RetrogeneDB ID: retro_dnov_1519

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2251:85104..85450(-)
• Located in intron of: ENSDNOG00000001398

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_1519
ACTGGGTATTCTTATGAAATCTATGTTGATCCTGAGAGAGAAATTTGTAAAAGATTGGGAATGAAAAGAGGTGAAGAAAT
TGCTGCCTCAGGACAGAGCCCCTGTGTAAAATCAAATATACTCTCAGGATGTGTTCAGATCCTGTGGTGGGTGGTGACTG
GCCCTTTTTATGATTTTCAAGGAGACCCAGGTTAGGAAGGTGGAACTGTCATTTTAGGTCCAGGTAGTAACATTTATTTT
ATACACAGAGATAAGATTTGATTGGATCACAAGTCCATCAACTGTTATACAGCTTGTAGGAGTTCAGCATGTGAACTTTA
CAAGAAGTCCTTCAGTTATGCATATG

Alignment

ORF - retro_dnov_1519 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 61.41 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGYSYEIYVDPEREIYKRLGMKRGEEIAASGQSPHVKSNILSGSIRSLWRAVTGPLFDFQGDPAQQGGTL
          TGYSYEIYVDPEREI.KRLGMKRGEEIAASGQSP.VKSNILSG....LW..VTGP..DFQGDP...GGT.
Retrocopy TGYSYEIYVDPEREICKRLGMKRGEEIAASGQSPCVKSNILSGCVQILWWVVTGPFYDFQGDPG*EGGTV

Parental  ILGP--NIHFIHHDRNRLDH-NPNNSVLQHVGV-HVSFTSRLSVVHL
          ILGP..NI.FIH.D...LDH..P...V.Q.VGV.HV.FT...SV.H.
Retrocopy ILGPGSNIYFIHRDKI*LDH>SP-STVIQLVGVQHVNFTRSPSVMHM

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	0.58 RPM	8.36 RPM
SRP012922_cerebellum	0.00 RPM	5.09 RPM
SRP012922_heart	0.93 RPM	6.03 RPM
SRP012922_kidney	0.27 RPM	7.12 RPM
SRP012922_liver	0.00 RPM	7.12 RPM
SRP012922_lung	0.31 RPM	12.52 RPM
SRP012922_quadricep_muscle	1.04 RPM	6.58 RPM
SRP012922_spleen	0.57 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_1519 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.

---

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,