RetrogeneDB ID: retro_dnov_378

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4238:59482..59831(-)
• Located in intron of: ENSDNOG00000019948

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000002470
• Aliases: None
• Description: None

Sequence

>retro_dnov_378
ATGAAGTTCAATCCCTTTGTGACCTCTGATAGGAGCAGGAACGTAAAAGGTATTTCAATGCACCTTCCCACATTTGGAAG
AGGATTATGTCTTCCCCTCTTTCCAAGGAGCTGAGACAGAAATATAATGTTCTATCCATGCCTATCTGAAAAGATGATGC
AGTTCATGTTGTGCAAGGACATTATAGAGATCAGCAAATTGGCAAAGTAGTCCAGGTTTACAGGAAGAAATATGTCATCT
ACATCAAATGGGTGCATTGGGAGATGGCTAATGGCACCACTCTCCATATGGGCATTCACCCCAGCAAGGTGGTTATCACT
ATGCTAAACTGGGTAAAGACCACAAAAAG

Alignment

ORF - retro_dnov_378 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.83 %
• Parental protein coverage: 76.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKN-RKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVXVVRGHYKGQQIGK
          MKFNPFVTSDRS.N.RKR.FNAPSHI...IMSSPLSKELRQKYNV.SMPI.KDD.V.VV.GHY..QQIGK
Retrocopy MKFNPFVTSDRSRN<RKRYFNAPSHIWKRIMSSPLSKELRQKYNVLSMPI*KDDAVHVVQGHYRDQQIGK

Parental  VVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRL-KLDKDRKK
          VVQVYRKKYVIYI..V..E.ANGTT.H.GIHPSKVVIT.L.KL.KD.KK
Retrocopy VVQVYRKKYVIYIKWVHWEMANGTTLHMGIHPSKVVITML<KLGKDHKK

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	252.81 RPM
SRP012922_cerebellum	0.00 RPM	157.26 RPM
SRP012922_heart	0.00 RPM	154.53 RPM
SRP012922_kidney	0.00 RPM	395.63 RPM
SRP012922_liver	0.00 RPM	152.02 RPM
SRP012922_lung	0.00 RPM	419.69 RPM
SRP012922_quadricep_muscle	0.00 RPM	198.87 RPM
SRP012922_spleen	0.00 RPM	374.17 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_378 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 148 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002453	7 retrocopies	retro_amel_1175, retro_amel_1535, retro_amel_1885, retro_amel_1934, retro_amel_360, retro_amel_499, retro_amel_900,
Bos taurus	ENSBTAG00000012344	2 retrocopies	retro_btau_1090, retro_btau_230,
Choloepus hoffmanni	ENSCHOG00000004703	10 retrocopies	retro_chof_149, retro_chof_1893, retro_chof_2147, retro_chof_2276, retro_chof_2333, retro_chof_2383, retro_chof_244, retro_chof_312, retro_chof_816, retro_chof_942,
Callithrix jacchus	ENSCJAG00000014372	8 retrocopies	retro_cjac_110, retro_cjac_119, retro_cjac_240, retro_cjac_250, retro_cjac_270, retro_cjac_297, retro_cjac_321, retro_cjac_362,
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306, retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Dasypus novemcinctus	ENSDNOG00000002470	3 retrocopies	retro_dnov_2054, retro_dnov_2174, retro_dnov_378 ,
Felis catus	ENSFCAG00000011259	13 retrocopies	retro_fcat_1090, retro_fcat_1151, retro_fcat_1198, retro_fcat_1236, retro_fcat_1257, retro_fcat_1309, retro_fcat_1412, retro_fcat_1652, retro_fcat_1801, retro_fcat_1845, retro_fcat_1965, retro_fcat_497, retro_fcat_801,
Homo sapiens	ENSG00000161970	27 retrocopies	retro_hsap_1137, retro_hsap_1309, retro_hsap_1376, retro_hsap_1394, retro_hsap_191, retro_hsap_2108, retro_hsap_2165, retro_hsap_2253, retro_hsap_253, retro_hsap_267, retro_hsap_2946, retro_hsap_3118, retro_hsap_3260, retro_hsap_3324, retro_hsap_3490, retro_hsap_3700, retro_hsap_3803, retro_hsap_3813, retro_hsap_3914, retro_hsap_4043, retro_hsap_4061, retro_hsap_4874, retro_hsap_4932, retro_hsap_642, retro_hsap_691, retro_hsap_915, retro_hsap_998,
Gorilla gorilla	ENSGGOG00000023944	4 retrocopies	retro_ggor_2565, retro_ggor_270, retro_ggor_51, retro_ggor_974,
Myotis lucifugus	ENSMLUG00000002176	1 retrocopy	retro_mluc_232,
Macaca mulatta	ENSMMUG00000003448	22 retrocopies	retro_mmul_1117, retro_mmul_1361, retro_mmul_1398, retro_mmul_1497, retro_mmul_1710, retro_mmul_1773, retro_mmul_1899, retro_mmul_1986, retro_mmul_2052, retro_mmul_2163, retro_mmul_2332, retro_mmul_2344, retro_mmul_325, retro_mmul_360, retro_mmul_398, retro_mmul_405, retro_mmul_448, retro_mmul_548, retro_mmul_805, retro_mmul_903, retro_mmul_920, retro_mmul_992,
Monodelphis domestica	ENSMODG00000006201	2 retrocopies	retro_mdom_36, retro_mdom_64,
Nomascus leucogenys	ENSNLEG00000009981	1 retrocopy	retro_nleu_76,
Otolemur garnettii	ENSOGAG00000017070	3 retrocopies	retro_ogar_118, retro_ogar_255, retro_ogar_66,
Sarcophilus harrisii	ENSSHAG00000006890	1 retrocopy	retro_shar_458,
Sus scrofa	ENSSSCG00000028850	9 retrocopies	retro_sscr_261, retro_sscr_363, retro_sscr_426, retro_sscr_427, retro_sscr_471, retro_sscr_485, retro_sscr_508, retro_sscr_609, retro_sscr_736,