RetrogeneDB ID: retro_dnov_643

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_7159:21024..21241(-)
• Located in intron of: ENSDNOG00000010215

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXYD4
• Ensembl ID: ENSDNOG00000017385
• Aliases: None
• Description: FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]

Sequence

>retro_dnov_643
CTGCCTGCTTTGGAAGCCAGTGGCCTGGTTGATAAACACAGTCGCCTCTAGTCGGACAGGAAAAGCCTCCAGCTGCACTG
CTGGTCTGTGCAGAGATCACATGCCTGGCTGGATCCTCTTTACTGTGCATGACAAATGCCAACGCAAGGCCAGAGGGAAG
CACAGCCCCTTACCTGAGAAAGCCCCTCTGCTCATCCGTGGGGGCTCCTCCTGCGCC

Alignment

ORF - retro_dnov_643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.21 %
• Parental protein coverage: 91.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LPVLEANDLVADKHSPFYYDWESLQL-AGLICAGALCLIG-ILFTVYGKCKCKAKEKHSPLPEKPTPLIT
          LP.LEA..LV.DKHS....D..SLQL.A.L.CA...CL.G.ILFTV..KC..KA..KHSPLPEK...LI.
Retrocopy LPALEASGLV-DKHSRL*SDRKSLQL<ALLVCAEITCLAG<ILFTVHDKCQRKARGKHSPLPEKAPLLIR

Parental  EGSASA
          .GS..A
Retrocopy GGSSCA

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	2.33 RPM
SRP012922_cerebellum	0.00 RPM	0.14 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	9.04 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.23 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_643 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024923	1 retrocopy	retro_cfam_1820,
Dasypus novemcinctus	ENSDNOG00000017385	1 retrocopy	retro_dnov_643 ,
Erinaceus europaeus	ENSEEUG00000010030	4 retrocopies	retro_eeur_148, retro_eeur_264, retro_eeur_524, retro_eeur_559,
Felis catus	ENSFCAG00000022417	2 retrocopies	retro_fcat_284, retro_fcat_990,
Monodelphis domestica	ENSMODG00000027578	1 retrocopy	retro_mdom_976,
Oryctolagus cuniculus	ENSOCUG00000006722	1 retrocopy	retro_ocun_1050,
Tupaia belangeri	ENSTBEG00000016033	1 retrocopy	retro_tbel_1911,
Tarsius syrichta	ENSTSYG00000014460	3 retrocopies	retro_tsyr_1494, retro_tsyr_70, retro_tsyr_875,