RetrogeneDB ID: retro_dnov_1981

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_40214:30957..31336(+)
• Located in intron of: None

Retrocopy information

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

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_1981
CTTTTCAAGCTGCTCCTGATCCGGGACTCGGGAGTGGGGAAGGCCTGCGTCCTTTCTCGTTTTTCGGGTGATGCCTTCAA
TACCACCTTTTATTTCCACCAGAGGAATAGACGTTAAGATCAAAACAATTGAATTACAAGGGAAGAAGATCAAGCTACAG
ATACGGGATACAGCAGGCCAGGAGCGATTCCACACCATCACGACCTCCTACTACAGAGGAGCTATGGGTATCATGCTAGT
ACATGACACCACCAATGGTAAAAGTTTTGAAAACATCAGCAAATGGCTTAGAAACATAGATGAGCATGCTAACGAAGATG
TGCAAAGAATGTTACTAGGAAACAAGTGTGATATGGACCATAAAAGAGTTGTGCCTAGA

Alignment

ORF - retro_dnov_1981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 63. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LFKLLLISDSRVSKTCLLFRFSEDAFNTTF-ISTIGIDFKIRTIELDGKKIKLQIWDTAGQERFRTITTA
          LFKLLLI.DS.V.K.C.L.RFS.DAFNTTF.IST.GID.KI.TIEL.GKKIKLQI.DTAGQERF.TITT.
Retrocopy LFKLLLIRDSGVGKACVLSRFSGDAFNTTF>ISTRGIDVKIKTIELQGKKIKLQIRDTAGQERFHTITTS

Parental  YYRGAMGIMLVYDITNEKSFDNIKNWIRNIEEHASSDVERMILGNKCDMNDKRQVSK
          YYRGAMGIMLV.D.TN.KSF.NI..W.RNI.EHA..DV.RM.LGNKCDM..KR.V..
Retrocopy YYRGAMGIMLVHDTTNGKSFENISKWLRNIDEHANEDVQRMLLGNKCDMDHKRVVPR

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	5.06 RPM	3.89 RPM
SRP012922_cerebellum	2.34 RPM	2.34 RPM
SRP012922_heart	2.78 RPM	1.16 RPM
SRP012922_kidney	1.64 RPM	1.10 RPM
SRP012922_liver	1.55 RPM	0.31 RPM
SRP012922_lung	1.68 RPM	3.21 RPM
SRP012922_quadricep_muscle	4.15 RPM	0.87 RPM
SRP012922_spleen	4.46 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_1981 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,