RetrogeneDB ID: retro_dnov_219

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2716:127436..128172(+)
• Located in intron of: ENSDNOG00000012085

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC9
• Ensembl ID: ENSDNOG00000010614
• Aliases: None
• Description: exosome component 9 [Source:HGNC Symbol;Acc:9137]

Sequence

>retro_dnov_219
ATGAAAGAGATGCCACTTTCAAACTGAGAGCACTGCTTCTTACTCCATGCTATCAAAAAGAATAAGCAGCTTCATGGTAG
ACAAACGTATGATTATTGGAACATCAAGATCTCATCTGGAACAGATTACGGGTGCTGTACTGTGGAACCTGGAAAACAAG
ACTTCTTGGACAGGTTTCCTGTGAACTTGTTTCTCCAAAACTCAACAGGGCAATGGAAAGTACTCTTTTTTTAACCTTGA
ATGCTCTCAGATGGCTGCCCCAGTTTTTGAACTTGGTAGGCAATCAAATCTCTTGGTGAAGTTCAATCAACTGTTGGAAA
GATGTCTAAGAAATTCGAAGTGTATAGACACTGAATCTCTCTGTATTGTTGCCGGTGAAAAGGTCTGGCAAATATGCGTG
GACTTATATTTATTATATCACGAAGGGAATATTATTGATTCTGCCAGCATTGCTGCAGTTGTGGCCCTGTGTCACTTTCG
AAGAGCTGATGTGTTGGTTCAAGGAGATAAAGTAACACTGAATATACCTGAAGAGTGCAACCCTGTACCATTGAGTATAC
TCCACATGCCCAAATGTGTCCGTTTTGCATTCTTCCAGCAAGGAACATATTTACTGGTGTATCCCAATAAACGAGAAGAA
CATGTAATGGGTAGCTTGGTGGTGACTGCCAAGAACAAGCTTTGAGAGATTTGGACCATCCAATCTAGTGGTGGAATAAC
GCTACTAAAAGATCAA

Alignment

ORF - retro_dnov_219 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.23 %
• Parental protein coverage: 63.73 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKETPLSNCERRFLLRAIEEKKRLDGRQTYDYRNIKISFGTDYGCCIVELGK-TRVLGQVSCELVSPKLN
          MKE.PLSN.E..FLL.AI...K.L.GRQTYDY.NIKIS.GTDYGCC.VE.GK.TR.LGQVSCELVSPKLN
Retrocopy MKEMPLSN*EHCFLLHAIKKNKQLHGRQTYDYWNIKISSGTDYGCCTVEPGK<TRLLGQVSCELVSPKLN

Parental  RATEGILF-FNLELSQMAAPAFEPGRQSDLLVKLNRLLERCLRNSKCIDTESLCVVAGEKVWQIRVDLHL
          RA.E..LF.FNLE.SQMAAP.FE.GRQS.LLVK.N.LLERCLRNSKCIDTESLC.VAGEKVWQI.VDL.L
Retrocopy RAMESTLF<FNLECSQMAAPVFELGRQSNLLVKFNQLLERCLRNSKCIDTESLCIVAGEKVWQICVDLYL

Parental  LNHDGNIIDAASIAAIVALCHFRRPDVSVQGDEVTLYTPEERDPVPLSIHHMPICVSFAFFQQGTYLLVD
          L.H.GNIID.ASIAA.VALCHFRR.DV.VQGD.VTL..PEE..PVPLSI.HMP.CV.FAFFQQGTYLLV.
Retrocopy LYHEGNIIDSASIAAVVALCHFRRADVLVQGDKVTLNIPEECNPVPLSILHMPKCVRFAFFQQGTYLLVY

Parental  PNEREERVMGGLLVIAMNKHREICTIQSSGGIMLLKDQ
          PN.REE.VMG.L.V.A.NK..EI.TIQSSGGI.LLKDQ
Retrocopy PNKREEHVMGSLVVTAKNKL*EIWTIQSSGGITLLKDQ

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	0.00 RPM	17.11 RPM
SRP012922_cerebellum	0.00 RPM	21.58 RPM
SRP012922_heart	0.00 RPM	16.71 RPM
SRP012922_kidney	0.00 RPM	14.78 RPM
SRP012922_liver	0.00 RPM	13.00 RPM
SRP012922_lung	0.15 RPM	31.31 RPM
SRP012922_quadricep_muscle	0.00 RPM	16.62 RPM
SRP012922_spleen	0.00 RPM	31.48 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_219 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010614	1 retrocopy	retro_dnov_219 ,
Dasypus novemcinctus	ENSDNOG00000019133	1 retrocopy	retro_dnov_1273,