RetrogeneDB ID: retro_dnov_2602

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_89389:790..1009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: YWHAE
• Ensembl ID: ENSDNOG00000003808
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide [Source:HGNC Symbol;Acc:12851]

Sequence

>retro_dnov_2602
GAAATTCTTAAATCCCCTGACCATGCCTGCAGGTTGGCCAAAGCAGCTTTTGATGATGCAATTGCAGAACTGGATACCCT
GAGTGAAGGAAGCTATAAGGACTCTACACTTATCATGTAGTTATTCCGTGATAATCTGACACTATGGACTTCCGACATGC
AGGGTGATGGTGAAGAGCAGAATAAAGAAGTGCTGCAGGATGTGGAAGATGAAAATCAG

Alignment

ORF - retro_dnov_2602 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.67 %
• Parental protein coverage: 55.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EILNSPDRACRLAKAAFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDXXXQNKEALQDVED
          EIL.SPD.ACRLAKAAFDDAIAELDTLSE.SYKDSTLIM.L.RDNLTLWTSDMQGD...QNKE.LQDVED
Retrocopy EILKSPDHACRLAKAAFDDAIAELDTLSEGSYKDSTLIM*LFRDNLTLWTSDMQGDGEEQNKEVLQDVED

Parental  ENQ
          ENQ
Retrocopy ENQ

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	84.98 RPM
SRP012922_cerebellum	0.00 RPM	119.87 RPM
SRP012922_heart	0.00 RPM	57.08 RPM
SRP012922_kidney	0.00 RPM	72.28 RPM
SRP012922_liver	0.00 RPM	35.30 RPM
SRP012922_lung	0.00 RPM	62.01 RPM
SRP012922_quadricep_muscle	0.00 RPM	81.87 RPM
SRP012922_spleen	0.00 RPM	49.68 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_2602 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 9 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010861	2 retrocopies	retro_chof_1912, retro_chof_905,
Ciona intestinalis	ENSCING00000023856	1 retrocopy	retro_cint_15,
Ciona savignyi	ENSCSAVG00000011723	2 retrocopies	retro_csav_13, retro_csav_9,
Dasypus novemcinctus	ENSDNOG00000001672	10 retrocopies	retro_dnov_1007, retro_dnov_117, retro_dnov_1354, retro_dnov_1579, retro_dnov_1769, retro_dnov_1907, retro_dnov_1993, retro_dnov_2588, retro_dnov_892, retro_dnov_99,
Dasypus novemcinctus	ENSDNOG00000003808	2 retrocopies	retro_dnov_1452, retro_dnov_2602 ,
Echinops telfairi	ENSETEG00000012056	2 retrocopies	retro_etel_1762, retro_etel_738,
Gorilla gorilla	ENSGGOG00000016840	1 retrocopy	retro_ggor_2596,
Oryctolagus cuniculus	ENSOCUG00000014607	2 retrocopies	retro_ocun_1062, retro_ocun_1576,
Pongo abelii	ENSPPYG00000007769	4 retrocopies	retro_pabe_1644, retro_pabe_1646, retro_pabe_2107, retro_pabe_3219,