RetrogeneDB ID: retro_dnov_376

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4226:744473..745276(-)
• Located in intron of: ENSDNOG00000015865

Retrocopy information

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

Parental gene information

• Parental gene symbol: CENPT
• Ensembl ID: ENSDNOG00000016760
• Aliases: None
• Description: centromere protein T [Source:HGNC Symbol;Acc:25787]

Sequence

>retro_dnov_376
GGGAAACCAGCCCAACCTCTAGCAGGAAGGGCAGAAGAAGTCAATGTTCTTGATATGGGCTCCCCAAACACTGGCAGCAG
TGTCTCTGGAAAAGGTATAGTAGAGCCCTTAGAGGACGGAGTTGGTGAGGAGATAAAGGAAAGATGGAAGAAGACTTGAA
CATAAGTGAAGTGTAGGAGGCACCAGGAGTTCAAGGGTCTGCCAGAGCAGAAAAACATTAAGGGTGCACAGAGGTGGGGG
AAGCTGAGGGATCCCAGGGAACTATTGAGGACTCAGAGCCAGAAGGATCTTCAGGGGATGAGGACACCTCTGGTGGGATA
GTAAGCCCAGAGTTGGCCTCCAGCACCCCTAAGTTTCTCTGGGCCAGATGACTTCATCAGTTTCTTGAGGCAACTCCACC
ACACAGTGCTGCAGACTTAGGTTCAGAACCTCTTGGGCCTCTTTTTGGCCAGTCTTCCCCCCCAGGACTTGAACTGTTAG
ATCCAGGCCTCATAAAGATCCCTATGAGGCTGGACTGAGCCACTATGTCAAACTCTTTAGCTTTTATGCTAAAATGCATA
AAATGCTCTTGAGATGGTAGAGAAATACCTGGACAGGTATTTCCAGCCTTTCTGCAATAATCTGGAGGTATTTGCTGTTC
ATTCTAGCTGCAAGACTGTGAGGCCAGAGGACTTAGAGCTGCTGATGTGAAGACAAGTCCTGGTCACCGCCAAGTCTCAC
TGTATGTGCTTGTGGAGCATCACCTGCCCCTGGAGTACAGGCAGCTGCTCATCCCCTGTGCATTCAGCTGCAACTCTGTC
TTC

Alignment

ORF - retro_dnov_376 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.09 %
• Parental protein coverage: 51.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  GKPAQPLVERAEEVNALDMGFPNINSSVSGEGGVKPLEDRVGEEAEER-MEEGLSISEMKEATGVQRSAK
          GKPAQPL..RAEEVN.LDMG.PN..SSVSG.G.V.PLED.VGEE..ER.MEE.L.ISE..EA.GVQ.SA.
Retrocopy GKPAQPLAGRAEEVNVLDMGSPNTGSSVSGKGIVEPLEDGVGEEIKER<MEEDLNISEV*EAPGVQGSAR

Parental  AEEHEGHTEVQEAEGSQGAIEAMEPEGSSGDEDTSGGTATPELASNTPEFLQARRLHQFLEPTPPPSAAD
          AE.H.G.TEV.EAEGSQG.IE..EPEGSSGDEDTSGG...PELAS.TP.FL.AR.LHQFLE.TPP.SAAD
Retrocopy AEKH*GCTEVGEAEGSQGTIEDSEPEGSSGDEDTSGGIVSPELASSTPKFLWAR*LHQFLEATPPHSAAD

Parental  LCSEP-LGPLSARLPP-RARTIGPRPHKDPYKAGLSHYVKLFSFCAKMPMEK-KTLEMVEKCMDKYFQHL
          L.SEP.LG...A.LPP.R..T...RPHKDPY.AGLSHYVKLFSF.AK..M.K...LEMVEK..D.YFQ..
Retrocopy LGSEP>LGLFLASLPP>RT*TVRSRPHKDPYEAGLSHYVKLFSFYAK--MHK<NALEMVEKYLDRYFQPF

Parental  CDDLEVFAAHAGRKTVKPEDLELLMRRQGLVT-DQVSLYVLVERHLPLEYRQLLIPCAFSGNSVF
          C..LEVFA.H...KTV.PEDLELLM.RQ.LVT..QVSLYVLVE.HLPLEYRQLLIPCAFS.NSVF
Retrocopy CNNLEVFAVHSSCKTVRPEDLELLM*RQVLVT<RQVSLYVLVEHHLPLEYRQLLIPCAFSCNSVF

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	13.03 RPM
SRP012922_cerebellum	0.27 RPM	31.07 RPM
SRP012922_heart	0.00 RPM	3.02 RPM
SRP012922_kidney	0.00 RPM	1.92 RPM
SRP012922_liver	0.00 RPM	2.48 RPM
SRP012922_lung	0.00 RPM	9.62 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.79 RPM
SRP012922_spleen	0.23 RPM	35.37 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_376 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	ENSDNOG00000016760	1 retrocopy	retro_dnov_376 ,
Myotis lucifugus	ENSMLUG00000010268	1 retrocopy	retro_mluc_1854,