RetrogeneDB ID: retro_dnov_1313

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_180499:528..890(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000007148
• Aliases: None
• Description: None

Sequence

>retro_dnov_1313
GAAGCAGCCAAGAGGGCAAACATCCGACTGCCGCCTGAGATAAATCGGATTTTGTATATAAGAAATTTGCTGAACAAAAT
CACAGCTGAAGAAATGTACAATACATTTGGGAAGTATGGACCTATTCATCAAATCAGAGTAGGGAACACACCTGAAACTA
GAGGAACAGCTTATGTGGTCTATGAAGACATCTTTGATTCCAAGAATGCCTATGATCACCTCTCAATAGTCAACTCTGTA
ACTGATACCTCCTGGTTTTGTACTGTAACGCCAACACAGCATTTCAGAAGATGAACACAAGAAAGGAGGAACAGTTGAAG
CTTCTCAAGGAGAAATATGGCATCAACACAGATCCACCAAAA

Alignment

ORF - retro_dnov_1313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.74 %
• Parental protein coverage: 97.6 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QAAKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA
          .AAKRANIRLPPE.NRILYIRNL..KITAEEMY..FGKYGPI.QIRVGNTPETRGTAYVVYEDIFD.KNA
Retrocopy EAAKRANIRLPPEINRILYIRNLLNKITAEEMYNTFGKYGPIHQIRVGNTPETRGTAYVVYEDIFDSKNA

Parental  CDHLSGFN-VCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDPPK
          .DHLS..N..CN.YL.VLY.NAN.AFQKM.T..KEEQLKLLKEKYGINTDPPK
Retrocopy YDHLSIVN<LCN*YLLVLYCNANTAFQKMNT-RKEEQLKLLKEKYGINTDPPK

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	56.98 RPM
SRP012922_cerebellum	0.00 RPM	48.11 RPM
SRP012922_heart	0.00 RPM	28.31 RPM
SRP012922_kidney	0.00 RPM	71.46 RPM
SRP012922_liver	0.00 RPM	42.57 RPM
SRP012922_lung	0.00 RPM	68.88 RPM
SRP012922_quadricep_muscle	0.00 RPM	24.75 RPM
SRP012922_spleen	0.00 RPM	55.51 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_1313 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002786	1 retrocopy	retro_amel_1594,
Bos taurus	ENSBTAG00000003407	1 retrocopy	retro_btau_606,
Choloepus hoffmanni	ENSCHOG00000000689	3 retrocopies	retro_chof_1217, retro_chof_2457, retro_chof_351,
Callithrix jacchus	ENSCJAG00000007716	2 retrocopies	retro_cjac_2632, retro_cjac_487,
Dasypus novemcinctus	ENSDNOG00000007148	1 retrocopy	retro_dnov_1313 ,
Equus caballus	ENSECAG00000015618	1 retrocopy	retro_ecab_733,
Felis catus	ENSFCAG00000031365	1 retrocopy	retro_fcat_247,
Homo sapiens	ENSG00000115128	1 retrocopy	retro_hsap_1773,
Macaca mulatta	ENSMMUG00000001282	1 retrocopy	retro_mmul_1262,
Mustela putorius furo	ENSMPUG00000013957	1 retrocopy	retro_mputfur_882,
Nomascus leucogenys	ENSNLEG00000000815	1 retrocopy	retro_nleu_2806,
Otolemur garnettii	ENSOGAG00000004468	1 retrocopy	retro_ogar_2877,
Pongo abelii	ENSPPYG00000012603	2 retrocopies	retro_pabe_1098, retro_pabe_1461,
Pan troglodytes	ENSPTRG00000011709	1 retrocopy	retro_ptro_1187,
Sorex araneus	ENSSARG00000011902	1 retrocopy	retro_sara_638,