RetrogeneDB ID: retro_dnov_594

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6641:10578..11192(-)
• Located in intron of: ENSDNOG00000002158

Retrocopy information

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

Parental gene information

• Parental gene symbol: SVOPL
• Ensembl ID: ENSDNOG00000006558
• Aliases: None
• Description: SVOP-like [Source:HGNC Symbol;Acc:27034]

Sequence

>retro_dnov_594
TGGCTGGGAATCGCTTTCGCCTATACGGTAGTCATCCTGGCCAGTGCCGAGTTGATGGAGAGGGAACTGGTCTGTGGTTC
ACGGTCAGAGCCTGAGGTGGTAGTATCTGCAGAAGACTCAGAGGGGAGCCAGAGCCCCTGCCACTGCCACATGTTTGCCC
CCTCCGACTACCAAACAATGATTATCAGCACCATTGGCGAAATTGCTTTGAATCCTTTAAATATCCTGGGAATCAATTTC
CTGGGAAGACGGCTGATCCTTTCTATTACCATGGGATGCACAGCTTTATTCTTCCCTCTCCTCAAAATTTGTACTTCAAG
AGCTGGCCTAATTGGCTTCCTCTTCATGCTGAGAGCTCTTGAGGCAGCAAACTTCATTACCATCTACATTTACACTGCTG
CGGTCTACCCTATGGCAATTCGTGCTTTGGGCAGGGAATCAGCGGCTCCCTGTGTCGCATTGGTGCAATGGTGGCACCAT
TCATATCACAGGTTCTTATGAATGCATCATTCCTGGGGGCCCTGTGTCTTTTCTCATCTGTCTGTGTCGCATGTGCCATT
TCTGCATTTACGCTCCCCATTGAGACCAGAGGACAGGCCTTACAGCAAATTAAA

Alignment

ORF - retro_dnov_594 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.23 %
• Parental protein coverage: 89.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  WLGISFAYYGVILASAELLERDLVCGSRSELEVVVSAGDSEGSQSPCHCHMFAPSDYQTMIISTIGEIAL
          WLGI.FAY..VILASAEL.ER.LVCGSRSE.EVVVSA.DSEGSQSPCHCHMFAPSDYQTMIISTIGEIAL
Retrocopy WLGIAFAYTVVILASAELMERELVCGSRSEPEVVVSAEDSEGSQSPCHCHMFAPSDYQTMIISTIGEIAL

Parental  NPLNILGINFLGRRLSLSITMGCTALFFLLLKICTSRAGLIGFLFMLRALVAANFITIYIYTAEVYPTAM
          NPLNILGINFLGRRL.LSITMGCTALFF.LLKICTSRAGLIGFLFMLRAL.AANFITIYIYTA.VYP.A.
Retrocopy NPLNILGINFLGRRLILSITMGCTALFFPLLKICTSRAGLIGFLFMLRALEAANFITIYIYTAAVYPMAI

Parental  RAL-GMGISGSLCRIGAMVAPFISQVLMNASFLGALCLFSSVCVACAISAFTLPIETRGRALQQIK
          RAL.G.GISGSLCRIGAMVAPFISQVLMNASFLGALCLFSSVCVACAISAFTLPIETRG.ALQQIK
Retrocopy RAL<GQGISGSLCRIGAMVAPFISQVLMNASFLGALCLFSSVCVACAISAFTLPIETRGQALQQIK

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	0.19 RPM
SRP012922_cerebellum	0.00 RPM	0.69 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	0.82 RPM
SRP012922_liver	0.00 RPM	0.15 RPM
SRP012922_lung	0.00 RPM	1.22 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.04 RPM
SRP012922_spleen	0.00 RPM	1.26 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_594 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000012965	1 retrocopy	retro_cjac_403,
Dasypus novemcinctus	ENSDNOG00000006558	2 retrocopies	retro_dnov_594 , retro_dnov_904,