RetrogeneDB ID: retro_dnov_2203

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_55420:7114..7563(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ10B
• Ensembl ID: ENSDNOG00000003229
• Aliases: None
• Description: coenzyme Q10 homolog B (S. cerevisiae) [Source:HGNC Symbol;Acc:25819]

Sequence

>retro_dnov_2203
ATGGCAGCTCGGAAGGCTTTAAGAAGGGTGGTCTCGGGATGCTGTCCGAAGGCCAGGGCGGCGACGCGAGCCCCGGCTCC
AGTACAGGAATCTGCATGGAACGTCAGATATTTAACTTCCTGTGGCATTTTGATGAGCAGAACTCTTCCACTTCATTCTT
CAGTTGTGTCTAAGGAGATGTATGCAAGAACATTCTTCAAAATTGCTGCACCATTATAAACAAAAGAAAAGAATATTCAG
AGAGGAAAATCATAGTGTATTCTATACAGGAAATCTATGATGTGGTATCAGGAGTGGAAGATTATAAGCATTTTGTTCCT
TGGTGTAAAAAATCAAATGTAATATCAAAGAGATCTGGATACTGTAAAACACAATTAGAAATTGGGTTGCCTCCTGTCTT
GAAACGATATACCTTAGTAGTAATCTTGGTGAAACCACATTTGGTAAAG

Alignment

ORF - retro_dnov_2203 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.77 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAARRALRRVVPGCCPKAGAATGARAPAQESARNVRYLASCGILMSRTLPLHTSIVPKEMYARTFFKIAA
          MAAR.ALRRVV.GCCPKA.AAT.A.AP.QESA.NVRYL.SCGILMSRTLPLH.S.V.KEMYARTFFKIAA
Retrocopy MAARKALRRVVSGCCPKARAATRAPAPVQESAWNVRYLTSCGILMSRTLPLHSSVVSKEMYARTFFKIAA

Parental  PL-INKRKEY-ERRIIGYSMQEMYDVVSGVEDYKHFVPWCKKSDVISKRSGYCKTRLEIGFPPVLERYTS
          PL.INKRKEY.ER.II.YS.QE.YDVVSGVEDYKHFVPWCKKS.VISKRSGYCKT.LEIG.PPVL.RYT.
Retrocopy PL<INKRKEYSERKIIVYSIQEIYDVVSGVEDYKHFVPWCKKSNVISKRSGYCKTQLEIGLPPVLKRYTL

Parental  VVTLVKPHLVK
          VV.LVKPHLVK
Retrocopy VVILVKPHLVK

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	11.67 RPM
SRP012922_cerebellum	0.00 RPM	12.92 RPM
SRP012922_heart	0.00 RPM	13.46 RPM
SRP012922_kidney	0.00 RPM	17.25 RPM
SRP012922_liver	0.00 RPM	16.41 RPM
SRP012922_lung	0.00 RPM	12.37 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.27 RPM
SRP012922_spleen	0.00 RPM	12.25 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_2203 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 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203 ,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,