RetrogeneDB ID: retro_dnov_1496

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_21889:129..468(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000024987
• Aliases: None
• Description: None

Sequence

>retro_dnov_1496
TTGAGCACTGCCAAGGCCAACTGCTGGGCATGGCTGCTGATACTCAGCTTCATGTTTTAGTGCAAAGTCCTTAGGCCTCC
TCTTGTCATTCTCTTCTCCTTCATGTCTAGGTTGTTGCAAAAGCATGTAGAACAGGAGGCGCATATGAGAGCAGAGATCC
AGGGTATGAAGCAAGAGCTCACCACTGTCAACATGATGGATGAGTTTGTCAGATATGCCAGACTGGAAAGAAAGATCAAC
AGATGGATAACTGATAACCTCAAAACTCAAATGAACGCATGGATGGCTCAAATAAGCAAGATAAAATAGGTTATCAGTGT
TGCTTTATATGCATCTCAA

Alignment

ORF - retro_dnov_1496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.26 %
• Parental protein coverage: 64.37 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCAAEADRWAWLLVLSFVFGCNVLRILLPSFSSFMSRVLQKDAEQEAQMRAEIQGMKQELSTVNMMDEFA
          ...A.A..WAWLL.LSF.F.C.VLR..L....SFMSR.LQK..EQEA.MRAEIQGMKQEL.TVNMMDEF.
Retrocopy LSTAKANCWAWLLILSFMF*CKVLRPPLVILFSFMSRLLQKHVEQEAHMRAEIQGMKQELTTVNMMDEFV

Parental  RYARLERKINK-MTDKLKTHVKARTAQLAKIKWVISVAFYVLQ
          RYARLERKIN...TD.LKT...A..AQ..KIK.VISVA.Y..Q
Retrocopy RYARLERKINRWITDNLKTQMNAWMAQISKIK*VISVALYASQ

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	4.08 RPM
SRP012922_cerebellum	0.55 RPM	12.65 RPM
SRP012922_heart	0.00 RPM	5.34 RPM
SRP012922_kidney	0.00 RPM	4.93 RPM
SRP012922_liver	0.00 RPM	4.80 RPM
SRP012922_lung	0.00 RPM	10.84 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.02 RPM
SRP012922_spleen	0.00 RPM	7.67 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_1496 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005714	2 retrocopies	retro_cjac_2153, retro_cjac_3208,
Dasypus novemcinctus	ENSDNOG00000024987	1 retrocopy	retro_dnov_1496 ,
Homo sapiens	ENSG00000182093	1 retrocopy	retro_hsap_3080,
Gorilla gorilla	ENSGGOG00000013144	1 retrocopy	retro_ggor_2116,
Microcebus murinus	ENSMICG00000015808	1 retrocopy	retro_mmur_1275,
Macaca mulatta	ENSMMUG00000020654	2 retrocopies	retro_mmul_1966, retro_mmul_853,
Mus musculus	ENSMUSG00000023147	1 retrocopy	retro_mmus_1452,
Nomascus leucogenys	ENSNLEG00000013146	1 retrocopy	retro_nleu_2014,
Otolemur garnettii	ENSOGAG00000026761	1 retrocopy	retro_ogar_2691,
Pongo abelii	ENSPPYG00000011427	1 retrocopy	retro_pabe_2552,
Pan troglodytes	ENSPTRG00000013915	1 retrocopy	retro_ptro_2078,
Ictidomys tridecemlineatus	ENSSTOG00000012736	1 retrocopy	retro_itri_1744,
Tursiops truncatus	ENSTTRG00000015373	1 retrocopy	retro_ttru_1711,