RetrogeneDB ID: retro_dnov_192

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2475:113136..113570(-)
• Located in intron of: ENSDNOG00000008110

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOJ
• Ensembl ID: ENSDNOG00000001761
• Aliases: None
• Description: ras homolog family member J [Source:HGNC Symbol;Acc:688]

Sequence

>retro_dnov_192
ATGCTCAAGTGCGTGGTGGTCGGCAACGGGGCAGTGGGCAAGATGTGCCTACTCATGAGCTATGCCAATGACGCCTTCCC
GGAGGAGTACGTGCCCACCGTCTTCAACCACTACGCAGTTAGCATCACCGTGGGGGCAAGCAGTACTTCCTGGGACTCTA
TGACTTGGCCCGACAGGAAGACTATGACCGTCTGAGGCCTTTATCTTATCCCATGACTGATGTCTTCCTTATATACTTCT
CTGTGGAAAATCCAGCCTCATTTCAAAACGTGAAGGAGGAGTGGGTACCAGAGCTTAAGGAATATGCATCAAATATACCC
TTTTTATTAATAGGAACTCAGATTGATCTCCGAGATGACCCCAAAACTTTAGCAAGACTGAATGATATGAAAGAAAAGCC
TGTATGTGTGGAACAAGGACAGAAACTAGCGAAA

Alignment

ORF - retro_dnov_192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.86 %
• Parental protein coverage: 87.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLKCVVVGDGAVGKTCLLMSYANDAFPEEYVPTVFDHYAVTVTVG-GKQHLLGLYDTAGQEDYNQLRPLS
          MLKCVVVG.GAVGK.CLLMSYANDAFPEEYVPTVF.HYAV..TVG.GKQ..LGLYD.A.QEDY..LRPLS
Retrocopy MLKCVVVGNGAVGKMCLLMSYANDAFPEEYVPTVFNHYAVSITVG<GKQYFLGLYDLARQEDYDRLRPLS

Parental  YPNTDVFLICFSVVNPASYHNVQEEWVPELKDCMPHVPYVLIGTQXXXXXXXXXXXRLLYMKEKPLTYEH
          YP.TDVFLI.FSV.NPAS..NV.EEWVPELK......P..LIGTQ...........RL..MKEKP...E.
Retrocopy YPMTDVFLIYFSVENPASFQNVKEEWVPELKEYASNIPFLLIGTQIDLRDDPKTLARLNDMKEKPVCVEQ

Parental  GVKLAK
          G.KLAK
Retrocopy GQKLAK

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	0.19 RPM	6.42 RPM
SRP012922_cerebellum	0.14 RPM	0.96 RPM
SRP012922_heart	0.23 RPM	3.02 RPM
SRP012922_kidney	0.00 RPM	1.37 RPM
SRP012922_liver	0.00 RPM	0.46 RPM
SRP012922_lung	0.00 RPM	10.08 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.73 RPM
SRP012922_spleen	0.23 RPM	4.35 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_192 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001761	2 retrocopies	retro_dnov_192 , retro_dnov_927,
Gorilla gorilla	ENSGGOG00000007948	1 retrocopy	retro_ggor_22,
Pan troglodytes	ENSPTRG00000006424	4 retrocopies	retro_ptro_1643, retro_ptro_2091, retro_ptro_2971, retro_ptro_910,
Vicugna pacos	ENSVPAG00000004859	2 retrocopies	retro_vpac_574, retro_vpac_588,