RetrogeneDB ID: retro_dnov_200

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2546:44548..44762(-)
• Located in intron of: ENSDNOG00000017242

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPLP2
• Ensembl ID: ENSDNOG00000011513
• Aliases: None
• Description: ribosomal protein, large, P2 [Source:HGNC Symbol;Acc:10377]

Sequence

>retro_dnov_200
GTCGTCAGTGAGCTACAATGGAAAAAACATTGACGATGGAATTGACCAGGGTGTTGGCAAGGTGGCCGGCGTGACTGCCA
GTGGGTCTGTGGCCGTGGCTGCCGCCCTGAGCTCTGCTGCTCCTGCTGCCAGCTCAGCCCTAGTTACAGCAGAGAAGAAG
GAAGACGAAAAGGAGGAAGAGTTGGGTGACAAAATGGGATTTGACTTGTTTGAT

Alignment

ORF - retro_dnov_200 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.33 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VISEL-NGKNIEDVIAQGIGKLASVPAGGAVAVAAAPGSAAPAASSAPAAAEEKKDEKKEESEESDDDMG
          V.SEL.NGKNI.D.I.QG.GK.A.V.A.G.VAVAAA..SAAPAASSA...AE.K.DEK.EE.....D.MG
Retrocopy VVSEL>NGKNIDDGIDQGVGKVAGVTASGSVAVAAALSSAAPAASSALVTAEKKEDEKEEE---LGDKMG

Parental  FGLFD
          F.LFD
Retrocopy FDLFD

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	0.39 RPM	146.43 RPM
SRP012922_cerebellum	0.55 RPM	56.09 RPM
SRP012922_heart	0.00 RPM	86.78 RPM
SRP012922_kidney	0.27 RPM	148.40 RPM
SRP012922_liver	0.00 RPM	63.47 RPM
SRP012922_lung	0.31 RPM	186.17 RPM
SRP012922_quadricep_muscle	0.00 RPM	121.68 RPM
SRP012922_spleen	0.11 RPM	181.08 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_200 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 11 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000001777	2 retrocopies	retro_btau_117, retro_btau_1399,
Canis familiaris	ENSCAFG00000009523	1 retrocopy	retro_cfam_18,
Ciona intestinalis	ENSCING00000000626	1 retrocopy	retro_cint_34,
Dasypus novemcinctus	ENSDNOG00000011513	12 retrocopies	retro_dnov_143, retro_dnov_1464, retro_dnov_1498, retro_dnov_1522, retro_dnov_1655, retro_dnov_1693, retro_dnov_1768, retro_dnov_200 , retro_dnov_2104, retro_dnov_2293, retro_dnov_335, retro_dnov_366,
Felis catus	ENSFCAG00000008417	1 retrocopy	retro_fcat_860,
Macaca mulatta	ENSMMUG00000020627	2 retrocopies	retro_mmul_221, retro_mmul_311,
Nomascus leucogenys	ENSNLEG00000026860	5 retrocopies	retro_nleu_1948, retro_nleu_2144, retro_nleu_2296, retro_nleu_2762, retro_nleu_85,
Otolemur garnettii	ENSOGAG00000016296	2 retrocopies	retro_ogar_156, retro_ogar_275,
Rattus norvegicus	ENSRNOG00000002116	3 retrocopies	retro_rnor_257, retro_rnor_320, retro_rnor_388,
Sarcophilus harrisii	ENSSHAG00000001056	1 retrocopy	retro_shar_321,
Sus scrofa	ENSSSCG00000012842	1 retrocopy	retro_sscr_54,