RetrogeneDB ID: retro_dnov_668

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_7447:453030..453505(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MXI1
• Ensembl ID: ENSDNOG00000002479
• Aliases: None
• Description: MAX interactor 1, dimerization protein [Source:HGNC Symbol;Acc:7534]

Sequence

>retro_dnov_668
GCTACACATGATGAGCTGGAAAAGAATTGACGTGCTCACCTGCGCCGGTGTTTAAAAACGCTTAAAGGTACTGATTCCAC
TAGGACCAGACTGCATCAGACATAGAACACTCGGATTGTGCAACAAAGCCAAAGCATACATGAAGAAACTTTAAAGAAGC
TAAAAGGAAGAGCCAGCACTAGCTTAAGAACTTGGAAGGAGAACAAAGATTTTTAAAGCGGCGATTGGAACAGCAGCAGG
TTCCTCCGAAAATGGAACGAATACAAATGGACAGCACTTATCAACTATTTTGTCAGATCGATCTGATTCAGAGCAAGAGG
AAATTGAAGCTGATGTTGAAAGCACAGAATTCTCCCGTGGAGAAGTAGACAATACCAGTTCCAGCAGCATCAGTGTTGTT
CATAACCACAGCAGCCTCTGGAGCATTGAAAGTGATGATTATTCCAGGGCCAGTGTCGCACTTTCCTTCCCTTCC

Alignment

ORF - retro_dnov_668 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.46 %
• Parental protein coverage: 53.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  STHNELEKNRRAHLRLCLE-RLKVLIPLGPDCTRHTTLGLLNKAKAHIKKL-EEAERKSQHQLENLEREQ
          .TH.ELEKN.RAHLR.CL..RLKVLIPLGPDC.RH.TLGL.NKAKA..KKL..EA.RKSQH.L.NLE.EQ
Retrocopy ATHDELEKN*RAHLRRCLK>RLKVLIPLGPDCIRHRTLGLCNKAKAYMKKL>KEAKRKSQH*LKNLEGEQ

Parental  RFLKRRLEQLQGPQEMERIRMDSIG-STISSDRSDSEREEIEVDVESTEFSHGEVDNISTTSISDIDDHS
          RFLKRRLEQ.Q.P..MERI.MDS...STI.SDRSDSE.EEIE.DVESTEFS.GEVDN.S..SIS....HS
Retrocopy RFLKRRLEQQQVPPKMERIQMDSTY<STILSDRSDSEQEEIEADVESTEFSRGEVDNTSSSSISVVHNHS

Parental  SLQSIGSDEGYSSASVKLSFTS
          SL.SI.SD..YS.ASV.LSF.S
Retrocopy SLWSIESDD-YSRASVALSFPS

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	17.70 RPM
SRP012922_cerebellum	0.00 RPM	28.04 RPM
SRP012922_heart	0.00 RPM	9.05 RPM
SRP012922_kidney	0.00 RPM	13.96 RPM
SRP012922_liver	0.00 RPM	8.98 RPM
SRP012922_lung	0.31 RPM	18.17 RPM
SRP012922_quadricep_muscle	0.00 RPM	23.02 RPM
SRP012922_spleen	0.00 RPM	37.09 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_668 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 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006556	2 retrocopies	retro_chof_1350, retro_chof_1817,
Cavia porcellus	ENSCPOG00000022901	1 retrocopy	retro_cpor_574,
Dasypus novemcinctus	ENSDNOG00000002479	2 retrocopies	retro_dnov_1336, retro_dnov_668 ,
Mus musculus	ENSMUSG00000025025	1 retrocopy	retro_mmus_1948,
Sus scrofa	ENSSSCG00000022128	1 retrocopy	retro_sscr_947,
Vicugna pacos	ENSVPAG00000003400	2 retrocopies	retro_vpac_483, retro_vpac_595,