RetrogeneDB ID: retro_dnov_258

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3080:124848..125559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SETD8
• Ensembl ID: ENSDNOG00000010371
• Aliases: None
• Description: SET domain containing (lysine methyltransferase) 8 [Source:HGNC Symbol;Acc:29489]

Sequence

>retro_dnov_258
CTGCAGGAAGAGACCTCAGTCCCACATCAGGAAGTCAAATGCCAGGGAAACCAGTAGCTGGAATTTACAGGGGGGTGGAA
GAGAACAGAAACTCTGGCAATGCAACACGGAGCAACATGAAGTCCCGAGAGCAGATCAGGGACGCCAGGAGAGGTCTCCT
GGCACCTTTTCCAAACCCAAAATCTGAAGCAGCAGAACCTCCAAAACTCCCACCGCGTCTTGGGATCCCACCAACGCAGC
TGTCACCAAGCAAACTGAAAAAGCCTGTCCAGGGCAAACAAGCCCCTCCAAATAAGCTCGCAGGGATACTCAACAAGGCA
AACTCCCTGTCCAGCAGAGCTCCAGGAAGAGCGAGGCTGAGCTGCAGGCTGAAGAAGGGACGAGAATAGACGAGTTGGTG
GGAAGTGGGAAGGAGGCAGGAATGAGGATTGGTCTCATCGGTGGCGAGGGCAGGGGAGTTATTGACAACCAAGCTGCTCT
CCAGGGCGAGTTTGTGGTGAAATACCACGGGGACCTCATCGAGATCACTGACGCCAAGAAGTGGGGGGCACTGTGTGCAC
AAGACCCCCCCAGAAGCTGCTACATGGACTATTTTCAGCATCTTGAACAAAACTACTGTGCAGATGAAGCTAGAGAGACG
AATCACCTGGGAAGACTGGTCAACCCAGCAAATGTGGGACCTGCCAGGCCCAGCTGCGCGGCCCTGGAGGC

Alignment

ORF - retro_dnov_258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.29 %
• Parental protein coverage: 69.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LQEENSVAHHEVKCQG-KPIAGIYRRREEKRNTGNAARSTMKSEEQKLKDARRGPLAPFPNQKSEAAEPP
          LQEE.SV.H.EVKCQG.KP.AGIYR..EE.RN.GNA.RS.MKS.EQ...DARRG.LAPFPN.KSEAAEPP
Retrocopy LQEETSVPHQEVKCQG<KPVAGIYRGVEENRNSGNATRSNMKSREQ-IRDARRGLLAPFPNPKSEAAEPP

Parental  K-TPTSSCDSANTAVTKQTLKKPGKGKQAPRKKGQGKTQQNRKLTDFYPVRRSSRKSKAELQSEERKRID
          K.TPT.S.D..N.AVTKQT..K...G...P.K.....TQQ..KL......R.S.....AE....E..RID
Retrocopy K<TPTASWDPTNAAVTKQT-EKACPGQTSPSK*ARRDTQQG-KLPVQQSSRKSEAELQAE----EGTRID

Parental  ELIESGKEEGMKIDLIDGKGRGVIATKQFSRGEFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQY
          EL..SGKE.GM.I.LI.G.GRGVI.......GEFVV.YHGDLIEITDAKK..AL.AQDP...CYM.YFQ.
Retrocopy ELVGSGKEAGMRIGLIGGEGRGVIDNQAALQGEFVVKYHGDLIEITDAKKWGALCAQDPPRSCYMDYFQH

Parental  LSKTYCVDATRETNRLGRLIN-HSKCGNCQTKLHDIGG
          L...YC.D..RETN.LGRL.N..SKCG.CQ..L...GG
Retrocopy LEQNYCADEARETNHLGRLVN<PSKCGTCQAQLRGPGG

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	91.21 RPM
SRP012922_cerebellum	0.00 RPM	25.84 RPM
SRP012922_heart	0.00 RPM	20.88 RPM
SRP012922_kidney	0.00 RPM	24.64 RPM
SRP012922_liver	0.00 RPM	20.28 RPM
SRP012922_lung	0.00 RPM	74.53 RPM
SRP012922_quadricep_muscle	0.00 RPM	30.29 RPM
SRP012922_spleen	0.00 RPM	89.51 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_258 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010371	1 retrocopy	retro_dnov_258 ,
Rattus norvegicus	ENSRNOG00000001062	4 retrocopies	retro_rnor_1551, retro_rnor_2837, retro_rnor_38, retro_rnor_679,
Sarcophilus harrisii	ENSSHAG00000015376	2 retrocopies	retro_shar_110, retro_shar_115,