RetrogeneDB ID: retro_dnov_303

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3448:141065..141714(+)
• Located in intron of: ENSDNOG00000015795

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSRC2
• Ensembl ID: ENSDNOG00000008912
• Aliases: None
• Description: arginine/serine-rich coiled-coil 2 [Source:HGNC Symbol;Acc:30559]

Sequence

>retro_dnov_303
AGGGAGGGAAAACATTGGATCAGATCTCATTTCCACTAAAGAGCAAGACACAGAGATAGGAATAGAAGCAGAAATAGAAC
AAGGAGTAGAAGTATTGATAAAAAGAAGAGAATTGAAAATCCAAGAAGGTTTAGCAGAAGTTTAAGCCAGACTCCTAGTT
CATCTCCCTTTAGAGGTGAGAACACAGCAATGGATGCACAAGAAGCCTTAGTTATGAGGTTGGAAAGGGCAAAGCAATTA
CAAGAATAATGAGAAAAGAAAATGGTTGAAAAACAACTAGAAATAGCTGCAGCAGCTACAGCTACTGGAGGTTCCTCAAT
GTTTCAGACCTTTGGCATCCAGAATACAAGTAACTCCTCATATAGCTATGGCAGCTCAAATGGCACCCTGTAAGCTAAAG
TTCTGGCAGACATTGGAATAGCTGTACCTAGATATTATAACCCAGTAGCTGTGAATCCAATGAAATTTGCCAAATGAGAG
AGAAAGGAAAATGCTTTGGCAAGGCATGAAAGAAAGGGGACAAATACCAGTCTGCTGAAGCATGGGAAAAATTGAATTTT
GGGAACAAGGACCAAATGTGAAATTTAGGAAATTAATGGGTATTAAGGGTGAAGATGAAGATGCATGCAGCTCATTTGAT
GAAGAAAGT

Alignment

ORF - retro_dnov_303 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.33 %
• Parental protein coverage: 50.69 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RERKRRIRSRSRSRSRHRHRSRSRSRTRSRSRDRKKRIEKPRRFSRSLSRTPSPPPFRGRNTAMDAQEAL
          RE.K..IRS....R.RHR.R.RSR.RTRSRS.D.KKRIE.PRRFSRSLS.TPS..PFRG.NTAMDAQEAL
Retrocopy REGKHWIRSHFH*RARHRDRNRSRNRTRSRSIDKKKRIENPRRFSRSLSQTPSSSPFRGENTAMDAQEAL

Parental  ARRLERAKKLQEQREKEMVEKQKQQEIAAAAATGGS-VLNVAAL-LASGTQVTPQIAMAAQMA-ALQAKA
          ..RLERAK.LQE..EK.MVEKQ...EIAAAA...G...LNV..L.LAS..QVTP.IAMAAQMA..L.AK.
Retrocopy VMRLERAKQLQE**EKKMVEKQL--EIAAAATATGG<FLNVSDL<LASRIQVTPHIAMAAQMA<TL*AKV

Parental  LAETGIAVPSYYNPAAVNPMKFAEQEKKRKMLWQGK-KEGDKSQSAEISYKSNFGNKDQ-NVKFRKLMGI
          LA..GIAVP.YYNP.AVNPMKFA..E.K...L.....K.GDK.QSAE...K.NFGNKDQ.NVKFRKLMGI
Retrocopy LADIGIAVPRYYNPVAVNPMKFAK*ERKENALARHE<KKGDKYQSAEAWEKLNFGNKDQ<NVKFRKLMGI

Parental  KSEDEAGCSSVDEES
          K.EDE..CSS.DEES
Retrocopy KGEDEDACSSFDEES

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	80.51 RPM
SRP012922_cerebellum	0.27 RPM	91.55 RPM
SRP012922_heart	0.00 RPM	39.91 RPM
SRP012922_kidney	0.00 RPM	62.43 RPM
SRP012922_liver	0.00 RPM	29.10 RPM
SRP012922_lung	0.15 RPM	101.41 RPM
SRP012922_quadricep_muscle	0.00 RPM	36.52 RPM
SRP012922_spleen	0.00 RPM	78.75 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_303 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020419	1 retrocopy	retro_cjac_468,
Dasypus novemcinctus	ENSDNOG00000008912	1 retrocopy	retro_dnov_303 ,
Macaca mulatta	ENSMMUG00000004412	1 retrocopy	retro_mmul_1179,
Mus musculus	ENSMUSG00000029422	1 retrocopy	retro_mmus_2465,
Rattus norvegicus	ENSRNOG00000001238	1 retrocopy	retro_rnor_1536,