RetrogeneDB ID: retro_dnov_1607

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_246723:306..663(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSDNOG00000004111
• Aliases: None
• Description: mitochondrial ribosomal protein L11 [Source:HGNC Symbol;Acc:14042]

Sequence

>retro_dnov_1607
CGAGGCACCTCCACCAGCCAGTGCTGCAAGGAATTCAACAAGAAGACAAAGGGCACCACAGAAGGCATTCCTCTGCCTAT
TAAGATTTCTGCGAAGCCTGACAGGACGTTTGAAATCAAGACTGGACAACCCACTGTTTCCTGCTTTCTGGAGGCAGCTG
CTGATATTGAGAAGGGGGCCCGGCAGACAGAGAAAGGTGGCAGGCCTGGTGACCCTGAAGCACAGGCATGAGGTTGCCCA
CGTCAAAGCTCAGGACGATGCCCTTCCCTGCAGGACATGCCCTTGTCCTCGGCTGTCCACTCCCTCATCGACTCTGCCTA
TTCTCTGGGCTTTCCTGTGCTGAAGGAACTGGCAGCT

Alignment

ORF - retro_dnov_1607 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.2 %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RGVSISQFCKEFNEKTKDIIEGIPLPTKIFVKPDRTFEIKIGQ-PTVSYFLKAAAGIEKGARQTGKEVAG
          RG.S.SQ.CKEFN.KTK...EGIPLP.KI..KPDRTFEIK.GQ.P....F.........G.....K.VAG
Retrocopy RGTSTSQCCKEFNKKTKGTTEGIPLPIKISAKPDRTFEIKTGQ>PLFPAFWRQLLILRRGPGRQRK-VAG

Parental  LVTLKHVYEIARIKAQDDAF-ALQDVPLSSVVRSIIGSARSLGIRVVKDLSS
          LVTLKH..E.A..KAQDDA...LQD.PLSS.V.S.I.SA.SLG..V.K.L..
Retrocopy LVTLKHRHEVAHVKAQDDAL<SLQDMPLSSAVHSLIDSAYSLGFPVLKELAA

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	41.62 RPM
SRP012922_cerebellum	0.00 RPM	20.76 RPM
SRP012922_heart	0.00 RPM	33.18 RPM
SRP012922_kidney	0.00 RPM	53.94 RPM
SRP012922_liver	0.00 RPM	27.87 RPM
SRP012922_lung	0.00 RPM	22.76 RPM
SRP012922_quadricep_muscle	0.00 RPM	41.89 RPM
SRP012922_spleen	0.00 RPM	21.40 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_1607 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607 , retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754, retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,