RetrogeneDB ID: retro_dnov_1866

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_34255:10414..11017(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC25A39
• Ensembl ID: ENSDNOG00000008556
• Aliases: None
• Description: solute carrier family 25, member 39 [Source:HGNC Symbol;Acc:24279]

Sequence

>retro_dnov_1866
CTCTGGAGAAGCCTTCCGGTGGCCCTAGTGATGACTGTGCCGGCCACCGCCGCCTACTTCGCTGCATAACACCAACGCAG
CGCCTTCCTGTGCGGCCGAGCACTGACCTCTGATCTCTACGCACCCATGGTGGCTGGTGCGCTGGCCCGCCTGGGCGCGG
CGACTGTGATCAGCCCCTTGGAGCTGGTGCGGACAAGCTGCAGGCTTAGCATACATCGTACCGTGAGCTGGGCCCTGTGT
CCAGGCCATGGTGGCTCAGGGTAGCTGGCACTCCTTGTGACTGGGCTGGGACCCCACAGACCGGAGGGATGTGCCCTTTA
CAGCCCTGCATTGATTCAAGTATGAGCTGCTGAAGCGCTGGCTGAGTGGCTCAGGCCAAAGAACCAGTCATTCATAGGTA
TCAGCCTTTTGGCTGGTGGCATCTTAGGGACAGTGGCAGCCATCCTGACTCTGCTCTTCAATATAGTAAAGCCACATCAC
CAGGTGGCACTGGGAGTGGTAGAGACTGTGCTATTGATGCCCCCATGCGCCGACTCCACCTGGCTGCCACTGTGAAGGAT
CCAGGCTGAGTCGGGCACCCGGGGCCACTTTGCAGGCAAGCTG

Alignment

ORF - retro_dnov_1866 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.76 %
• Parental protein coverage: 58.09 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LWSGLPATLVMTVPATAAYFTVYDQLRAFLCSRALTSDLYAPMVAGALARLATVTVISPLELVRT-KLQA
          LW..LP..LVMTVPATAAYF....Q..AFLC.RALTSDLYAPMVAGALARL...TVISPLELVRT.KLQA
Retrocopy LWRSLPVALVMTVPATAAYFAA*HQRSAFLCGRALTSDLYAPMVAGALARLGAATVISPLELVRT<KLQA

Parental  QHLSYREL-GTCVRAAVTQ-SDRSLWLGWGPTAMRDVPFSALYWFNYELVKRWLSG-LRSKDETLVGISF
          .H.SYREL.G.CV.A.V.Q.S..SL.LGW.PT..RDVPF.AL..F.YEL.KRWLSG.LR.K.....GIS.
Retrocopy *HTSYREL<GPCVQAMVAQGSWHSL*LGWDPTDRRDVPFTALH*FKYELLKRWLSG<LRPKNQSFIGISL

Parental  LAGGISGMVAAILTLPFDVVKTQRQMALGTVEAVRVTPPRADSTWLLLRRIRAESGTRGLFAGFL
          LAGGI.G.VAAILTL.F..VK...Q.ALG.VE.V...PP.ADSTWL.L.RI.AESGTRG.FAG.L
Retrocopy LAGGILGTVAAILTLLFNIVKPHHQVALGVVETVLLMPPCADSTWLPL*RIQAESGTRGHFAGKL

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	0.19 RPM	136.71 RPM
SRP012922_cerebellum	0.00 RPM	27.08 RPM
SRP012922_heart	0.00 RPM	41.77 RPM
SRP012922_kidney	0.00 RPM	180.98 RPM
SRP012922_liver	0.15 RPM	70.75 RPM
SRP012922_lung	0.00 RPM	69.80 RPM
SRP012922_quadricep_muscle	0.00 RPM	41.02 RPM
SRP012922_spleen	0.00 RPM	203.51 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_1866 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000008556	1 retrocopy	retro_dnov_1866 ,
Echinops telfairi	ENSETEG00000002713	1 retrocopy	retro_etel_823,
Homo sapiens	ENSG00000013306	1 retrocopy	retro_hsap_290,
Myotis lucifugus	ENSMLUG00000001925	2 retrocopies	retro_mluc_2296, retro_mluc_646,
Monodelphis domestica	ENSMODG00000011561	1 retrocopy	retro_mdom_1102,
Pongo abelii	ENSPPYG00000008333	1 retrocopy	retro_pabe_383,
Pan troglodytes	ENSPTRG00000009272	1 retrocopy	retro_ptro_239,
Rattus norvegicus	ENSRNOG00000020994	2 retrocopies	retro_rnor_1892, retro_rnor_2884,
Ictidomys tridecemlineatus	ENSSTOG00000004189	1 retrocopy	retro_itri_447,