RetrogeneDB ID: retro_dnov_2004

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_41552:4713..5187(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARL10
• Ensembl ID: ENSDNOG00000002678
• Aliases: None
• Description: ADP-ribosylation factor-like 10 [Source:HGNC Symbol;Acc:22042]

Sequence

>retro_dnov_2004
CTGGGGCCCGATGGCTCCGGAAAAATCCCGTTCCTGCACGTGCTTTACCGGAAACCACCCGCGGAAGTCCACATCCCCGC
CTGGGGCTTCAACTCCACGAGGCTGCCCACCAAAGACTTGTTCAAGGTGGACCTGCTAGAGATTGGTGTCAGCCAGAAGC
TGAGCTTCCACTAGAAGGAGTTTGTGAATGAGGTGGATGCTGGTGTTGTGGTGGATTCTGCTGAGGGCCTCCGGCTGCCC
TGGGCCCAACAGGAGCCGCACAAGCTGCTGGATAAGGACCCTCTCCTGCCGGTCAGTGTGGTGGCCATGAGGGAGGCCAT
GCGTGTGGTGGAGCTGTGGTGGGAGCTGGGCCTGCAGGCTGTCCACAGCCAGCCGGAGCTCTTCCTCCTGGCAGCCAGTG
TTGCTCCCTCAGGGCCTGGCTTTCACAAACCTGGCACCGTGCACATCCAGAGGCTGCTCTTGGAACTTCTCTCC

Alignment

ORF - retro_dnov_2004 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.39 %
• Parental protein coverage: 99.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LGLDGCGKSTFLRVLSGKPPLEGHVPTWGFNSVRLPTKD-FEVDLLEIGGSQNLRFYWKEFVNEVDVLVF
          LG.DG.GK..FL.VL..KPP.E.H.P.WGFNS.RLPTKD.F.VDLLEIG.SQ.L.F..KEFVNEVD..V.
Retrocopy LGPDGSGKIPFLHVLYRKPPAEVHIPAWGFNSTRLPTKDLFKVDLLEIGVSQKLSFH*KEFVNEVDAGV-

Parental  VVDSADRLRLPWARQELHKLLDKDPDLPVVVVANKQDLSEAMSVVELQRELGLQAVDSQREVFLLAASIA
          VVDSA..LRLPWA.QE.HKLLDKDP.LPV.VVA......EAM.VVEL..ELGLQAV.SQ.E.FLLAAS.A
Retrocopy VVDSAEGLRLPWAQQEPHKLLDKDPLLPVSVVA----MREAMRVVELWWELGLQAVHSQPELFLLAASVA

Parental  PAGPGFGEPGTVHIWRLLLELLS
          P.GPGF..PGTVHI.RLLLELLS
Retrocopy PSGPGFHKPGTVHIQRLLLELLS

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	1.75 RPM
SRP012922_cerebellum	0.00 RPM	2.75 RPM
SRP012922_heart	0.00 RPM	1.39 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	2.17 RPM
SRP012922_lung	0.00 RPM	3.21 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	7.10 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_2004 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001642	3 retrocopies	retro_cpor_136, retro_cpor_1479, retro_cpor_933,
Dasypus novemcinctus	ENSDNOG00000002678	1 retrocopy	retro_dnov_2004 ,
Oryctolagus cuniculus	ENSOCUG00000016961	1 retrocopy	retro_ocun_219,