RetrogeneDB ID: retro_dnov_1860

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_33733:48574..48895(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD4
• Ensembl ID: ENSDNOG00000013425
• Aliases: None
• Description: COMM domain containing 4 [Source:HGNC Symbol;Acc:26027]

Sequence

>retro_dnov_1860
GAGTTGCAGCAGCTGGGCCTGCCCAAAGAGCACGCAGCCAGCCTATGCCTCTGTTACTAGGAGAAGCAAAGCCCTCTGCA
GAAACACCTGCAGGCCTGCAGCCTGCACATGAACAGGCTGATGAGCATGGGCTGGCGCATAGACTACACACTGAGCTCCA
GCCTGCTGCAGACTGTGGAGGAGTCCATGGTACACCTGAGGCTGCATGTGGCAGCTGCAACAGGGGAAAAGGCCCAGCCC
ATCAACATGTTCCTCTCAGCAGACAAGTTCCAGGTCCTGCCGGCAGAACTGAGGCAGGCCCAGACCCTGATGAGCTCGCT
G

Alignment

ORF - retro_dnov_1860 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.05 %
• Parental protein coverage: 53.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELQQLGLPKEHAASLCRCYEEKQSPLQEHLRACSLRVNRLAGVGWRVDYTLSSSLLQTVEEPMVHLRLDV
          ELQQLGLPKEHAASLC.CY.EKQSPLQ.HL.ACSL..NRL...GWR.DYTLSSSLLQTVEE.MVHLRL.V
Retrocopy ELQQLGLPKEHAASLCLCY*EKQSPLQKHLQACSLHMNRLMSMGWRIDYTLSSSLLQTVEESMVHLRLHV

Parental  AAALGEKAQPITMSLSADKFQVLLAELRQAQTLMSSL
          AAA.GEKAQPI.M.LSADKFQVL.AELRQAQTLMSSL
Retrocopy AAATGEKAQPINMFLSADKFQVLPAELRQAQTLMSSL

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	37.14 RPM
SRP012922_cerebellum	0.00 RPM	38.49 RPM
SRP012922_heart	0.00 RPM	23.90 RPM
SRP012922_kidney	0.00 RPM	52.84 RPM
SRP012922_liver	0.00 RPM	12.85 RPM
SRP012922_lung	0.00 RPM	35.74 RPM
SRP012922_quadricep_muscle	0.00 RPM	17.48 RPM
SRP012922_spleen	0.00 RPM	43.61 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_1860 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010909	1 retrocopy	retro_cjac_2080,
Dasypus novemcinctus	ENSDNOG00000013425	1 retrocopy	retro_dnov_1860 ,
Loxodonta africana	ENSLAFG00000006259	1 retrocopy	retro_lafr_1099,