RetrogeneDB ID: retro_dnov_266

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3144:150351..151035(+)
• Located in intron of: ENSDNOG00000006446

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIAS
• Ensembl ID: ENSDNOG00000007417
• Aliases: None
• Description: lipoic acid synthetase [Source:HGNC Symbol;Acc:16429]

Sequence

>retro_dnov_266
GTATTTGGAAGATATTTATGCAGCCTGGTCAGAGTACTGAGCTCCTTGCCAGACGAAAAAAAGGAATTTTTACAGAATGG
ATCAGACTTTCAAGATTTTGTATCTGGTGATCTTGCAGACAAGGGTACCTGAGCTGAATATAAAGGAAACTTAAAATGCC
AGAAAGGAGAATGGTTAAGACTACCTTCATGGTTAAACACAGAGATTCCCATGGTGAAAAATTACAATAAATTGAAAAAT
ACATTGCAAATTAAATCTCCATACAGTGTGTGAGAAGCTAGATGTCCAAATATTGGGGAGTTTTGGGGAGGTGAGAATAT
GCCACAGTCATAGCCACAATCATGTTGATGGGTGATACATGTACAAGAGGTTGTAGATTTTGTTCTGTGAAAACTGCAAG
AAATCCACCTCTACTGGATATCAATGAGCCCCTTCAATACTGCAAAGGCGACTGCAGAGTGGGGTCTGGATTATGTTGCC
TGACATCTGTGGATTGAGATGATATGCCTGATGGGGGGAGCTGAGCACTTTGCAAAGACGGTTATGCTTAAAGGAAAGGA
ATCCAAAAATTCTTATGGAATCCCTCACCCCTGATTTCTGAGGAGACCTTAAAGCAATAGAGAAAGTTGCTCTGTCAGAT
TAGATGTGCACACACATAATGTGCAAACAGTTTAAGAATTAAAG

Alignment

ORF - retro_dnov_266 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 64.43 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  IFGRCLCSPIRTLSSLPEERKEFLRNGPDLQDFVSGDLADKNTWVEYKGNLKRQKGERLRLPPWLKTEIP
          .FGR.LCS..R.LSSLP.E.KEFL.NG.D.QDFVSGDLADK.T..EYKGNLK.QKGE.LRLP.WL.TEIP
Retrocopy VFGRYLCSLVRVLSSLPDEKKEFLQNGSDFQDFVSGDLADKGT*AEYKGNLKCQKGEWLRLPSWLNTEIP

Parental  MGKNYNKLKNILRNLNLHTVCEEARCPNIGECWGGG-EYATATATIMLMGDTCTRGCRFCSVKTARNPPP
          M.KNYNKLKN.L.......V..EARCPNIGE.WGG..EYAT..ATIMLMGDTCTRGCRFCSVKTARNPP.
Retrocopy MVKNYNKLKNTLQIKSPYSV-*EARCPNIGEFWGGE<EYATVIATIMLMGDTCTRGCRFCSVKTARNPPL

Parental  LDANE-PYNTAKAIAEWGLDYVV-LTSVDRDDMPD-GGAEHFAKTVSCLK-ERNPKILVECLTPDFRGDL
          LD.NE.P.NTAKA.AEWGLDYV..LTSVD.DDMPD.GGAEHFAKTV..LK.ERNPKIL.E.LTPDF.GDL
Retrocopy LDINE>PFNTAKATAEWGLDYVA<LTSVD*DDMPD>GGAEHFAKTV-MLK>ERNPKILMESLTPDF*GDL

Parental  KAIEKVALSG-LDVYAHNVETVPELQ
          KAIEKVALS..LDV..HNV.TV.EL.
Retrocopy KAIEKVALSD<LDVHTHNVQTV*ELK

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	12.45 RPM
SRP012922_cerebellum	0.00 RPM	8.80 RPM
SRP012922_heart	0.00 RPM	16.01 RPM
SRP012922_kidney	0.00 RPM	16.43 RPM
SRP012922_liver	0.00 RPM	13.78 RPM
SRP012922_lung	0.00 RPM	6.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.17 RPM
SRP012922_spleen	0.11 RPM	9.27 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_266 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012946	2 retrocopies	retro_chof_1942, retro_chof_2555,
Dasypus novemcinctus	ENSDNOG00000007417	1 retrocopy	retro_dnov_266 ,
Myotis lucifugus	ENSMLUG00000004602	2 retrocopies	retro_mluc_1985, retro_mluc_347,
Mus musculus	ENSMUSG00000029199	1 retrocopy	retro_mmus_3029,
Tursiops truncatus	ENSTTRG00000014293	1 retrocopy	retro_ttru_1371,