RetrogeneDB ID: retro_dnov_2410

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_725:174892..175195(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UQCRB
• Ensembl ID: ENSDNOG00000017312
• Aliases: None
• Description: ubiquinol-cytochrome c reductase binding protein [Source:HGNC Symbol;Acc:12582]

Sequence

>retro_dnov_2410
GCAGCATGAGGCCGTTGGCTGGATGGTATTCAAAAATGGTATTGCAGTGCTGCAGGGTTCAATAAACTAGGGTTAACGCA
AGATGATACAATAGCCAAGAATGAAGATGTAAAAGAAGCCATAACTGAAAACCTTTATCATGACAGGATGTTTCGCATTA
AGAGAGCACTAGACCTGACCATGAAGCATCAGATCTTGCCTAAAAAGCAGTGGACAAAATAGGAGGAGGATAAATTCTAC
CTTGAATCATATCTAAAAGAAGTTATTCAGGAAAGAAAAGAGAGAGAAGAATGGGCAAAGAAA

Alignment

ORF - retro_dnov_2410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASSGQWLDSIQKQYHRVVEGREKGLMRDDTY-ENEDVKEAIKRLPENVYNDRMFRIKRALDLTMKHQILP
          A..G.WLD.IQK.Y.........GL..DDT...NEDVKEAI....EN.Y.DRMFRIKRALDLTMKHQILP
Retrocopy AA*GRWLDGIQKWYCSAAGFNKLGLTQDDTIAKNEDVKEAIT---ENLYHDRMFRIKRALDLTMKHQILP

Parental  KEQWTKYEEDKFYLEPYLKEVIREIKEREEWAKK
          K.QWTK.EEDKFYLE.YLKEVI.E.KEREEWAKK
Retrocopy KKQWTK*EEDKFYLESYLKEVIQERKEREEWAKK

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	50.95 RPM
SRP012922_cerebellum	0.14 RPM	14.30 RPM
SRP012922_heart	0.00 RPM	91.19 RPM
SRP012922_kidney	0.00 RPM	31.76 RPM
SRP012922_liver	0.00 RPM	24.15 RPM
SRP012922_lung	0.00 RPM	17.87 RPM
SRP012922_quadricep_muscle	0.00 RPM	60.58 RPM
SRP012922_spleen	0.00 RPM	17.51 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_2410 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 9 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009449	4 retrocopies	retro_cfam_1504, retro_cfam_1509, retro_cfam_1531, retro_cfam_792,
Dasypus novemcinctus	ENSDNOG00000017312	8 retrocopies	retro_dnov_1109, retro_dnov_1163, retro_dnov_1706, retro_dnov_2410 , retro_dnov_2518, retro_dnov_369, retro_dnov_608, retro_dnov_798,
Latimeria chalumnae	ENSLACG00000004465	1 retrocopy	retro_lcha_127,
Myotis lucifugus	ENSMLUG00000007182	1 retrocopy	retro_mluc_1601,
Nomascus leucogenys	ENSNLEG00000026670	1 retrocopy	retro_nleu_1357,
Ochotona princeps	ENSOPRG00000008892	2 retrocopies	retro_opri_109, retro_opri_688,
Rattus norvegicus	ENSRNOG00000024967	1 retrocopy	retro_rnor_290,
Ictidomys tridecemlineatus	ENSSTOG00000008017	1 retrocopy	retro_itri_46,
Drosophila melanogaster	FBgn0030733	1 retrocopy	retro_dmel_22,