RetrogeneDB ID: retro_dnov_80

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1346:234437..234620(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP1R14C
• Ensembl ID: ENSDNOG00000017261
• Aliases: None
• Description: protein phosphatase 1, regulatory (inhibitor) subunit 14C [Source:HGNC Symbol;Acc:14952]

Sequence

>retro_dnov_80
TGCCAGGAAGAAGAGCTCCCAGAAGAGGAGATGGATGTGGATGAGCTCCTGGACATGGAGAGTGATGCTACGTGGGCTGC
CAGGGTAGAGGAGATGCTGGCTGACTGCTACAAACCCACTGAGGCCTTCTCTGGCCTACTGGACAAGATCCTGGGCATGC
AGAAGCTGAGCACACCCAGAAGA

Alignment

ORF - retro_dnov_80 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.23 %
• Parental protein coverage: 72.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CQEEEMPDVEIDIDDLLDADSEEERALKLQEALIDCYKPTEEFIKELLSRIRGMRKLSPPQK
          CQEEE.P..E.D.D.LLD..S....A....E.L.DCYKPTE.F...LL..I.GM.KLS.P..
Retrocopy CQEEELPEEEMDVDELLDMESDATWAARVEEMLADCYKPTEAF-SGLLDKILGMQKLSTPRR

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	0.19 RPM	2.14 RPM
SRP012922_cerebellum	0.14 RPM	1.51 RPM
SRP012922_heart	0.00 RPM	9.28 RPM
SRP012922_kidney	0.27 RPM	3.29 RPM
SRP012922_liver	0.15 RPM	0.00 RPM
SRP012922_lung	0.15 RPM	7.94 RPM
SRP012922_quadricep_muscle	0.00 RPM	24.23 RPM
SRP012922_spleen	0.46 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_80 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 6 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000026586	2 retrocopies	retro_btau_161, retro_btau_571,
Dasypus novemcinctus	ENSDNOG00000017261	2 retrocopies	retro_dnov_1661, retro_dnov_80 ,
Myotis lucifugus	ENSMLUG00000023245	2 retrocopies	retro_mluc_1095, retro_mluc_499,
Mus musculus	ENSMUSG00000040653	2 retrocopies	retro_mmus_2089, retro_mmus_3721,
Pongo abelii	ENSPPYG00000017102	4 retrocopies	retro_pabe_1880, retro_pabe_2079, retro_pabe_3001, retro_pabe_3232,
Tarsius syrichta	ENSTSYG00000002873	1 retrocopy	retro_tsyr_245,