RetrogeneDB ID: retro_dnov_79

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1343:104743..105000(-)
• Located in intron of: ENSDNOG00000004897

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018469
• Aliases: None
• Description: None

Sequence

>retro_dnov_79
ATGCCCAAGAGAAAAGCTGACAGGGATATTAAAGGAGATAAAGCCAAGGAAAAGGACAAGCCACAGAGAAGATCTACAAG
GTTACCTGCTCAACTTGCTCCTCCAAAGCCAGAACCCAAGCCTAAGAAGGTCCCTGCAAAGAAGAGTGAGAAGGTACCCA
AAGGGAAAAAGGAAAAGCTGATGCTGTCAAGGATGGAATAACCCTGCAGAAAATGGAGACCAGACACAAAAAAGCTGAAG
GTGCTAGAGATGCCAAG

Alignment

ORF - retro_dnov_79 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPKRKAEGDVKGDKAKVKDEPQRRSARLSAKPAPPKPEPKPKKAPAKKGEKVPKGK-KGKADAGKDG-NN
          MPKRKA..D.KGDKAK.KD.PQRRS.RL.A..APPKPEPKPKK.PAKK.EKVPKGK.KGKADA.KDG.NN
Retrocopy MPKRKADRDIKGDKAKEKDKPQRRSTRLPAQLAPPKPEPKPKKVPAKKSEKVPKGK<KGKADAVKDG<NN

Parental  PAENGDAKTDQAQK-AEGAGDAK
          PAENGD....Q.QK.AEGA.DAK
Retrocopy PAENGD----QTQK>AEGARDAK

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	171.91 RPM
SRP012922_cerebellum	0.14 RPM	56.64 RPM
SRP012922_heart	0.00 RPM	37.82 RPM
SRP012922_kidney	0.00 RPM	69.27 RPM
SRP012922_liver	0.00 RPM	25.23 RPM
SRP012922_lung	0.00 RPM	112.56 RPM
SRP012922_quadricep_muscle	0.00 RPM	29.94 RPM
SRP012922_spleen	0.00 RPM	232.70 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_79 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 5 parental genes, and 74 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018469	56 retrocopies	retro_dnov_1067, retro_dnov_1087, retro_dnov_112, retro_dnov_1178, retro_dnov_1316, retro_dnov_1321, retro_dnov_1350, retro_dnov_1409, retro_dnov_1414, retro_dnov_1461, retro_dnov_1518, retro_dnov_155, retro_dnov_1551, retro_dnov_1552, retro_dnov_1563, retro_dnov_1962, retro_dnov_1992, retro_dnov_2011, retro_dnov_2017, retro_dnov_2099, retro_dnov_2105, retro_dnov_2111, retro_dnov_2131, retro_dnov_2227, retro_dnov_2254, retro_dnov_2274, retro_dnov_2314, retro_dnov_2333, retro_dnov_2366, retro_dnov_2384, retro_dnov_2415, retro_dnov_2441, retro_dnov_2510, retro_dnov_2541, retro_dnov_2550, retro_dnov_2596, retro_dnov_2630, retro_dnov_2688, retro_dnov_354, retro_dnov_37, retro_dnov_411, retro_dnov_419, retro_dnov_478, retro_dnov_48, retro_dnov_495, retro_dnov_541, retro_dnov_583, retro_dnov_587, retro_dnov_717, retro_dnov_732, retro_dnov_79 , retro_dnov_808, retro_dnov_809, retro_dnov_912, retro_dnov_916, retro_dnov_995,
Felis catus	ENSFCAG00000012812	3 retrocopies	retro_fcat_1842, retro_fcat_4, retro_fcat_530,
Macropus eugenii	ENSMEUG00000010966	8 retrocopies	retro_meug_1178, retro_meug_126, retro_meug_1859, retro_meug_1910, retro_meug_1997, retro_meug_248, retro_meug_369, retro_meug_76,
Mus musculus	ENSMUSG00000003038	2 retrocopies	retro_mmus_202, retro_mmus_2582,
Tursiops truncatus	ENSTTRG00000005681	5 retrocopies	retro_ttru_1392, retro_ttru_1443, retro_ttru_3, retro_ttru_345, retro_ttru_788,