RetrogeneDB ID: retro_dnov_688

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_824:216920..217316(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP6V1E1
• Ensembl ID: ENSDNOG00000014592
• Aliases: None
• Description: ATPase, H+ transporting, lysosomal 31kDa, V1 subunit E1 [Source:HGNC Symbol;Acc:857]

Sequence

>retro_dnov_688
GACTTACTAAATGAAACAAAGTAGAGGCTCGGCAAGGTGGGAAAAGCTGCAACCAGGGACTAATTGCTGCTGGATGGACT
GGTCCTCTATGGTTTGTTCCAGTTGCTGGAGCCCCGAATTTGTTGCAAGAAACAGGATTTCCCACTGGTAAAGGCTGCCG
TACAAAAAGCGATTCCTATGTACAAAATTGCCTCCAAGAAAGATATTGATGTCCAAATTGATCAGGAGGCCTCCCTGCCT
GAGGATATAGCTGGTGGTGTTGAGATCTGTAGTGGCAAGCAAACAATAAAGGTTTCCAAAACCCTAGAAAGCTGGGTGGA
TCTCATACACTAGCAGATAATGTCAGAAGTACTGGGAGCCTTGTTTGATGCAAATTCCAACAGGAAGTTTTTGGAC

Alignment

ORF - retro_dnov_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.63 %
• Parental protein coverage: 59.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLLNEAKQRLSKVVKDTTRYQVLLDGLVLQGLYQLLEPRMIIRCRKQDFPLVKAAVQKAIPMYKIATKKE
          DLLNE.K.RL.KV.K..TR...LLDGLVL.GL.QLLEPR..I.C.KQDFPLVKAAVQKAIPMYKIA.KK.
Retrocopy DLLNETK*RLGKVGKAATRD*LLLDGLVLYGLFQLLEPR--ICCKKQDFPLVKAAVQKAIPMYKIASKKD

Parental  VDVQIDQEAFLPEDVAGGVEIYSGDRKIKVSNTLESRLDLIAQQMMPEVRGALFGANANRKFLD
          .DVQIDQEA.LPED.AGGVEI.SG...IKVS.TLES..DLI..Q.M.EV.GALF.AN.NRKFLD
Retrocopy IDVQIDQEASLPEDIAGGVEICSGKQTIKVSKTLESWVDLIH*QIMSEVLGALFDANSNRKFLD

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	42.20 RPM
SRP012922_cerebellum	0.41 RPM	102.41 RPM
SRP012922_heart	0.00 RPM	23.67 RPM
SRP012922_kidney	0.00 RPM	58.59 RPM
SRP012922_liver	0.00 RPM	24.00 RPM
SRP012922_lung	0.31 RPM	34.36 RPM
SRP012922_quadricep_muscle	0.00 RPM	14.54 RPM
SRP012922_spleen	0.11 RPM	46.59 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_688 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 14 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017489	2 retrocopies	retro_amel_116, retro_amel_1502,
Canis familiaris	ENSCAFG00000016151	7 retrocopies	retro_cfam_1050, retro_cfam_1260, retro_cfam_1354, retro_cfam_1379, retro_cfam_1446, retro_cfam_1997, retro_cfam_73,
Callithrix jacchus	ENSCJAG00000017277	1 retrocopy	retro_cjac_1160,
Dasypus novemcinctus	ENSDNOG00000014592	3 retrocopies	retro_dnov_2037, retro_dnov_44, retro_dnov_688 ,
Echinops telfairi	ENSETEG00000019283	2 retrocopies	retro_etel_1384, retro_etel_6,
Loxodonta africana	ENSLAFG00000003802	4 retrocopies	retro_lafr_1220, retro_lafr_123, retro_lafr_134, retro_lafr_742,
Myotis lucifugus	ENSMLUG00000014876	2 retrocopies	retro_mluc_312, retro_mluc_57,
Monodelphis domestica	ENSMODG00000018452	4 retrocopies	retro_mdom_1456, retro_mdom_1853, retro_mdom_248, retro_mdom_489,
Mustela putorius furo	ENSMPUG00000018109	2 retrocopies	retro_mputfur_23, retro_mputfur_4,
Oryctolagus cuniculus	ENSOCUG00000006964	1 retrocopy	retro_ocun_88,
Ochotona princeps	ENSOPRG00000004591	2 retrocopies	retro_opri_184, retro_opri_539,
Procavia capensis	ENSPCAG00000016094	1 retrocopy	retro_pcap_455,
Rattus norvegicus	ENSRNOG00000011905	1 retrocopy	retro_rnor_383,
Sarcophilus harrisii	ENSSHAG00000008300	2 retrocopies	retro_shar_501, retro_shar_780,