RetrogeneDB ID: retro_dnov_504

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5388:173245..173558(+)
• Located in intron of: ENSDNOG00000016536

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000008426
• Aliases: None
• Description: None

Sequence

>retro_dnov_504
GGCAATGTTGTGGAGCGTTTTGATAAGGCAGCCTTGAACGCGTTGCAGCCACCCGAATTCAGAACTGAAAATTCATTAGC
ATCTACACTGAAGACGCTCCTGGTTCTTCACCGCTTTAATGATCACTGTTCCAATTGGGTTATATTTTACAACTAAATCT
TACCTATTTGAAGGTGCCTTGGGGATGTCCAATAGGGACAGCTATTTTTATGCTGCTATTGTTGCAGTGGTAGCCGCCCA
TGTGGTGCTGGCTCTCTTTGTGTACGTGGCCTGGAATGAAGGCTCATGACAGTGGCGAGAAGGCAAACAGGAT

Alignment

ORF - retro_dnov_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.19 %
• Parental protein coverage: 66.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSLLELRSRPLATSHPPPSGGRTESSLASTLKTLL-FFTALMITVPIGLYFTTKSYLFEGALGMSNRDSY
          G...E...........PP...RTE.SLASTLKTLL.FFTALMITVPIGLYFTTKSYLFEGALGMSNRDSY
Retrocopy GNVVERFDKAALNALQPPEF-RTENSLASTLKTLL>FFTALMITVPIGLYFTTKSYLFEGALGMSNRDSY

Parental  FYAAIVAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          FYAAIVAVVA.HVVLALFVYVAWNEGS.QWREGKQD
Retrocopy FYAAIVAVVAAHVVLALFVYVAWNEGS*QWREGKQD

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	1.56 RPM	2.72 RPM
SRP012922_cerebellum	0.27 RPM	3.44 RPM
SRP012922_heart	0.46 RPM	2.32 RPM
SRP012922_kidney	0.27 RPM	2.19 RPM
SRP012922_liver	0.31 RPM	2.48 RPM
SRP012922_lung	0.76 RPM	3.05 RPM
SRP012922_quadricep_muscle	0.52 RPM	2.25 RPM
SRP012922_spleen	0.57 RPM	4.01 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_504 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504 ,
Echinops telfairi	ENSETEG00000006467	1 retrocopy	retro_etel_528,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Pan troglodytes	ENSPTRG00000022372	1 retrocopy	retro_ptro_2521,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,