RetrogeneDB ID: retro_dnov_1229

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_166736:3498..4073(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000004334
• Aliases: None
• Description: None

Sequence

>retro_dnov_1229
TGCCAGAAATGCCATGCCATCCCTGAGCAATAATCTCTGATATTCAAGAATGGCACTCGCCATCCAGATCTCTTCAACTG
TGCCAACTGCAGGAAGGAGCTGACTCTCAGTGCCTGGGAGCTGAAAGGAGAACTGTACTGCTTGCCGTGCCATGATAAAA
ATGGGTGACCCCATCTGTGGTGCTTATCGACAGCCCATGGAAAGGGCATGTGGTAAATGCCATGGGCAAGCAGTGGCATT
TGGAGCATTTTGCTTGTGCCAAGTGTGAAAAGTCATTTCTTGGACATTGCCATTATGAGAAAAAGGGCCTGGTGTACTGT
GAGATCCACTATAACCAGCTCTTTGGTGATGTTTGTTTCCCGGGTAACCATGTTATGGAAGGAGATGTGGTTCCTGCTCT
TAATAAGGCCTGGTGTGTGAACTGTTTTGCCTGTTCTACCTGCAACACTAAATTAACATTCAAGAATAAATTTGTGTAGT
TTGACATGAAGCCAGTCTGTAAGAAGTGTTACGAGAAATTTCCATTGGAACTGAAGAAAAGACTGAAGAAACTAGCTGAG
ACCTTAGGGAGGAAA

Alignment

ORF - retro_dnov_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.79 %
• Parental protein coverage: 58.77 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CQKCHAIIDEQPLIFKNDPYHPDHFNCANCGRKLTADARELKGELYCLPCHEK-IGVPICSACRRPIE-G
          CQKCHAI.....LIFKN...HPD.FNCANC...LT..A.ELKGELYCLPCH.K..G.PIC.A.R.P.E.G
Retrocopy CQKCHAIPEQ*SLIFKNGTRHPDLFNCANCRKELTLSAWELKGELYCLPCHDK>MGDPICGAYRQPME>G

Parental  RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDVCFHCNRVIEGDVVSALNKAWC
          .VVNAMGKQWH.EHF.CAKCEK.FLGH.HYE.KGL.YCE.HYNQLFGDVCF..N.V.EGDVV.ALNKAWC
Retrocopy HVVNAMGKQWHLEHFACAKCEKSFLGHCHYEKKGLVYCEIHYNQLFGDVCFPGNHVMEGDVVPALNKAWC

Parental  VNCFACSTCNTKLTLKNKFVEFDMKPVCKKCYEKFPLELKKRLKKLAETLGRK
          VNCFACSTCNTKLT.KNKFV.FDMKPVCKKCYEKFPLELKKRLKKLAETLGRK
Retrocopy VNCFACSTCNTKLTFKNKFV*FDMKPVCKKCYEKFPLELKKRLKKLAETLGRK

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	18.86 RPM
SRP012922_cerebellum	0.41 RPM	6.46 RPM
SRP012922_heart	0.00 RPM	4.41 RPM
SRP012922_kidney	0.00 RPM	10.68 RPM
SRP012922_liver	0.00 RPM	4.64 RPM
SRP012922_lung	0.00 RPM	19.24 RPM
SRP012922_quadricep_muscle	0.00 RPM	11.94 RPM
SRP012922_spleen	0.11 RPM	37.89 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_1229 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013902	1 retrocopy	retro_chof_817,
Dasypus novemcinctus	ENSDNOG00000004334	1 retrocopy	retro_dnov_1229 ,
Otolemur garnettii	ENSOGAG00000001879	1 retrocopy	retro_ogar_2992,
Rattus norvegicus	ENSRNOG00000037765	1 retrocopy	retro_rnor_432,