RetrogeneDB ID: retro_dnov_406

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4444:5951..6644(+)
• Located in intron of: ENSDNOG00000010084

Retrocopy information

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

Parental gene information

• Parental gene symbol: C8orf33
• Ensembl ID: ENSDNOG00000015805
• Aliases: None
• Description: chromosome 8 open reading frame 33 [Source:HGNC Symbol;Acc:26104]

Sequence

>retro_dnov_406
GCAGCGCTTGGCAGTCCCTGGACACCCTACTCAGGAGACCAGCCCTCGGGTGCTGCTTGTGTGTCTCACACTCCCAAGCT
CTCTGGCCCTGTTCCCAGTGCCCTGAGTCTTTCCACTGTAAGGTCCCATCCAGTCTGTCTCTGCTCAGGGCACCCCACCT
GTAATGACACTGTCTCTAGGGTGCACTCTGTAGGTGGTGGAGGCCATGCAACCTTTAAGAAGCAAAAGAAGAAGAAAACA
TTGGAACAGGGTCTTTGTGACCAATGGAGGCAGGAAGACCTCAGGAAAGCCCGTGAAGAGGAGCTCCTCAGTGCTGAGGG
CCAGGTGGAGCAGCTGGCCCAGGAACTGGCTAGGCATGTGGAGCAGCTCGAGCTCAGTCTCAGGACTCAGAGACCCAGCC
CAAAACAGAAAGAGCAGACTACTTGGGCAATCCAGACCCTGTGCAGTGAAAGAACCCACCTGCCCCAGAAGAAGCAGCTG
ATGCATTTCTTATTTGGAAACTACAGGGCTCAGATGGAAGCAGAATGGAGGGAGGCCCTGCTGGCTCTCAGGGCTGCAGC
CCACTCAGCCCAGGTGAAGCCTGTGAGTCAGGCCACCAGAAAGAAAAGCTGAAGGGTCTACACGCACTGCCCATTGAGGG
CAGCCAAGGCCATCCTGGACACTCCTGGTGAAGAGTTTAGGTTCAGTTTCTTT

Alignment

ORF - retro_dnov_406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.26 %
• Parental protein coverage: 99.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AVSGHPARETAAAAAPGAARAPHAPRPPGPALSAPTLSSATSPPARLCPGRPTCKDAVPRVLPAGDDGDA
          A..G.P..........GAA...H.P...GP..SA..LS...S.P..LC.G.PTC.D.V.RV...G..G.A
Retrocopy AALGSPWTPYSGDQPSGAACVSHTPKLSGPVPSALSLSTVRSHPVCLCSGHPTCNDTVSRVHSVGGGGHA

Parental  ASKKQKKKKKTRDGAS-VADGGGKASEKLVP-EEPLSAEAQAEQLAQELAWCVEQLQLGLRTQRPSPKQK
          ..KKQKK.KKT......V..GG.K.S.K.V..EE.LSAE.Q.EQLAQELA..VEQL.L.LRTQRPSPKQK
Retrocopy TFKKQKK-KKTLEQGL>VTNGGRKTSGKPVK<EELLSAEGQVEQLAQELARHVEQLELSLRTQRPSPKQK

Parental  EQATGAIRTLLSERTPLPRKRQLMRSLFGDYRTQMEAERRETLQALRAAAHSSQVKPVSKAARKKSRRVC
          EQ.T.AI.TL.SERT.LP.K.QLM..LFG.YR.QMEAE.RE.L.ALRAAAHS.QVKPVS.A.RKKS.RV.
Retrocopy EQTTWAIQTLCSERTHLPQKKQLMHFLFGNYRAQMEAEWREALLALRAAAHSAQVKPVSQATRKKS*RVY

Parental  RPRPVGAVTAILDTPNEEFRFNFF
          ...P..A..AILDTP.EEFRF.FF
Retrocopy THCPLRAAKAILDTPGEEFRFSFF

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	12.64 RPM
SRP012922_cerebellum	0.00 RPM	6.05 RPM
SRP012922_heart	0.00 RPM	5.10 RPM
SRP012922_kidney	0.00 RPM	18.34 RPM
SRP012922_liver	0.00 RPM	4.95 RPM
SRP012922_lung	0.00 RPM	15.27 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.23 RPM
SRP012922_spleen	0.00 RPM	13.96 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_406 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015805	3 retrocopies	retro_dnov_1578, retro_dnov_406 , retro_dnov_521,
Macaca mulatta	ENSMMUG00000016084	1 retrocopy	retro_mmul_1436,
Monodelphis domestica	ENSMODG00000028791	2 retrocopies	retro_mdom_1056, retro_mdom_388,
Mustela putorius furo	ENSMPUG00000005972	1 retrocopy	retro_mputfur_1096,
Rattus norvegicus	ENSRNOG00000034107	1 retrocopy	retro_rnor_436,