RetrogeneDB ID: retro_dnov_95

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1509:429432..429815(-)
• Located in intron of: ENSDNOG00000018133

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000010652
• Aliases: None
• Description: None

Sequence

>retro_dnov_95
ATGTCAGCTTCATTAGTCTAGGCCACTGTTCAGACTGTGAGTTAGAGGAAGATGCAGCCCCCCCAAACTGGCCTTGGTCT
TACACCTTTGGCAGTAAACAAGATAAAACAACTTCTTAAAGATAAGTCTAAGCATGTTATATGAAAGTTGATATCCAAAT
AAGGGGTTGTAATGGCCTTTATTATACTCCAGATTTTACGAAGACAAAGGGAGACAGTGATAAAGAAGTTGTTCAAGATG
GAATTAGGGTGTCCATCAAAAAGAAAGTACAGCTAACACTTTTAGAAACAGAAACGGAATATGTAGAAGACAAATTACCC
AGTGAGTTTGTGTTCAATAACCCAAACATCAAAGGAATTTGTGGTTGTGGAGAAAGTTTTAAT

Alignment

ORF - retro_dnov_95 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.64 %
• Parental protein coverage: 99.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSASLVRATVRAVS-RKLQPTRAALTLTSSAVNKIKQLLKDKPEHV-GVKVGVRTRGCNGLSYTLDYTKT
          MSASLV.ATV..VS.RK.QP....L.LT..AVNKIKQLLKDK..HV...KV....RGCNGL.YT.D.TKT
Retrocopy MSASLV*ATVQTVS*RKMQPPQTGLGLTPLAVNKIKQLLKDKSKHV<YMKVDIQIRGCNGLYYTPDFTKT

Parental  KGDSDEEVVQDGVRVFIEKKAQLTLLGTEMDYVEDKLSSEFVFNNPNIKGTCGCGESFN
          KGDSD.EVVQDG.RV.I.KK.QLTLL.TE..YVEDKL.SEFVFNNPNIKG.CGCGESFN
Retrocopy KGDSDKEVVQDGIRVSIKKKVQLTLLETETEYVEDKLPSEFVFNNPNIKGICGCGESFN

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	51.15 RPM
SRP012922_cerebellum	0.00 RPM	39.87 RPM
SRP012922_heart	0.00 RPM	105.57 RPM
SRP012922_kidney	0.00 RPM	70.09 RPM
SRP012922_liver	0.00 RPM	43.35 RPM
SRP012922_lung	0.00 RPM	71.63 RPM
SRP012922_quadricep_muscle	0.00 RPM	191.09 RPM
SRP012922_spleen	0.00 RPM	125.11 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_95 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 24 parental genes, and 65 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000046526	2 retrocopies	retro_btau_1787, retro_btau_506,
Canis familiaris	ENSCAFG00000001336	1 retrocopy	retro_cfam_1087,
Callithrix jacchus	ENSCJAG00000001940	6 retrocopies	retro_cjac_1623, retro_cjac_1734, retro_cjac_1870, retro_cjac_2608, retro_cjac_350, retro_cjac_672,
Cavia porcellus	ENSCPOG00000011872	2 retrocopies	retro_cpor_1383, retro_cpor_768,
Dasypus novemcinctus	ENSDNOG00000010652	5 retrocopies	retro_dnov_1162, retro_dnov_142, retro_dnov_1956, retro_dnov_431, retro_dnov_95 ,
Equus caballus	ENSECAG00000011465	1 retrocopy	retro_ecab_936,
Echinops telfairi	ENSETEG00000016537	1 retrocopy	retro_etel_1857,
Homo sapiens	ENSG00000135070	6 retrocopies	retro_hsap_1556, retro_hsap_1768, retro_hsap_1975, retro_hsap_2314, retro_hsap_317, retro_hsap_3329,
Gorilla gorilla	ENSGGOG00000007518	2 retrocopies	retro_ggor_1182, retro_ggor_92,
Microcebus murinus	ENSMICG00000003889	1 retrocopy	retro_mmur_1399,
Myotis lucifugus	ENSMLUG00000001288	1 retrocopy	retro_mluc_1620,
Macaca mulatta	ENSMMUG00000003399	3 retrocopies	retro_mmul_1230, retro_mmul_1365, retro_mmul_2211,
Monodelphis domestica	ENSMODG00000003559	1 retrocopy	retro_mdom_583,
Mus musculus	ENSMUSG00000044792	1 retrocopy	retro_mmus_278,
Nomascus leucogenys	ENSNLEG00000005129	5 retrocopies	retro_nleu_1674, retro_nleu_1725, retro_nleu_2330, retro_nleu_2618, retro_nleu_2782,
Oryctolagus cuniculus	ENSOCUG00000010945	1 retrocopy	retro_ocun_1685,
Otolemur garnettii	ENSOGAG00000015628	5 retrocopies	retro_ogar_1267, retro_ogar_1545, retro_ogar_2186, retro_ogar_2813, retro_ogar_935,
Pongo abelii	ENSPPYG00000019339	5 retrocopies	retro_pabe_1287, retro_pabe_2043, retro_pabe_2744, retro_pabe_2745, retro_pabe_367,
Pan troglodytes	ENSPTRG00000021075	7 retrocopies	retro_ptro_1047, retro_ptro_1185, retro_ptro_1316, retro_ptro_1689, retro_ptro_2149, retro_ptro_256, retro_ptro_2842,
Pteropus vampyrus	ENSPVAG00000004588	1 retrocopy	retro_pvam_956,
Rattus norvegicus	ENSRNOG00000018343	4 retrocopies	retro_rnor_1177, retro_rnor_1805, retro_rnor_2254, retro_rnor_2956,
Sus scrofa	ENSSSCG00000010953	1 retrocopy	retro_sscr_558,
Tarsius syrichta	ENSTSYG00000012826	2 retrocopies	retro_tsyr_1060, retro_tsyr_1698,
Tursiops truncatus	ENSTTRG00000004231	1 retrocopy	retro_ttru_1317,