RetrogeneDB ID: retro_dnov_928

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_122688:4670..4889(-)
• 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_928
ATGGGGCTGTGTTTTCCTTGCCCCGGGGAGGCTGAGCCTCCCTCAGCGGACCCAGAAGAGAAAAGAACAAAACTTGCAGA
AGCTACTGAGAGAAGACAGAGGTAGGCTGCATCTCGGGGCATTTTGGATGTTCAATCTGTGGAAGAAAAGAGGAAGAAAA
AGGAAAGATTAGAAAAACAAATCACTACAACTGGACCCCCACCAGAAGGTGGACTTAGA

Alignment

ORF - retro_dnov_928 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.97 %
• Parental protein coverage: 96.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGLCFPCPGEAEPPSPDPEEKRAKLAEAAERRQREAASRGILNVQSVEEKRKKKERLEKQITTTGPPPEG
          MGLCFPCPGEAEPPS.DPEEKR.KLAEA.ERRQR.AASRGIL.VQSV..............TTTGPPPEG
Retrocopy MGLCFPCPGEAEPPSADPEEKRTKLAEATERRQR*AASRGILDVQSVXXXXXXXXXXXXXXTTTGPPPEG

Parental  GLR
          GLR
Retrocopy GLR

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	0.14 RPM	9.62 RPM
SRP012922_heart	0.00 RPM	6.03 RPM
SRP012922_kidney	0.00 RPM	5.75 RPM
SRP012922_liver	0.00 RPM	2.63 RPM
SRP012922_lung	0.00 RPM	7.64 RPM
SRP012922_quadricep_muscle	0.17 RPM	9.87 RPM
SRP012922_spleen	0.00 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_928 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,