RetrogeneDB ID: retro_dnov_396

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4358:130752..131098(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5G3
• Ensembl ID: ENSDNOG00000010440
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C3 (subunit 9) [Source:HGNC Symbol;Acc:843]

Sequence

>retro_dnov_396
GCATACAGATGAATTTTTGCATCACTGTTATCTTGACTAGAGATAAGACTGGGGAGGACTCTACGGTATTCAGTTGAGCC
TAGAATGGTGTGTCTTAGCTAATCCAAAGGGAGTTTCAGACCAGTGCAATCAGCAGAGGCATTGAAACTGCTGTCAAATT
TATTGGTGCAGGTGCTGCCACAGTAGGAGGGCTGGCTCTATTGCTGGTATTGGGACAGTCTTTGGCAGCCTCATCTTTGG
TTATGTGAGAAACCCTTTGCTGAAGAAGCACCTTTTCTCATATGCTATCCTGGGGTTTCCCTTTTCTGAAGCTATGGGTC
TCTTTTGTTTGAAGGTTGATTTCTTG

Alignment

ORF - retro_dnov_396 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.97 %
• Parental protein coverage: 82.27 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AYRPISASVLSRPE-DRTGEGSTVFSRAHNGVSQLIQREFQTSAISRDIDTAAKFIGAGAATVGV-AGSG
          AYR.I.AS.LS..E.D.TGE.STVFS.A.NGVS.LIQREFQTSAISR.I.TA.KFIGAGAATVG..AGS.
Retrocopy AYR*IFASLLS*LE<DKTGEDSTVFS*A*NGVS*LIQREFQTSAISRGIETAVKFIGAGAATVGG<AGSI

Parental  AGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMVAFL
          AGIGTVFGSLI.GY.RNP.LK..LFSYAILGF..SEAMGLFCL.V.FL
Retrocopy AGIGTVFGSLIFGYVRNPLLKKHLFSYAILGFPFSEAMGLFCLKVDFL

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	711.17 RPM
SRP012922_cerebellum	0.69 RPM	190.53 RPM
SRP012922_heart	0.00 RPM	581.47 RPM
SRP012922_kidney	0.00 RPM	360.86 RPM
SRP012922_liver	0.00 RPM	202.64 RPM
SRP012922_lung	0.46 RPM	74.22 RPM
SRP012922_quadricep_muscle	0.00 RPM	368.32 RPM
SRP012922_spleen	0.23 RPM	86.65 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_396 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 19 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012367	1 retrocopy	retro_amel_1829,
Bos taurus	ENSBTAG00000002944	1 retrocopy	retro_btau_838,
Canis familiaris	ENSCAFG00000013366	2 retrocopies	retro_cfam_4, retro_cfam_5,
Choloepus hoffmanni	ENSCHOG00000012592	3 retrocopies	retro_chof_189, retro_chof_2561, retro_chof_508,
Callithrix jacchus	ENSCJAG00000008207	3 retrocopies	retro_cjac_279, retro_cjac_38, retro_cjac_4183,
Cavia porcellus	ENSCPOG00000006194	1 retrocopy	retro_cpor_479,
Dasypus novemcinctus	ENSDNOG00000010440	2 retrocopies	retro_dnov_235, retro_dnov_396 ,
Loxodonta africana	ENSLAFG00000010768	1 retrocopy	retro_lafr_120,
Myotis lucifugus	ENSMLUG00000012822	1 retrocopy	retro_mluc_23,
Macaca mulatta	ENSMMUG00000003954	1 retrocopy	retro_mmul_148,
Monodelphis domestica	ENSMODG00000009520	3 retrocopies	retro_mdom_1070, retro_mdom_295, retro_mdom_545,
Mustela putorius furo	ENSMPUG00000013986	1 retrocopy	retro_mputfur_818,
Oryctolagus cuniculus	ENSOCUG00000012164	1 retrocopy	retro_ocun_949,
Otolemur garnettii	ENSOGAG00000027578	1 retrocopy	retro_ogar_1938,
Rattus norvegicus	ENSRNOG00000001596	1 retrocopy	retro_rnor_1106,
Sorex araneus	ENSSARG00000006733	1 retrocopy	retro_sara_82,
Ictidomys tridecemlineatus	ENSSTOG00000013572	4 retrocopies	retro_itri_1091, retro_itri_1236, retro_itri_324, retro_itri_438,
Tupaia belangeri	ENSTBEG00000012159	1 retrocopy	retro_tbel_54,
Tursiops truncatus	ENSTTRG00000011524	3 retrocopies	retro_ttru_268, retro_ttru_510, retro_ttru_588,