RetrogeneDB ID: retro_dnov_880

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_117658:3242..3530(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000756
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VIMP
• Ensembl ID: ENSDNOG00000010694
• Aliases: None
• Description: VCP-interacting membrane protein [Source:HGNC Symbol;Acc:30396]

Sequence

>retro_dnov_880
GAGTCCCTGTCCCTACAGCTGGCCCTTAAGACCGAGGGGCTGCTCTTCCTGCATGTCACCCTGGGCTCGCTGCTGGCCAC
TTATGGCTGGTACATCATCTTTAGCTGTATCCCCCTCTACATGGCCTTTCAGAAGCTTTTTGCCCAGCTGAGGGCCTTGA
GGCAGAGGCAGCTGGACCGAGCAGCGGCTGTGGAACCTGATATTGTTGTTAAACAAGTAGCAGCTGCTTGTTTGAAAATG
CAAGAAGAGTTAAATGCACAAGCAGAAAAGCATAAGGAAAAAGCTAAA

Alignment

ORF - retro_dnov_880 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.0 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELLSTRPAFETEGLRFLHVTVGSLLATYGWYIVFSCVLLYVVFQKLSTRLRALRQRQLDRAAAAVEPDIV
          E.LS...A..TEGL.FLHVT.GSLLATYGWYI.FSC..LY..FQKL...LRALRQRQLDRAAA.VEPDIV
Retrocopy ESLSLQLALKTEGLLFLHVTLGSLLATYGWYIIFSCIPLYMAFQKLFAQLRALRQRQLDRAAA-VEPDIV

Parental  VKRQEAVAAARLKMQEELNAQAEKHKEKLK
          VK....VAAA.LKMQEELNAQAEKHKEK.K
Retrocopy VKQ---VAAACLKMQEELNAQAEKHKEKAK

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	35.98 RPM
SRP012922_cerebellum	0.00 RPM	19.25 RPM
SRP012922_heart	0.00 RPM	22.04 RPM
SRP012922_kidney	0.00 RPM	16.15 RPM
SRP012922_liver	0.00 RPM	22.14 RPM
SRP012922_lung	0.00 RPM	32.38 RPM
SRP012922_quadricep_muscle	0.00 RPM	17.48 RPM
SRP012922_spleen	0.00 RPM	35.25 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_880 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007115	1 retrocopy	retro_amel_177,
Bos taurus	ENSBTAG00000000640	1 retrocopy	retro_btau_1044,
Dasypus novemcinctus	ENSDNOG00000010694	2 retrocopies	retro_dnov_207, retro_dnov_880 ,
Echinops telfairi	ENSETEG00000011401	1 retrocopy	retro_etel_2096,
Felis catus	ENSFCAG00000028822	1 retrocopy	retro_fcat_1524,
Pteropus vampyrus	ENSPVAG00000012873	1 retrocopy	retro_pvam_1334,