RetrogeneDB ID: retro_dnov_2308

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_62730:6276..6769(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RND3
• Ensembl ID: ENSDNOG00000004736
• Aliases: None
• Description: Rho family GTPase 3 [Source:HGNC Symbol;Acc:671]

Sequence

>retro_dnov_2308
TCTCCTTACTATGACAATGTCCGGCCCCTTTCTTACCCAGATTCTGATGCTGTGCTGATTTGCTTTGACATCAATAGACC
AGAGACTCTGGACAGTGTCCTTAAAAAGTGAAAAGATGAAATTCAGGAGTTTTGTCCCAACACCAAAATGCTCTTGGTCG
GCTGCAAGTCTGATCTTCGGACAGATGTTAGTACTTTAGTAGAGCCTCTCAAATCACAGGCAGACACCAGTGTCCTATGA
CCAGGGGGAAAATATGGCCAAACAGGTTGGAGCAGCTACTTATATTGAATGCTTAGCTTTACAGTCAGAAAATAGCGTCA
GAGACATTTCTCACGCTGCCACCTTAGCCTGTGTGAACAAGACAAATTAAAACGTTAAGCGGAACAAATCGCAGAGGGCC
ACAAAGCGGATTTCACACATCCCTAGCAGACCAGAACTCTCAACAGTTGCTACGGACTTACGAAAAGACAAAGCGAAGAG
CTGCACTGTGATG

Alignment

ORF - retro_dnov_2308 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPYYDNVRPLSYPDSDAVLICFDISRPETLDSVLKKWKGEIQEFCPNTKMLLVGCKSDLRTDVSTLVE-L
          SPYYDNVRPLSYPDSDAVLICFDI.RPETLDSVLKK.K.EIQEFCPNTKMLLVGCKSDLRTDVSTLVE.L
Retrocopy SPYYDNVRPLSYPDSDAVLICFDINRPETLDSVLKK*KDEIQEFCPNTKMLLVGCKSDLRTDVSTLVE>L

Parental  SNHRQTPVSYDQGANMAKQIGAATYIECSALQSENSVRDIFHVATLACVNKTNKNVKRNKSQRATKRISH
          SNHRQTPVSYDQG.NMAKQ.GAATYIEC.ALQSENSVRDI.H.ATLACVNKTN.NVKRNKSQRATKRISH
Retrocopy SNHRQTPVSYDQGENMAKQVGAATYIECLALQSENSVRDISHAATLACVNKTN*NVKRNKSQRATKRISH

Parental  MPSRPELSTVATDLRKDKAKSCTVM
          .PSRPELSTVATDLRKDKAKSCTVM
Retrocopy IPSRPELSTVATDLRKDKAKSCTVM

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	4.86 RPM	20.61 RPM
SRP012922_cerebellum	0.41 RPM	1.24 RPM
SRP012922_heart	3.71 RPM	17.63 RPM
SRP012922_kidney	0.82 RPM	5.75 RPM
SRP012922_liver	2.17 RPM	20.74 RPM
SRP012922_lung	3.51 RPM	14.05 RPM
SRP012922_quadricep_muscle	1.90 RPM	3.29 RPM
SRP012922_spleen	0.80 RPM	4.81 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_2308 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004736	1 retrocopy	retro_dnov_2308 ,
Dasypus novemcinctus	ENSDNOG00000012825	6 retrocopies	retro_dnov_1012, retro_dnov_1814, retro_dnov_1904, retro_dnov_2090, retro_dnov_29, retro_dnov_326,
Echinops telfairi	ENSETEG00000004538	1 retrocopy	retro_etel_353,