RetrogeneDB ID: retro_dnov_1019

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_13579:4166..4856(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCNM1
• Ensembl ID: ENSDNOG00000004323
• Aliases: None
• Description: sodium channel modifier 1 [Source:HGNC Symbol;Acc:23136]

Sequence

>retro_dnov_1019
ATGTCTTTCAAGAGGGAAGGGGACGATGGGAGTTAACTCAGTGTGCTCAAAACACAAAAAGTCGGTGACTTTTTGGCCAG
TAATATTCCAGAGAATGAGGCACTGATGCTGCGGGATGGACGCTTTGCTTGTGTCATCTGCCCACACCAGCCTGTACTGG
ACACCCTGGCCATGATGACTGACCACTGTGCAGGCAAGAAACGTCGGATCAGCTTGCAGCTGTTCTATGGGCCAAAAGCA
GCCAGATAGGGGAATGGAGCAGAATCCAAAATAGGAGAATGAATTGAGGAGGGAGGAGACCAAATCTGAGGCTCCTCTGC
TGGCCCAACCTCGGTTTACCACCCAGGGTGCTCTGCACAGAGCCCCCCACTTGAACAGTTGCTGCCGCCGCAAGTACAGA
CCAGAAGCCCCAGGTCCTTCTGTCTCCCGTTCCCCTTTGCCACCCCCAGAAGTTGAATTCCACAGCAGGAAGATCAGCAG
GGAACCTGAGCCCGGGACTAACCCACAGGCCAAGGAGTCAGCAACTGCCTCGGCGCCTCCACCCATGAGCCCACAGGAAG
ATAAGCCCTGGATCATTACCTCACCGTTCAAAGCTCTGGATGGATCCCATATGGACGAGGTCGATAGGTGAAAGATGGCA
ACGTTGAGTTTGACTCTGATCAGAAAGAACCCCCTGGTCTCCCTTTGGAC

Alignment

ORF - retro_dnov_1019 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.29 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSFKREGDDWSQLNVLKKRRVGDLLASYIPEDEALMLRDGRXXXXXXPHRPVL-TLAMLTAHRAGKKHLS
          MSFKREGDD.S.L.VLK...VGD.LAS.IPE.EALMLRDGR......PH.PVL.TLAM.T.H.AGKK...
Retrocopy MSFKREGDDGS*LSVLKTQKVGDFLASNIPENEALMLRDGRFACVICPHQPVLDTLAMMTDHCAGKKRRI

Parental  SLQLFYG-KKQTGRGMEQNPKQQSELR-EETKSEAPLLAQTRFITQSALHRAPHYNSCCRRKYRPEAPGP
          SLQLFYG..KQ..RGMEQNPK...ELR.EETKSEAPLLAQ.RF.TQ.ALHRAPH.NSCCRRKYRPEAPGP
Retrocopy SLQLFYG>QKQPDRGMEQNPK*ENELRREETKSEAPLLAQPRFTTQGALHRAPHLNSCCRRKYRPEAPGP

Parental  SVPHSALPPPEVECHSGKTSREPEPGAGPQANESATASAPPPMS-PTRRRALDHYLTLRSSGWIPDGRGR
          SV..S.LPPPEVE.HS.K.SREPEPG..PQA.ESATASAPPPMS.PT.R.ALDHYLT..SSGWIP.GRGR
Retrocopy SVSRSPLPPPEVEFHSRKISREPEPGTNPQAKESATASAPPPMS<PTGR*ALDHYLTVQSSGWIPYGRGR

Parental  WVKDENVEFDSDEEEPPDLPLD
          .VKD.NVEFDSD..EPP.LPLD
Retrocopy *VKDGNVEFDSDQKEPPGLPLD

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	12.83 RPM
SRP012922_cerebellum	0.00 RPM	26.81 RPM
SRP012922_heart	0.00 RPM	8.12 RPM
SRP012922_kidney	0.00 RPM	27.11 RPM
SRP012922_liver	0.00 RPM	5.11 RPM
SRP012922_lung	0.00 RPM	31.77 RPM
SRP012922_quadricep_muscle	0.00 RPM	12.12 RPM
SRP012922_spleen	0.00 RPM	21.40 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_1019 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004323	1 retrocopy	retro_dnov_1019 ,
Oryctolagus cuniculus	ENSOCUG00000026766	1 retrocopy	retro_ocun_925,
Rattus norvegicus	ENSRNOG00000021092	1 retrocopy	retro_rnor_2550,