RetrogeneDB ID: retro_dnov_672

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_7501:500530..501215(-)
• Located in intron of: ENSDNOG00000016579

Retrocopy information

• Ensembl ID: ENSDNOG00000006036
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PSMD6
• Ensembl ID: ENSDNOG00000005852
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 [Source:HGNC Symbol;Acc:9564]

Sequence

>retro_dnov_672
ATGCCGCTGGAGAACTTGGAGGAAGAGGGTCTGCCCAAGAACCCCGACCTTCGCATCGCTCAGCTGCGCTTCCTGCTCAG
CCTGCCGGAGCACCGTGGGGACACGGCCGTGTGCGACGAGCTGATGGCGGCAGTCCGCGATAACAATATGGCCCCTTACT
ATGAAGCCTTGTGCAAATCTCTTGACTGGCAGATGGACATGGACCTCCTCAATAAAATGAAGAATGGCAAATGAAGAAGA
GTTGAAACGTTTGGATGAAGAGCTGGAAGATGCAGAGAAGAATCTGGGAGAGAGCGAAATCCGTGATGCAATGATGACAA
AGGCCGAGTACCTCTGTCGGATAGGTGACAAGGAGGGAGCCCTGACAGCTTTTCGCAAGACATACGACAAAACCGTGGCC
TTGGGTCACCGACTGGATATTGTGTTCTATCTCCTCAGGATTGGTTTATTTTATATGGATAATGATCTTATCACACGAAA
TACAGAAAAGGCCAAAAGTTTAATAGAGGAAGGAGGAGACTGGGACAGGAGAAACCGCTTAAAAGTGTATCAAGGTCTTT
ATTGTGTGGCTATTCGTGATTTCAAACAGGCTGCTGAACTCTTTCTTGACACTGTTTCCACATTTACATCCTATGAACTC
ATGGATTATAAAACCTTTGTGACTTATACTGTCTATGTCAGCATG

Alignment

ORF - retro_dnov_672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.38 %
• Parental protein coverage: 58.4 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDTAVRDELMAAVRDNNMAPYYEALCKSLDWQMDMDLL
          MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDTAV.DELMAAVRDNNMAPYYEALCKSLDWQMDMDLL
Retrocopy MPLENLEEEGLPKNPDLRIAQLRFLLSLPEHRGDTAVCDELMAAVRDNNMAPYYEALCKSLDWQMDMDLL

Parental  NKMKK-ANEEELKRLDEELEDAEKNLGESEIRDAMMTKAEYLCRIGDKEGALTAFRKTYDKTVALGHRLD
          NKMK..ANEEELKRLDEELEDAEKNLGESEIRDAMMTKAEYLCRIGDKEGALTAFRKTYDKTVALGHRLD
Retrocopy NKMKN>ANEEELKRLDEELEDAEKNLGESEIRDAMMTKAEYLCRIGDKEGALTAFRKTYDKTVALGHRLD

Parental  IVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRLKVYQGLYCVAIRDFKQAAELFLDTVSTFT
          IVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRLKVYQGLYCVAIRDFKQAAELFLDTVSTFT
Retrocopy IVFYLLRIGLFYMDNDLITRNTEKAKSLIEEGGDWDRRNRLKVYQGLYCVAIRDFKQAAELFLDTVSTFT

Parental  SY--LDYKTFVTYTVYVSM
          SY...DYKTFVTYTVYVSM
Retrocopy SYELMDYKTFVTYTVYVSM

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	23.92 RPM	41.81 RPM
SRP012922_cerebellum	14.43 RPM	21.86 RPM
SRP012922_heart	17.17 RPM	29.93 RPM
SRP012922_kidney	20.26 RPM	33.68 RPM
SRP012922_liver	11.61 RPM	20.74 RPM
SRP012922_lung	14.36 RPM	33.45 RPM
SRP012922_quadricep_muscle	20.94 RPM	34.62 RPM
SRP012922_spleen	16.83 RPM	29.76 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_672 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005852	1 retrocopy	retro_dnov_672 ,
Tupaia belangeri	ENSTBEG00000008485	2 retrocopies	retro_tbel_1619, retro_tbel_4345,