RetrogeneDB ID: retro_dnov_1226

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_166355:220..610(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AAED1
• Ensembl ID: ENSDNOG00000024562
• Aliases: None
• Description: AhpC/TSA antioxidant enzyme domain containing 1 [Source:HGNC Symbol;Acc:16881]

Sequence

>retro_dnov_1226
GTAGGACAGTTGTCCTGCCATCATTTTGAGCTTTTCTACAAACTGACTGAATATTTTCATGAAATCTATGTTGATACTGA
GAGAAAAATTTATAAAAGATTGGGAATGAAAAGACATGAAGAAATTGCTGTCTCAGGACAGTGCCCCCTATAAAATGTCA
AATATACTCTCAGGAAACATTCAGTACCTGTGGTGGGTAATGATTGGCCTACATTTTGATTTTCAAGGAGACCCACTCAG
CAAGACAGAACCCTCATTTTAGGTCCAGGTAATAACATTAATTTTATATGCCACAATAGGAAAAGATTGGATCACAAACC
TATCAACTCTGTTCTACAGCGTGTAGGAGTTCAGCATGTAAACTTTACAACACCTTCAGTTATCCATGTG

Alignment

ORF - retro_dnov_1226 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.66 %
• Parental protein coverage: 69.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IGQSSYHHIESFCKLTGYSYEIYVDPEREIYKRLGMKRGEEIAASGQ-SPHVKSNILSGSIRSLWRAVTG
          .GQ.S.HH.E.F.KLT.Y..EIYVD.ER.IYKRLGMKR.EEIA.SGQ..P...SNILSG.I..LW....G
Retrocopy VGQLSCHHFELFYKLTEYFHEIYVDTERKIYKRLGMKRHEEIAVSGQ>APYKMSNILSGNIQYLWWVMIG

Parental  PLFDFQGD-PAQQGGTLILGP--NIHFIHHDRNRLDHNPNNSVLQHVGV-HVSFTSRLSVVHL
          ..FDFQGD.P.QQ..TLILGP..NI.FI.H.R.RLDH.P.NSVLQ.VGV.HV.FT...SV.H.
Retrocopy LHFDFQGD<PTQQDRTLILGPGNNINFICHNRKRLDHKPINSVLQRVGVQHVNFTTP-SVIHV

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	0.19 RPM	8.36 RPM
SRP012922_cerebellum	0.00 RPM	5.09 RPM
SRP012922_heart	0.00 RPM	6.03 RPM
SRP012922_kidney	0.00 RPM	7.12 RPM
SRP012922_liver	0.00 RPM	7.12 RPM
SRP012922_lung	0.00 RPM	12.52 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.58 RPM
SRP012922_spleen	0.00 RPM	13.85 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_1226 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 10 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006422	1 retrocopy	retro_chof_1792,
Choloepus hoffmanni	ENSCHOG00000007723	7 retrocopies	retro_chof_1026, retro_chof_1037, retro_chof_1808, retro_chof_2079, retro_chof_2149, retro_chof_2642, retro_chof_811,
Callithrix jacchus	ENSCJAG00000005509	1 retrocopy	retro_cjac_4168,
Dasypus novemcinctus	ENSDNOG00000024562	4 retrocopies	retro_dnov_1226 , retro_dnov_1419, retro_dnov_1519, retro_dnov_1871,
Homo sapiens	ENSG00000158122	1 retrocopy	retro_hsap_4843,
Macaca mulatta	ENSMMUG00000008295	1 retrocopy	retro_mmul_2586,
Otolemur garnettii	ENSOGAG00000017058	1 retrocopy	retro_ogar_1866,
Procavia capensis	ENSPCAG00000003177	1 retrocopy	retro_pcap_269,
Pongo abelii	ENSPPYG00000019418	1 retrocopy	retro_pabe_3765,
Pan troglodytes	ENSPTRG00000021156	1 retrocopy	retro_ptro_3227,