RetrogeneDB ID: retro_dnov_2035

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_43513:6641..6857(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SVIP
• Ensembl ID: ENSDNOG00000016735
• Aliases: None
• Description: small VCP/p97-interacting protein [Source:HGNC Symbol;Acc:25238]

Sequence

>retro_dnov_2035
ATGGGGCTGTGTTTTCCTTGCCCTGGGGAGGCTGAGCCTCCCTTGCCAGACCTGAAAGAGAAAAGAGCAAAACTTGCAGA
AGCTGCAGAGAGAAGACAGAGGGAGGCTGCATCTCAGGGCATTTTGGATGTTCAATCTGTAGAAGAAAAGAGAAAGAAAA
AGGAAAGATTAGAAAAACAAATCACTACAACTGGACCCCCACCAGAAGGTGGACTT

Alignment

ORF - retro_dnov_2035 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75. %
• Parental protein coverage: 94.74 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLCFPCPGEAEPPSPDPEEKRAKLAEAAERRQREAASRGILNVQSVEEKRKKKERLEKQITTTGPPPEG
          MGLCFPCPGEAEPP.PD..EKRAKLAEAAERRQREAAS.GIL.VQS.............QITTTGPPPEG
Retrocopy MGLCFPCPGEAEPPLPDLKEKRAKLAEAAERRQREAASQGILDVQSXXXXXXXXXXXXXQITTTGPPPEG

Parental  GL
          GL
Retrocopy GL

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	2.53 RPM
SRP012922_cerebellum	0.41 RPM	9.62 RPM
SRP012922_heart	0.46 RPM	6.03 RPM
SRP012922_kidney	1.64 RPM	5.75 RPM
SRP012922_liver	0.00 RPM	2.63 RPM
SRP012922_lung	0.46 RPM	7.64 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.87 RPM
SRP012922_spleen	0.57 RPM	7.10 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_2035 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013152	4 retrocopies	retro_chof_1571, retro_chof_2005, retro_chof_2442, retro_chof_668,
Dasypus novemcinctus	ENSDNOG00000016735	4 retrocopies	retro_dnov_2035 , retro_dnov_2072, retro_dnov_928, retro_dnov_945,
Sus scrofa	ENSSSCG00000022838	1 retrocopy	retro_sscr_446,