RetrogeneDB ID: retro_dnov_2097

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_47568:6640..7071(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025332
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000017128
• Aliases: None
• Description: None

Sequence

>retro_dnov_2097
TCTTACTACTTTGACCGTGATGATGTGGCTTTGAAGAACTTTGCCAAATATTTTCTTCACCAATCTCATGAGGAGAGGGA
ACATGCTGAGAAACCAATGAAGCTACAGAACCAACGAGGCAGCCGAATCTTCCTTCAGGATATCAAGAAACCAGAACGAG
ATGACCGGGAGAGCGGACTGAATGCAATGGAGTGTGCATTACACTTGGAAAAAAGGGTGACTCAGTCACTCCTGGAACTG
TACAAGCTGGCTACTGACAAAAATGACCCCCATCTGTGTGACTTCACTGAGACCCATTACCTGAATGAGCAGGTGAAGTC
CCTCAAAGAACTGGGTGACTACGTAACCAGCCTGCGCAAGATGGGGGCCCGGATTCTGGCTTGGTAGCGTATCTCGTTGA
CAAGCACACTCTGGGAAGCAGTGATGAGAGC

Alignment

ORF - retro_dnov_2097 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SYYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQDIKKPERDDWESGLNAMECALHLE
          SYYFDRDDVALKNFAKYFLHQSHEEREHAEK.MKLQNQRG.RIFLQDIKKPERDD.ESGLNAMECALHLE
Retrocopy SYYFDRDDVALKNFAKYFLHQSHEEREHAEKPMKLQNQRGSRIFLQDIKKPERDDRESGLNAMECALHLE

Parental  KRVNQSLLELHKLATDKNDPHLCDFIETHYLNEQVKSIKELGDYVTNLRKMGA-PDSGLAEYLFDKHTLG
          KRV.QSLLEL.KLATDKNDPHLCDF.ETHYLNEQVKS.KELGDYVT.LRKMGA.PDSGL..YL.DKHTLG
Retrocopy KRVTQSLLELYKLATDKNDPHLCDFTETHYLNEQVKSLKELGDYVTSLRKMGA<PDSGLVAYLVDKHTLG

Parental  SSDES
          SSDES
Retrocopy SSDES

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	567.85 RPM
SRP012922_cerebellum	0.00 RPM	303.39 RPM
SRP012922_heart	0.23 RPM	263.36 RPM
SRP012922_kidney	0.00 RPM	890.66 RPM
SRP012922_liver	0.00 RPM	543.68 RPM
SRP012922_lung	0.15 RPM	953.15 RPM
SRP012922_quadricep_muscle	0.00 RPM	198.18 RPM
SRP012922_spleen	0.00 RPM	1034.61 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_2097 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 32 parental genes, and 355 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016831	1 retrocopy	retro_amel_115,
Bos taurus	ENSBTAG00000011184	10 retrocopies	retro_btau_1151, retro_btau_121, retro_btau_1255, retro_btau_1473, retro_btau_1708, retro_btau_1745, retro_btau_256, retro_btau_595, retro_btau_673, retro_btau_959,
Canis familiaris	ENSCAFG00000015901	1 retrocopy	retro_cfam_150,
Callithrix jacchus	ENSCJAG00000019089	16 retrocopies	retro_cjac_1570, retro_cjac_1634, retro_cjac_2115, retro_cjac_2233, retro_cjac_230, retro_cjac_232, retro_cjac_2320, retro_cjac_2531, retro_cjac_278, retro_cjac_2843, retro_cjac_2857, retro_cjac_485, retro_cjac_519, retro_cjac_699, retro_cjac_767, retro_cjac_804,
Cavia porcellus	ENSCPOG00000026586	3 retrocopies	retro_cpor_1309, retro_cpor_15, retro_cpor_157,
Dasypus novemcinctus	ENSDNOG00000002455	9 retrocopies	retro_dnov_1096, retro_dnov_1135, retro_dnov_1177, retro_dnov_1737, retro_dnov_2006, retro_dnov_2352, retro_dnov_2678, retro_dnov_473, retro_dnov_993,
Dasypus novemcinctus	ENSDNOG00000004126	5 retrocopies	retro_dnov_1263, retro_dnov_1490, retro_dnov_1760, retro_dnov_2329, retro_dnov_299,
Dasypus novemcinctus	ENSDNOG00000005577	36 retrocopies	retro_dnov_103, retro_dnov_1164, retro_dnov_1215, retro_dnov_130, retro_dnov_1382, retro_dnov_1441, retro_dnov_1515, retro_dnov_1568, retro_dnov_1657, retro_dnov_1812, retro_dnov_1815, retro_dnov_1918, retro_dnov_1991, retro_dnov_2014, retro_dnov_2134, retro_dnov_2187, retro_dnov_236, retro_dnov_2376, retro_dnov_2379, retro_dnov_247, retro_dnov_2575, retro_dnov_2658, retro_dnov_2667, retro_dnov_285, retro_dnov_305, retro_dnov_432, retro_dnov_439, retro_dnov_543, retro_dnov_598, retro_dnov_642, retro_dnov_807, retro_dnov_841, retro_dnov_846, retro_dnov_849, retro_dnov_861, retro_dnov_897,
Dasypus novemcinctus	ENSDNOG00000007848	2 retrocopies	retro_dnov_1049, retro_dnov_1476,
Dasypus novemcinctus	ENSDNOG00000016683	8 retrocopies	retro_dnov_1134, retro_dnov_1329, retro_dnov_2023, retro_dnov_2194, retro_dnov_2228, retro_dnov_56, retro_dnov_757, retro_dnov_886,
Dasypus novemcinctus	ENSDNOG00000017128	83 retrocopies	retro_dnov_1017, retro_dnov_1074, retro_dnov_1078, retro_dnov_110, retro_dnov_1179, retro_dnov_1188, retro_dnov_1196, retro_dnov_1201, retro_dnov_1205, retro_dnov_1271, retro_dnov_1352, retro_dnov_1356, retro_dnov_1369, retro_dnov_1397, retro_dnov_1415, retro_dnov_1425, retro_dnov_1446, retro_dnov_1489, retro_dnov_1526, retro_dnov_1535, retro_dnov_1554, retro_dnov_1565, retro_dnov_162, retro_dnov_1627, retro_dnov_1640, retro_dnov_1777, retro_dnov_1787, retro_dnov_1792, retro_dnov_1827, retro_dnov_1851, retro_dnov_1865, retro_dnov_1875, retro_dnov_189, retro_dnov_197, retro_dnov_2005, retro_dnov_2065, retro_dnov_2093, retro_dnov_2097 , retro_dnov_2109, retro_dnov_2124, retro_dnov_2136, retro_dnov_2154, retro_dnov_2173, retro_dnov_220, retro_dnov_2216, retro_dnov_2231, retro_dnov_2241, retro_dnov_2251, retro_dnov_2356, retro_dnov_2388, retro_dnov_2399, retro_dnov_242, retro_dnov_2443, retro_dnov_2444, retro_dnov_2454, retro_dnov_2476, retro_dnov_2483, retro_dnov_2489, retro_dnov_2511, retro_dnov_2528, retro_dnov_2554, retro_dnov_2579, retro_dnov_2607, retro_dnov_2626, retro_dnov_2646, retro_dnov_304, retro_dnov_383, retro_dnov_409, retro_dnov_422, retro_dnov_471, retro_dnov_517, retro_dnov_52, retro_dnov_55, retro_dnov_589, retro_dnov_61, retro_dnov_661, retro_dnov_675, retro_dnov_722, retro_dnov_726, retro_dnov_810, retro_dnov_864, retro_dnov_890, retro_dnov_994,
Felis catus	ENSFCAG00000007382	1 retrocopy	retro_fcat_887,
Homo sapiens	ENSG00000167996	20 retrocopies	retro_hsap_1243, retro_hsap_139, retro_hsap_1432, retro_hsap_2240, retro_hsap_2351, retro_hsap_2662, retro_hsap_2835, retro_hsap_2985, retro_hsap_2996, retro_hsap_316, retro_hsap_3208, retro_hsap_3293, retro_hsap_3589, retro_hsap_4083, retro_hsap_4232, retro_hsap_4671, retro_hsap_484, retro_hsap_81, retro_hsap_87, retro_hsap_898,
Gorilla gorilla	ENSGGOG00000027722	7 retrocopies	retro_ggor_1313, retro_ggor_153, retro_ggor_1671, retro_ggor_1858, retro_ggor_2835, retro_ggor_64, retro_ggor_726,
Latimeria chalumnae	ENSLACG00000017426	1 retrocopy	retro_lcha_75,
Loxodonta africana	ENSLAFG00000004824	12 retrocopies	retro_lafr_106, retro_lafr_1080, retro_lafr_1129, retro_lafr_138, retro_lafr_321, retro_lafr_433, retro_lafr_523, retro_lafr_53, retro_lafr_624, retro_lafr_717, retro_lafr_760, retro_lafr_966,
Microcebus murinus	ENSMICG00000005851	6 retrocopies	retro_mmur_1227, retro_mmur_1303, retro_mmur_1370, retro_mmur_1609, retro_mmur_392, retro_mmur_509,
Myotis lucifugus	ENSMLUG00000025726	16 retrocopies	retro_mluc_1030, retro_mluc_1142, retro_mluc_1211, retro_mluc_1354, retro_mluc_1464, retro_mluc_1769, retro_mluc_1984, retro_mluc_2002, retro_mluc_2091, retro_mluc_212, retro_mluc_2635, retro_mluc_361, retro_mluc_532, retro_mluc_556, retro_mluc_850, retro_mluc_885,