RetrogeneDB ID: retro_dnov_1013

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_135020:241..678(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000013931
• Aliases: None
• Description: None

Sequence

>retro_dnov_1013
ATGGAGAACATTGAAAACTCAATGGATTCGAAATCCATTAAAAATTCAGAAACAAAGATCTTACTTGGAAGCGAATCAAT
GACTCTAGAATATCCTTGGACAGTAGTTGCAAATTGGGTTACCCTGAAATGGGTTTATGTATAATAATTAATAATAAAAA
CTTTCACAAAAGCACTGGAATGGCATCTTGGTCTGGCACAGATGTAGATGCAGCAAACCTCAGGGAAACATTCGGTAACT
TGAAATATCAAGGCAGCAATAGAAATTATCTTACAAGTGAAGAAAGCATGGAATTGTTATGCAATGTTTCTAAAGCCGAT
CGTAGCAAAGGAAGGAGTTTTATTTGTGTGAATCTAAGCCATGGTAAGGAAGGAATAATTTTTGGATCAAATGGACCTCT
TGATCTGAAAAAATTAACAAGTTTCTTCGGAGGGGAT

Alignment

ORF - retro_dnov_1013 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 52.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MENIENSVDSKSIKNSETKISLGSKSV-DSGISLDSSYKMDYPEMGLCIIINNKNFHKSTGMASRSGTDV
          MENIENS.DSKSIKNSETKI.LGS.S..DS.ISLDSS.K..YPEMGLCIIINNKNFHKSTGMAS.SGTDV
Retrocopy MENIENSMDSKSIKNSETKILLGSESM<DSRISLDSSCKLGYPEMGLCIIINNKNFHKSTGMASWSGTDV

Parental  DAANLRQTFGNLNYQVRNKNDLTREEIMELLRNVSKEDHSKRSSFICVILSHGEEGIIFGTDGPIDLKKL
          DAANLR.TFGNL.YQ..N.N.LT.EE.MELL.NVSK.D.SK..SFICV.LSHG.EGIIFG..GP.DLKKL
Retrocopy DAANLRETFGNLKYQGSNRNYLTSEESMELLCNVSKADRSKGRSFICVNLSHGKEGIIFGSNGPLDLKKL

Parental  TSFFRGD
          TSFF.GD
Retrocopy TSFFGGD

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	14.20 RPM
SRP012922_cerebellum	0.00 RPM	6.60 RPM
SRP012922_heart	0.00 RPM	1.86 RPM
SRP012922_kidney	0.00 RPM	5.20 RPM
SRP012922_liver	0.00 RPM	4.80 RPM
SRP012922_lung	0.00 RPM	7.18 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.15 RPM
SRP012922_spleen	0.00 RPM	11.45 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_1013 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 16 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450,
Dasypus novemcinctus	ENSDNOG00000001797	1 retrocopy	retro_dnov_1507,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013 ,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389, retro_mmur_691,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586,