RetrogeneDB ID: retro_dnov_178

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2366:79954..80226(+)
• Located in intron of: ENSDNOG00000008298

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL3
• Ensembl ID: ENSDNOG00000014498
• Aliases: None
• Description: mitochondrial ribosomal protein L3 [Source:HGNC Symbol;Acc:10379]

Sequence

>retro_dnov_178
AAAGCTGAAGCCATGTTGGAATTTTACCGACAACTTGGATTGCCCCAAAACGGAAAATTAAAATCTTTCATGTGACAGAT
AACACTGTAATTAAGCCAGGCACTCCACTTCATGCTGTGCACTTTCACCCAGGACGGTATGTGGATGTCACAGCTCAAAC
TATTGGTAAAGTTTTTCAAGGCGTCATGAAAAGATGGGGATTTAAAGGCCAGCCTGCTACTCATGGTCAAACGAAAACCC
ACAGGAGACCTAGAGCTATCTCAACTGGTGAT

Alignment

ORF - retro_dnov_178 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.78 %
• Parental protein coverage: 51.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAESILEFYRELGLP-PKQKIKIFHVTDNAIIKPGTPLYAAHFRPGQYVDVTAKTIGKGFQGVMKRWGFK
          KAE..LEFYR.LGLP.PK.KIKIFHVTDN..IKPGTPL.A.HF.PG.YVDVTA.TIGK.FQGVMKRWGFK
Retrocopy KAEAMLEFYRQLGLP<PKRKIKIFHVTDNTVIKPGTPLHAVHFHPGRYVDVTAQTIGKVFQGVMKRWGFK

Parental  GQPATHGQTKTHRRPGAISTGD
          GQPATHGQTKTHRRP.AISTGD
Retrocopy GQPATHGQTKTHRRPRAISTGD

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	4.47 RPM	16.53 RPM
SRP012922_cerebellum	4.81 RPM	14.30 RPM
SRP012922_heart	3.25 RPM	18.79 RPM
SRP012922_kidney	2.74 RPM	12.87 RPM
SRP012922_liver	1.08 RPM	4.95 RPM
SRP012922_lung	1.99 RPM	11.45 RPM
SRP012922_quadricep_muscle	5.37 RPM	15.75 RPM
SRP012922_spleen	3.66 RPM	13.28 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_178 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021216	1 retrocopy	retro_cpor_324,
Dasypus novemcinctus	ENSDNOG00000014498	1 retrocopy	retro_dnov_178 ,
Homo sapiens	ENSG00000114686	1 retrocopy	retro_hsap_1236,
Gorilla gorilla	ENSGGOG00000011128	1 retrocopy	retro_ggor_969,
Microcebus murinus	ENSMICG00000009524	1 retrocopy	retro_mmur_1106,
Ochotona princeps	ENSOPRG00000000501	1 retrocopy	retro_opri_589,
Pan troglodytes	ENSPTRG00000015396	1 retrocopy	retro_ptro_850,
Sus scrofa	ENSSSCG00000011179	1 retrocopy	retro_sscr_126,