RetrogeneDB ID: retro_dnov_1830

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_32323:17660..18128(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SET
• Ensembl ID: ENSDNOG00000002802
• Aliases: None
• Description: SET nuclear oncogene [Source:HGNC Symbol;Acc:10760]

Sequence

>retro_dnov_1830
ATGGCCCCCAAACGCCAGTCTTCACTCCTGCCTCCCATGAAGAAAGAAAAACAGCTCCCCGCCCCATGCCAGAGGAGACA
CTGGGCTGCTCTGGACTTGCCCAAAGGAGGAAAAGGAACAGCAGGGAGCAACTGAACATATTGATGGAGTACAAAAAGAA
ATAGACAGACCTAATGAACAAGCCAGTGAGGAGATTTTGAAAGTAGAACAGAAATATAATAAACTCCACCAACCATTCTT
TCAGAAGAGGTCAGAATTGATTGCTAAAATCCCAAATTTTTGGTAACAACATTTGTCAACCATCCGCAAGTGTCTGCACT
GCTTGGGGAGGAAGATGAAGAGGCCCTGCAGTATTTGACCAGAGCTGAAGTAACAGAATTTGAAGGTATTAAATCAGGTT
ACAGAATAGATTTTTATTTTGATGAAAATCCTTACTTCAAAAATGAAATTCTCTCCAAAGAATTTCAT

Alignment

ORF - retro_dnov_1830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.38 %
• Parental protein coverage: 54.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MVPKRQSSLLPHSKRAKLL-PIP-PEETP-AALDLPKG-EKEQQEAIEHIDEVQNEIDRLNEQASEEILK
          M.PKRQSSLLP..K..K.L.P.P.PEET..AALDLPKG.EKEQQ.A.EHID.VQ.EIDR.NEQASEEILK
Retrocopy MAPKRQSSLLPPMKKEKQL<PRPMPEETL>AALDLPKG>EKEQQGATEHIDGVQKEIDRPNEQASEEILK

Parental  VEQKYNKLRQPFFQKRSELIAKIPNFW-VTTFVNHPQVSALLGEEDEEALHYLTRVEVTEFEDIKSGYRI
          VEQKYNKL.QPFFQKRSELIAKIPNFW.VTTFVNHPQVSALLGEEDEEAL.YLTR.EVTEFE.IKSGYRI
Retrocopy VEQKYNKLHQPFFQKRSELIAKIPNFW<VTTFVNHPQVSALLGEEDEEALQYLTRAEVTEFEGIKSGYRI

Parental  DFYFDENPYFENKVLSKEFH
          DFYFDENPYF.N..LSKEFH
Retrocopy DFYFDENPYFKNEILSKEFH

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	2.33 RPM	34.62 RPM
SRP012922_cerebellum	2.06 RPM	23.92 RPM
SRP012922_heart	1.62 RPM	12.07 RPM
SRP012922_kidney	3.83 RPM	24.64 RPM
SRP012922_liver	0.77 RPM	14.86 RPM
SRP012922_lung	2.75 RPM	31.16 RPM
SRP012922_quadricep_muscle	1.04 RPM	14.37 RPM
SRP012922_spleen	4.24 RPM	54.14 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_1830 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 13 parental genes, and 106 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Canis familiaris	ENSCAFG00000032728	2 retrocopies	retro_cfam_47, retro_cfam_83,
Dasypus novemcinctus	ENSDNOG00000002802	3 retrocopies	retro_dnov_160, retro_dnov_1830 , retro_dnov_464,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta	ENSMMUG00000008532	11 retrocopies	retro_mmul_1133, retro_mmul_1261, retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Oryctolagus cuniculus	ENSOCUG00000007501	12 retrocopies	retro_ocun_1107, retro_ocun_1110, retro_ocun_1234, retro_ocun_1311, retro_ocun_1563, retro_ocun_276, retro_ocun_407, retro_ocun_421, retro_ocun_423, retro_ocun_476, retro_ocun_859, retro_ocun_923,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,
Ictidomys tridecemlineatus	ENSSTOG00000010546	6 retrocopies	retro_itri_1204, retro_itri_1588, retro_itri_477, retro_itri_529, retro_itri_603, retro_itri_876,