RetrogeneDB ID: retro_dnov_2473

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_78341:2668..3021(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL49
• Ensembl ID: ENSDNOG00000004494
• Aliases: None
• Description: mitochondrial ribosomal protein L49 [Source:HGNC Symbol;Acc:1176]

Sequence

>retro_dnov_2473
CATGAACACCAGTTTGTGGAGCACTTTATGCATCCCACCAGCATTCCAAAGCCCCAAGGCACAAACACATCCCATTGCCA
GTGACTGGCAGCACTCCCTCCCAGTCTCCACCCAGCCTGCCCTGTTTTGTGGGGCGCTCTCAGATGAACAACACTCCTGT
CTACAGGGACATCAGATATGGCAACTGTCAGATAACAGTGATCGAGAAGTTAGAAGGGTACATTGAAGCCCTGCAGAAGG
ATGTGGAGGATTTTCTGAGCCCACATCTGGGGAAGGCACCTTTTAGCCAGGTCAGTGGGGTGACACGTGCCCTGTTGGAT
CAAGGACTTCTGCGAGTCCCGCTGATCAGCTGG

Alignment

ORF - retro_dnov_2473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.46 %
• Parental protein coverage: 84.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HEYQFVERLIPPTSIPKP-PKHEQYSTPSGWQPPQDTPPNLPYFVRRSRMHNIPVYKDITHGNRQMTVIR
          HE.QFVE....PTSIPKP.P.H.....P.....P...PP.LP.FV.RS.M.N.PVY.DI..GN.Q.TVI.
Retrocopy HEHQFVEHFMHPTSIPKP<PRHKHIPLPVTGSTPSQSPPSLPCFVGRSQMNNTPVYRDIRYGNCQITVIE

Parental  KVEGDIWALQKDVEDFLSPLLGKTPVTQVNEVTGTLRVKGYVDQQLKAW
          K.EG.I.ALQKDVEDFLSP.LGK.P..QV..VT..L...G.....L..W
Retrocopy KLEGYIEALQKDVEDFLSPHLGKAPFSQVSGVTRALLDQGLLRVPLISW

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	8.11 RPM
SRP012922_heart	0.00 RPM	7.19 RPM
SRP012922_kidney	0.00 RPM	12.32 RPM
SRP012922_liver	0.00 RPM	3.10 RPM
SRP012922_lung	0.00 RPM	13.59 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.06 RPM
SRP012922_spleen	0.00 RPM	12.48 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_2473 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012855	1 retrocopy	retro_chof_1006,
Dasypus novemcinctus	ENSDNOG00000004494	6 retrocopies	retro_dnov_1396, retro_dnov_1488, retro_dnov_1941, retro_dnov_2272, retro_dnov_2473 , retro_dnov_2686,
Dipodomys ordii	ENSDORG00000003613	1 retrocopy	retro_dord_196,
Homo sapiens	ENSG00000149792	1 retrocopy	retro_hsap_3180,
Macropus eugenii	ENSMEUG00000009437	1 retrocopy	retro_meug_1151,
Microcebus murinus	ENSMICG00000016604	1 retrocopy	retro_mmur_629,
Macaca mulatta	ENSMMUG00000018778	1 retrocopy	retro_mmul_2031,
Nomascus leucogenys	ENSNLEG00000005505	1 retrocopy	retro_nleu_1659,
Oryctolagus cuniculus	ENSOCUG00000014882	1 retrocopy	retro_ocun_316,
Pan troglodytes	ENSPTRG00000003867	1 retrocopy	retro_ptro_2263,
Tupaia belangeri	ENSTBEG00000007929	2 retrocopies	retro_tbel_1350, retro_tbel_3334,