RetrogeneDB ID: retro_dnov_6

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_7686:5274..5988(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000012066
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000017212
• Aliases: None
• Description: None

Sequence

>retro_dnov_6
AATAGGAAGGTCGTTGATCATTCACCGTTTCAGGAATCTGGTGATGCTGATGACGATTATGGAAGAGATTCGGGCCCTCC
AGCTAAGAAAATTCCATCATCTCCCCGAGAAGCTACAAATAAGAGGCGATCTGGAAAGAATTCACAGGCAGATAGTGAAG
ACTCGGAAGAAAAAGAAGTAAAAACCAAGAAGGATGATTCTCACTCAGCAGAAGACAGCGAAGATGAAAAAGAAGATCAT
AAAAATGTGCGCCAGCAACAGCAGGCAGCATCTAAAGCAGCTTCTAAACAGAGAGAGATGCTCATGGAAGACATGGGGGG
TGAGGAAGAACAAGAAGAAGAGGATGAAGCACCATTCCAGGAGAAAGATTCTGGCAGTGATGAAGATTTCCTAATGGAAG
ATGATGACGATAGTGACTATGGCAGTTCAAAAAAGAAAAACAAAAAGATGGTTAAGAAGACCAAACCTGAGAGAAAAGAA
AAGAAAATGCCCAAACCCAGGCTAAAGGCCACCGTGACGCCAAGTCCAGTGAAAGGCAAAGGGAAAGTGGGTCGTCCCAC
AGCTTCAAAGGCATCAAAGGAAAAGACTCCTTCCCCCAAAGAAGAAGATGACGAACCAGAAAGCCCTCCAGAAAAGAAAA
CATCTGCAAGCCCTCCACCCGGAAAATCTGGGGGTGAAGGATCTGAAGATGAAGCTCAGTCTGGGGAAGATTAA

Alignment

ORF - retro_dnov_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.22 %
• Parental protein coverage: 69.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EDSEEKEVKTKKDDSHSAEDSEDEKEDHKNVRQQRQAASKAASKQREMLMEDVGSEEEQEEEDEAPFQEK
          EDSEEKEVKTKKDDSHSAEDSEDEKEDHKNVRQQ.QAASKAASKQREMLMED.G.EEEQEEEDEAPFQEK
Retrocopy EDSEEKEVKTKKDDSHSAEDSEDEKEDHKNVRQQQQAASKAASKQREMLMEDMGGEEEQEEEDEAPFQEK

Parental  DSGSDEDFLMEDDDDSDYGSSKKKNKKMVKKAKPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKAS
          DSGSDEDFLMEDDDDSDYGSSKKKNKKMVKK.KPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKAS
Retrocopy DSGSDEDFLMEDDDDSDYGSSKKKNKKMVKKTKPERKEKKMPKPRLKATVTPSPVKGKGKVGRPTASKAS

Parental  KEKTPSPKEDDDEPESPPEKKTSASPPPEKSGDEGSEDEAQSGED
          KEKTPSPKE.DDEPESPPEKKTSASPPP.KSG.EGSEDEAQSGED
Retrocopy KEKTPSPKEEDDEPESPPEKKTSASPPPGKSGGEGSEDEAQSGED

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	32.67 RPM	81.68 RPM
SRP012922_cerebellum	41.79 RPM	105.85 RPM
SRP012922_heart	17.63 RPM	52.67 RPM
SRP012922_kidney	38.88 RPM	145.11 RPM
SRP012922_liver	19.51 RPM	56.66 RPM
SRP012922_lung	42.61 RPM	136.99 RPM
SRP012922_quadricep_muscle	20.42 RPM	59.19 RPM
SRP012922_spleen	54.94 RPM	151.09 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_6 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348, retro_dnov_6 ,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,