RetrogeneDB ID: retro_dnov_139

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2007:24032..24680(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF13
• Ensembl ID: ENSDNOG00000014687
• Aliases: None
• Description: ring finger protein 13 [Source:HGNC Symbol;Acc:10057]

Sequence

>retro_dnov_139
ATGCTGCTCTCTATAGGAATGCTCATGCTGTCGGCCACTCAAGTCTACACCATCTTGACCGTCCAGTTGTTTGCATTCTT
AAACCTACCGCCTGTAGAAGCAGGCATTTTAGCATATAATTTTGAAAATGCATCTCAGACTTTTGATGACCTTCCTGCAA
AATTTGGTTATAGACTTCCAACTGAAGGTTTAAAGGGTTTTCTGATTAATTCAAAACCAGAGAATACCTGTGAACCTAAA
GTGCCTCCACCACTAAAAGATAATTCATCTGGCACTTTCATCGTGTTAATTAGAAGACTTGATTGCAATTTTGATATAAA
GATTTTAAATGCACAGAGAGCAGAATTCAAAGCCGCCATAGTTCACAATGTTGATTCTGATGACCTCATTAGCATGGGAT
GCAACGACACTGATAAGTTAAAGAAAATTGACATTCCATCGGTCTTCATTGGTGAATCATCAGCTAATTCCCTGAAAGAT
GAATTCACATATGAAAAAGGGGGCCACATTATTTTAGTTCCAGAATTTAGTCTTCCTGTGGAATACTACCTCATCCCCTT
CCTTATCACTGTGGGCATCTATCTCATCTTGATAGTCATTTTCATGATCACAAAAATTGTCCAGGATCGGCACAGAGCTA
GAAGAAAT

Alignment

ORF - retro_dnov_139 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 56.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLLSIGMLMLSATQVYTILTVQFFAFLNLLPVEADILAYNFENASQTFDDLPARFGYRLPAEGLKGFLIN
          MLLSIGMLMLSATQVYTILTVQ.FAFLNL.PVEA.ILAYNFENASQTFDDLPA.FGYRLP.EGLKGFLIN
Retrocopy MLLSIGMLMLSATQVYTILTVQLFAFLNLPPVEAGILAYNFENASQTFDDLPAKFGYRLPTEGLKGFLIN

Parental  SKPENACEPIVPPPLKDNSSGTFIVLIRRLDCNFDIKVLNAQRAGFKAAIVHNVDSDELISMGSNDIDVL
          SKPEN.CEP.VPPPLKDNSSGTFIVLIRRLDCNFDIK.LNAQRA.FKAAIVHNVDSD.LISMG.ND.D.L
Retrocopy SKPENTCEPKVPPPLKDNSSGTFIVLIRRLDCNFDIKILNAQRAEFKAAIVHNVDSDDLISMGCNDTDKL

Parental  KKIDIPSVFIGESSANSLKDEFIYEKGGHIILVPEFSLPLEYYLIPFII-VSICLILIVIFMITKFVQDR
          KKIDIPSVFIGESSANSLKDEF.YEKGGHIILVPEFSLP.EYYLIPF.I.V.I.LILIVIFMITK.VQDR
Retrocopy KKIDIPSVFIGESSANSLKDEFTYEKGGHIILVPEFSLPVEYYLIPFLITVGIYLILIVIFMITKIVQDR

Parental  HRARRN
          HRARRN
Retrocopy HRARRN

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	0.39 RPM	26.84 RPM
SRP012922_cerebellum	1.10 RPM	30.24 RPM
SRP012922_heart	0.23 RPM	12.99 RPM
SRP012922_kidney	0.82 RPM	26.56 RPM
SRP012922_liver	0.93 RPM	45.36 RPM
SRP012922_lung	1.68 RPM	79.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.69 RPM
SRP012922_spleen	3.20 RPM	79.21 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_139 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 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010433	1 retrocopy	retro_amel_311,
Canis familiaris	ENSCAFG00000008370	1 retrocopy	retro_cfam_815,
Dasypus novemcinctus	ENSDNOG00000011956	3 retrocopies	retro_dnov_2168, retro_dnov_534, retro_dnov_580,
Dasypus novemcinctus	ENSDNOG00000014687	1 retrocopy	retro_dnov_139 ,
Microcebus murinus	ENSMICG00000001221	1 retrocopy	retro_mmur_323,
Nomascus leucogenys	ENSNLEG00000003149	1 retrocopy	retro_nleu_627,
Pongo abelii	ENSPPYG00000014202	1 retrocopy	retro_pabe_2392,