RetrogeneDB ID: retro_dnov_2144

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_5099:44637..45561(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOP56
• Ensembl ID: ENSDNOG00000013699
• Aliases: None
• Description: NOP56 ribonucleoprotein [Source:HGNC Symbol;Acc:15911]

Sequence

>retro_dnov_2144
GTAGAGAAGTATGTGCTCAACCTGGGCAAGTTCCACAGCATTGCTCATCTCAGTGGCCTTTTGCCACTGGTCCTAGTCCC
AGCTGCCTTAGAAAATGCCAATGCTATGTCTGAAGCCATTGTTCATGAGGACCTCCACCTTCCCTTTGAGACCCACCTGC
CATCCAAAAAGAAGAAAGTCCTCTTAGGGGTTGGGCATCCCAAGATTGGTGCTGCTGTACAAGAGGAGTTAGGATACAAC
TGCCAGATTGGAAGTATGATAGCTGAGATCCTACGAGGAGTTCATCTCTACTTCCATAATCTGGTGAAGGGTCTCACCCA
TCTGCCAGCTTATAAAGCCCAGCTGGGCCTGGGACATAGCTATTCTCCTGCCAAAGTTAAGTTTTCTGTGAATGGGGTGG
ATAATAGGATTATCCAGTCCATAAGCCTCCAGGACCAGCTGGATAAAGACATCAAAATATTTTCTGTATATGTCAGGGAG
TGGTATGGTGACCACTTTCTGGAGCTAGTGAAGGTCAAGAACAAAACCACATACTGTTGCCTCACTCACTTCATTGGAAA
ACAAAGGGAGCTGAACAAAGACAAGTTGGAGAAGCCAGAGGAGTTGAAGATGGATGGAGCCAAGATCAAGGCTCTTCTGG
ATGCCTCATGGTCCTCCATGGACATGGACATGTTTACCATCAACTTGATAAACATTGAGAGTTTCTCTAGCCATGTGGTG
TGTTTGTCAGAATTCCACCAGAGCCTACACACTTACCTGCAATCCAAGATGAGCCAAGCAGTCTCCAGACTGTCAGCTCT
AACTGAGGAAGCACTAGGTGCCCATCTCATTGCTCACCCTGGCAGCCTCGCCAACCTGGCCAAGTACCTAGCGTCCACAG
TCCAGATCCTTGGGGTTGAAAAGGCCCTGTTCAGAGCCTTGGAG

Alignment

ORF - retro_dnov_2144 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.24 %
• Parental protein coverage: 54.59 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VEECVLNLGKFHSIVRL-VAFCPFSSSQ-AALENANAVSEGVVHEDLRLLLETHLPSKKKKVLLGVGDPK
          VE..VLNLGKFHSI..L.VAFC..S.SQ.AALENANA.SE..VHEDL.L..ETHLPSKKKKVLLGVG.PK
Retrocopy VEKYVLNLGKFHSIAHL>VAFCHWS*SQ<AALENANAMSEAIVHEDLHLPFETHLPSKKKKVLLGVGHPK

Parental  IGAAIQEELGYNCQTGGVIAEILRGVRLHFHNLVKGLTDLSACKAQLGLGHSYSRAKVKFNVNRVDNMII
          IGAA.QEELGYNCQ.G..IAEILRGV.L.FHNLVKGLT.L.A.KAQLGLGHSYS.AKVKF.VN.VDN.II
Retrocopy IGAAVQEELGYNCQIGSMIAEILRGVHLYFHNLVKGLTHLPAYKAQLGLGHSYSPAKVKFSVNGVDNRII

Parental  QSISLLDQLDKDINTFSMRVREWYGYHFPELVKVVSDNATYCRLAQFIGNRRELNEEKLEKLEELTMDGA
          QSISL.DQLDKDI..FS..VREWYG.HF.ELVK.V....TYC.L..FIG..RELN..KLEK.EEL.MDGA
Retrocopy QSISLQDQLDKDIKIFSVYVREWYGDHFLELVK-VKNKTTYCCLTHFIGKQRELNKDKLEKPEELKMDGA

Parental  KAKAILDASRSSMGMDISAIDLINIETFSSRVVSLSEYRQSLHTYLRSKMSQVAPSLSALIGEAVGARLI
          K.KA.LDAS.SSM.MD...I.LINIE.FSS.VV.LSE..QSLHTYL.SKMSQ....LSAL..EA.GA.LI
Retrocopy KIKALLDASWSSMDMDMFTINLINIESFSSHVVCLSEFHQSLHTYLQSKMSQAVSRLSALTEEALGAHLI

Parental  AHAGSLTNLAKYPASTVQILGAEKALFRALK
          AH.GSL.NLAKY.ASTVQILG.EKALFRAL.
Retrocopy AHPGSLANLAKYLASTVQILGVEKALFRALE

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	64.56 RPM
SRP012922_cerebellum	0.00 RPM	73.41 RPM
SRP012922_heart	0.00 RPM	19.72 RPM
SRP012922_kidney	0.00 RPM	59.96 RPM
SRP012922_liver	0.00 RPM	37.93 RPM
SRP012922_lung	0.00 RPM	51.77 RPM
SRP012922_quadricep_muscle	0.00 RPM	30.64 RPM
SRP012922_spleen	0.00 RPM	74.06 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_2144 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013699	1 retrocopy	retro_dnov_2144 ,