RetrogeneDB ID: retro_dnov_1181

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_15905:44099..44529(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VTCN1
• Ensembl ID: ENSDNOG00000013317
• Aliases: None
• Description: V-set domain containing T cell activation inhibitor 1 [Source:HGNC Symbol;Acc:28873]

Sequence

>retro_dnov_1181
GTCACAGATGCTGGCACCTACAAACATTACATCATCATCTCTAAGGGCAAGGGGAATGCTAACTTGGAATATAAAATTGG
TCCTTTCTGCATCCCAAAGTGAATGTGGACTATAATGCCCATTCAGAGATCTTACAGTATAATGCTCCCCAATGGTTCCC
CCCCTTCCACAGTGATCTGGGCATCCCAAGTTGACGAGGGAACCAACTTCTCAGAAGTCTCCAATATCGGCTTTGAGCTT
AACTCTGAGAATGTGATAAGGAAGGTAGTGTTCATGTTCTACACTGTAACAAATCAACAACACATATTCCTGTATGACTG
AGAACAACACTGTCAGAGCCACAGGGGATATCAAAGGGACAGACTCTGGTCAAAAGATGGAGTCACAGCTGCTAAACTCA
AAGGTTTTAGTGTATCTCTTCTTTCTCTGC

Alignment

ORF - retro_dnov_1181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.19 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LTDAGTYKCYIITSKGKGNANLEYKTGAFSV-PEVNVNYNASSESLRCEAPRWF-PQPTVVWASQADQGA
          .TDAGTYK.YII.SKGKGNANLEYK.G.F...P.VNV.YNA.SE.L...AP.WF.P..TV.WASQ.D.G.
Retrocopy VTDAGTYKHYIIISKGKGNANLEYKIGPFCI<PKVNVDYNAHSEILQYNAPQWF>PPSTVIWASQVDEGT

Parental  NFSEVST-SFELNSENVTMKVVSVLYNVT-INNTYSCMIENSIAKATGDIKVTDSEIKRQSHLQLLNSKA
          NFSEVS...FELNSENV..KVV...Y.VT.INNTYSCM.EN....ATGDIK.TDS..K..S..QLLNSK.
Retrocopy NFSEVSNIGFELNSENVIRKVVFMFYTVT>INNTYSCMTENNTVRATGDIKGTDSGQKMES--QLLNSKV

Parental  SLGVSSFC
          .......C
Retrocopy LVYLFFLC

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	1.36 RPM
SRP012922_cerebellum	0.00 RPM	0.00 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.46 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.11 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_1181 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005097	1 retrocopy	retro_chof_1322,
Dasypus novemcinctus	ENSDNOG00000013317	1 retrocopy	retro_dnov_1181 ,
Homo sapiens	ENSG00000134258	1 retrocopy	retro_hsap_2420,
Gorilla gorilla	ENSGGOG00000025814	1 retrocopy	retro_ggor_1505,
Macaca mulatta	ENSMMUG00000016964	1 retrocopy	retro_mmul_611,
Nomascus leucogenys	ENSNLEG00000005256	1 retrocopy	retro_nleu_2811,
Pan troglodytes	ENSPTRG00000001164	1 retrocopy	retro_ptro_1394,