDPAVAQCFLAENDWEMERA.NSYFEPCVEES.PESRPR
Retrocopy PEPRRRETTGSGEPRVKKRRLLCAEFASVANCDPAVAQCFLAENDWEMERAQNSYFEPCVEESAPESRPR

Parental  TPCRPEAYVDVSNEDTTDSTCSKITSSENIQQEDGSMFSLITWNIDGLDLNNLQERARGVCSYLTLYSPD
          TPC.PEA.VD.SNEDTTDS.CSKITSSENIQQEDGSMFSLITWNIDGLDLNNLQERARGVCSYLTLYSPD
Retrocopy TPCQPEACVDLSNEDTTDSNCSKITSSENIQQEDGSMFSLITWNIDGLDLNNLQERARGVCSYLTLYSPD

Parental  VICLQEVIPPYYSYLKKRASNYEIITGREEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVSVS
          VI.LQEVIPPYYSYLKKRASNYEIITGREEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVSVS
Retrocopy VIFLQEVIPPYYSYLKKRASNYEIITGREEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVSVS

Parental  GNELYLMTSHLESTRGHAKERINQLKVVLKKMQEAPETATVIFAGDTNLRDQEVTRCGGLPNNILDVWEF
          GNELYLMTSHLESTRGHAKERINQLKVVLKKMQEAPETATVIFAGDTNLRDQEVTRCGGLPNNILDVWEF
Retrocopy GNELYLMTSHLESTRGHAKERINQLKVVLKKMQEAPETATVIFAGDTNLRDQEVTRCGGLPNNILDVWEF

Parental  LGKPEHCQFTWDTQMNSNLGIPATCKLRFDRIFFRAAAEEGHIIPRSMDLLGLEKLD
          LGKPEHCQFTWDTQMN.NLGIPATCKLRFD.IFFRAAAEEGHIIPRSMDLLGLEKL.
Retrocopy LGKPEHCQFTWDTQMNFNLGIPATCKLRFD*IFFRAAAEEGHIIPRSMDLLGLEKLE

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
SRP012922_ascending_colon	0.97 RPM	19.06 RPM
SRP012922_cerebellum	1.10 RPM	14.71 RPM
SRP012922_heart	0.00 RPM	5.34 RPM
SRP012922_kidney	0.82 RPM	22.18 RPM
SRP012922_liver	0.31 RPM	11.30 RPM
SRP012922_lung	1.07 RPM	19.55 RPM
SRP012922_quadricep_muscle	0.69 RPM	14.02 RPM
SRP012922_spleen	1.26 RPM	15.34 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_500 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus 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 4 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012012	2 retrocopies	retro_chof_2007, retro_chof_616,
Callithrix jacchus	ENSCJAG00000006074	1 retrocopy	retro_cjac_363,
Dasypus novemcinctus	ENSDNOG00000010113	1 retrocopy	retro_dnov_500 ,
Ochotona princeps	ENSOPRG00000016299	2 retrocopies	retro_opri_261, retro_opri_939,