RetrogeneDB ID: retro_dnov_2110

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_48736:3398..3995(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLRX3
• Ensembl ID: ENSDNOG00000010387
• Aliases: None
• Description: glutaredoxin 3 [Source:HGNC Symbol;Acc:15987]

Sequence

>retro_dnov_2110
GGCGGCGGTGGTGGGGAAGTCGGCTCGGGCCGGGAGTGTGAGGAGCTGCTGCTCCTCAAAGCCAGATCCCTCCTTGTGGC
CCATTTTGGGGCACCACGGGCTCCACAGTGTGTGCAGACGACCGATGTGACGGTGGAGTTAGCTAAAGAACACCCTCAAG
TTTCATTTACGAAGTTGAAAGCTGAAGCTGTTCCTGAAGTGTCTGAAAGATATGAAATTAGTTCTGTTCCCACCTTTCTG
TTTTTCAAGAATTCTCAGAAAATTGACCGATTAGATGGTGCACCTGCCCCAGAGTTGACCAAAAGAGTTCAGCGACACGC
ACCTAGCGGCTCTTTGGCATCCGATCTGAACGAACATCCTAGAGAAGATTTCAACCTCCGTCTAAAGAAATTAACTAATG
CTGCCCCCTGCATGCAGTTCATGAAAGGAGCTCCTCAGCAAGCCCGCTGTGGTTCCAGCAAGCAGAGGGTGGAAATTCTT
AACAAACATAATATTCAGTTCAGCAGTTGTGATTCCTTCTCAGATGAAGAAGTTCGTCAGGGTCTCAAAACCTACTCCAG
TTGGCCCACCTATCCCCTCAGCTGTATGTCTCCGGAG

Alignment

ORF - retro_dnov_2110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.4 %
• Parental protein coverage: 63.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GAAAVEVGSAREFEELLRLKARSLLVVHFWAPWAPQCVQMNDVMVELAKEHPQVSFVKLEAEAVPEVSEK
          G....EVGS.RE.EELL.LKARSLLV.HF.AP.APQCVQ..DV.VELAKEHPQVSF.KL.AEAVPEVSE.
Retrocopy GGGGGEVGSGRECEELLLLKARSLLVAHFGAPRAPQCVQTTDVTVELAKEHPQVSFTKLKAEAVPEVSER

Parental  YEISSVPTFLFFKNSQKIDRLDGAHAPELTKRVQRHASSGSFAPAMNEHPKEELNLRLKKLTNAAPCMLF
          YEISSVPTFLFFKNSQKIDRLDGA.APELTKRVQRHA.SGS.A...NEHP.E..NLRLKKLTNAAPCM.F
Retrocopy YEISSVPTFLFFKNSQKIDRLDGAPAPELTKRVQRHAPSGSLASDLNEHPREDFNLRLKKLTNAAPCMQF

Parental  MKGTPQEPRCGFSKQMVEILNKHNIQFSSFDIFSDEEVRQGLKTYSNWPTYPQLYVSGE
          MKG.PQ..RCG.SKQ.VEILNKHNIQFSS.D.FSDEEVRQGLKTYS.WPTYP....S.E
Retrocopy MKGAPQQARCGSSKQRVEILNKHNIQFSSCDSFSDEEVRQGLKTYSSWPTYPLSCMSPE

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	44.53 RPM
SRP012922_cerebellum	0.00 RPM	45.50 RPM
SRP012922_heart	0.00 RPM	65.43 RPM
SRP012922_kidney	0.00 RPM	38.88 RPM
SRP012922_liver	0.00 RPM	20.59 RPM
SRP012922_lung	0.00 RPM	47.34 RPM
SRP012922_quadricep_muscle	0.17 RPM	69.06 RPM
SRP012922_spleen	0.00 RPM	45.33 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_2110 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
Ailuropoda melanoleuca	ENSAMEG00000003257	1 retrocopy	retro_amel_1348,
Bos taurus	ENSBTAG00000005027	1 retrocopy	retro_btau_659,
Canis familiaris	ENSCAFG00000013280	1 retrocopy	retro_cfam_285,
Callithrix jacchus	ENSCJAG00000014400	1 retrocopy	retro_cjac_158,
Dasypus novemcinctus	ENSDNOG00000010387	1 retrocopy	retro_dnov_2110 ,
Gorilla gorilla	ENSGGOG00000010771	1 retrocopy	retro_ggor_2308,
Microcebus murinus	ENSMICG00000008544	2 retrocopies	retro_mmur_1394, retro_mmur_89,
Myotis lucifugus	ENSMLUG00000005483	1 retrocopy	retro_mluc_377,
Mus musculus	ENSMUSG00000031068	1 retrocopy	retro_mmus_2480,
Nomascus leucogenys	ENSNLEG00000027088	2 retrocopies	retro_nleu_2322, retro_nleu_249,
Ochotona princeps	ENSOPRG00000017309	1 retrocopy	retro_opri_462,
Pongo abelii	ENSPPYG00000002768	1 retrocopy	retro_pabe_2830,
Pan troglodytes	ENSPTRG00000003060	1 retrocopy	retro_ptro_2320,