RetrogeneDB ID: retro_dnov_1273

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17383:73959..74440(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC8
• Ensembl ID: ENSDNOG00000019133
• Aliases: None
• Description: exosome component 8 [Source:HGNC Symbol;Acc:17035]

Sequence

>retro_dnov_1273
ACAATGCAACCTCTGGAGTACTACAAGAGATTTTTGAAAGAGAACTGCCACCATAATGGAAGAGAACTTGGTGAATTCAG
AATCACCACTATTAACATAGGTTCAATTAGTTCTGTAGATAGTTCTGCTTTAGAGTAGTTGGGAAATACTACAGTCATTT
GTGGAATTAAAGCAGAATTTGCAGCACCACCAACTGATGCCGGTGATAAAGGAAATGTTGTTCCCAATGTGGATCTCCCA
CCCTGTGTTCATTGAGATTTCGATCTGGACCTCCTCACATAGAGGTCCAAGTAGCTAGCCAGTTCGTTCAGATGTCATTG
AAAATTCACAGATAATTCAGAAAGAGGACTTATGCATTTCTCATGGAAAGCTTGCTTGGATTCTATACTGTGATCTCATT
TGCCTTGACTAAGATGGAAACATTTTGGTAACCTGTACCTTTCCTTTGTTAGTTGCTTTAAAAGATGCACAGTTGCCTGA
A

Alignment

ORF - retro_dnov_1273 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.37 %
• Parental protein coverage: 59.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TVEPLEYYRRFLKENCRPDGRELGEFRTTTVNIGSISTADGSALVKLGNTTVICGVKAEFAAPPTDAPDK
          T..PLEYY.RFLKENC...GRELGEFR.TT.NIGSIS..D.SAL..LGNTTVICG.KAEFAAPPTDA.DK
Retrocopy TMQPLEYYKRFLKENCHHNGRELGEFRITTINIGSISSVDSSALE*LGNTTVICGIKAEFAAPPTDAGDK

Parental  GYVVPNVDLPP-LCSSRFRSGPPGEEAQVASQFI-ADVIENSQIIQKEDLCISQGKLAWVLYCDLICLDY
          G.VVPNVDLPP.LCS.RFRSGPP..E.QVASQF...DVIENSQIIQKEDLCIS.GKLAW.LYCDLICLD.
Retrocopy GNVVPNVDLPP<LCSLRFRSGPPHIEVQVASQFV<SDVIENSQIIQKEDLCISHGKLAWILYCDLICLD*

Parental  DGNILDACTFALLAALKDVQLPE
          DGNIL..CTF.LL.ALKD.QLPE
Retrocopy DGNILVTCTFPLLVALKDAQLPE

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	23.78 RPM
SRP012922_heart	0.00 RPM	17.63 RPM
SRP012922_kidney	0.00 RPM	15.33 RPM
SRP012922_liver	0.00 RPM	8.51 RPM
SRP012922_lung	0.00 RPM	23.06 RPM
SRP012922_quadricep_muscle	0.00 RPM	15.06 RPM
SRP012922_spleen	0.00 RPM	33.42 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_1273 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009005	2 retrocopies	retro_chof_2014, retro_chof_664,
Dasypus novemcinctus	ENSDNOG00000010614	1 retrocopy	retro_dnov_219,
Dasypus novemcinctus	ENSDNOG00000019133	1 retrocopy	retro_dnov_1273 ,
Tupaia belangeri	ENSTBEG00000012040	9 retrocopies	retro_tbel_1492, retro_tbel_1680, retro_tbel_2932, retro_tbel_349, retro_tbel_3712, retro_tbel_4030, retro_tbel_419, retro_tbel_4649, retro_tbel_527,