RetrogeneDB ID: retro_dnov_2070

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_45559:11874..12385(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DERL3
• Ensembl ID: ENSDNOG00000011041
• Aliases: None
• Description: derlin 3 [Source:HGNC Symbol;Acc:14236]

Sequence

>retro_dnov_2070
CAGTTGGAACTGATCATACCTTTTCCATTGTACTTCAATCCTGAATTAATTTTTAAACGCTTTCGAATATGGAGGTTTAT
CAACAATTTCTTACTCTTTGGGCCAGTTGGATTCAATTTTTTAAAATACAATTTTTCTATATCGTTACTGTCAAATGCTT
AGAAAAAGGCTCTTTCTGAGGTCGGACAGCCGACTTTGTATTTATGTTCCTTTTTGGTGTATTCTTAATGATCCTTTTTG
GTTTGTTTGTGAGCTTAGTTTTCTTGGGTTAGGCCTTTACAATAATGCTTGTGTACGTGTGGAGCCGAAGGAACCCATAC
ATCTGCATGAGCTTCTTTGGTCCTCTAACTTCCAAGCCCCTTTTCCGCCCTGGGTGCTCATGGGCTTTTCATTGTCACTG
GGCATCTCAATCATTGTGGACCTCTTGGGTATTCCAGTTGGGCACATACATTTTTTCTTGGAAGATGTATTTCCAAATGA
GCCATGTAGAATAAGAATTCCGAAAACACCA

Alignment

ORF - retro_dnov_2070 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 86.8 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLELLSPFQLYFNPHLVFRKFQIWRLITNFLFF-GPLGFSFFFNMLFVFRYCRML-EEGSFRGRTADFVF
          QLEL..PF.LYFNP.L.F..F.IWR.I.NFL.F.G.L..S.F.N..F..RYC.ML.E.GSF.GRTADFVF
Retrocopy QLELIIPFPLYFNPELIFKRFRIWRFINNFLLF>GQLD-SIF*NTIFLYRYCQML>EKGSF*GRTADFVF

Parental  MFLFGGFLMILLGFLGSLFFLGQALMAMLVYVWSRRSPQIRVNFFGLLT-FQAPFLPWALMGFSMLLGNS
          MFLFG.FLMIL.G...SL.FLG.A...MLVYVWSRR.P.I...FFG.LT.FQAPF.PW.LMGFS..LG.S
Retrocopy MFLFGVFLMILFGLFVSLVFLG*AFTIMLVYVWSRRNPYICMSFFGPLT<FQAPFPPWVLMGFSLSLGIS

Parental  ILVDLLGIAVGHIYYFLEDVFPNQPGGKRLLLTP
          I.VDLLGI.VGHI..FLEDVFPN.P...R...TP
Retrocopy IIVDLLGIPVGHIHFFLEDVFPNEPCRIRIPKTP

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	9.14 RPM
SRP012922_cerebellum	0.00 RPM	0.27 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.00 RPM	0.62 RPM
SRP012922_lung	0.00 RPM	5.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.11 RPM	57.00 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_2070 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
Dasypus novemcinctus	ENSDNOG00000011041	2 retrocopies	retro_dnov_2070 , retro_dnov_2675,
Sus scrofa	ENSSSCG00000010069	1 retrocopy	retro_sscr_865,