RetrogeneDB ID: retro_dnov_23

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_208303:1423..1801(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000115
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RAB8B
• Ensembl ID: ENSDNOG00000023965
• Aliases: None
• Description: RAB8B, member RAS oncogene family [Source:HGNC Symbol;Acc:30273]

Sequence

>retro_dnov_23
GGAATTATGCTGGTCTATGACATCACAAATGAAAAATCCTTTGACAATATTAAAAATTGGATAAGAAACATTGAAGAGCA
TGCCTCTTCAGATGTTGAAAGAATGATCCTGGGTAACAAATGTGATATGAATGACAAAAGACAAGTATCAAAAGAAAGAG
GGGAGAAGTTAGCAATTGACTACGGGATTAAATTCTTGGAGACAAGTGCAAAATCCAGTACAAATGTAGAAGAGGCATTT
TTTACACTTGCACGAGATATAATGACAAAACTCAACCGAAAAATGAATGACAGCAATTCATCAGGAGCAGGTGGACCAGT
GAAAATAACAGAAAATCGATCAAAGAAGACCAGTTTCTTCCGTTGTTCACTACTCTGA

Alignment

ORF - retro_dnov_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 62.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GIMLVYDITNEKSFDNIKNWIRNIEEHASSDVERMILGNKCDMNDKRQVSKERGEKLAIDYGIKFLETSA
          GIMLVYDITNEKSFDNIKNWIRNIEEHASSDVERMILGNKCDMNDKRQVSKERGEKLAIDYGIKFLETSA
Retrocopy GIMLVYDITNEKSFDNIKNWIRNIEEHASSDVERMILGNKCDMNDKRQVSKERGEKLAIDYGIKFLETSA

Parental  KSSTNVEEAFFTLARDIMTKLNRKMNDSNSSGAGGPVKITENRSKKTSFFRCSLL
          KSSTNVEEAFFTLARDIMTKLNRKMNDSNSSGAGGPVKITENRSKKTSFFRCSLL
Retrocopy KSSTNVEEAFFTLARDIMTKLNRKMNDSNSSGAGGPVKITENRSKKTSFFRCSLL

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	0.78 RPM	3.89 RPM
SRP012922_cerebellum	0.27 RPM	2.34 RPM
SRP012922_heart	0.23 RPM	1.16 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.15 RPM	0.31 RPM
SRP012922_lung	0.76 RPM	3.21 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 RPM
SRP012922_spleen	2.75 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_23 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007196	3 retrocopies	retro_chof_1996, retro_chof_475, retro_chof_669,
Dasypus novemcinctus	ENSDNOG00000023965	3 retrocopies	retro_dnov_1191, retro_dnov_1981, retro_dnov_23 ,
Dasypus novemcinctus	ENSDNOG00000025047	1 retrocopy	retro_dnov_1758,
Microcebus murinus	ENSMICG00000007113	1 retrocopy	retro_mmur_503,
Sorex araneus	ENSSARG00000005217	2 retrocopies	retro_sara_366, retro_sara_725,