RetrogeneDB ID: retro_dnov_460

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5002:4699..5011(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDV3
• Ensembl ID: ENSDNOG00000010208
• Aliases: None
• Description: CDV3 homolog (mouse) [Source:HGNC Symbol;Acc:26928]

Sequence

>retro_dnov_460
GATGAAGATGAGTGGAAAGAATTTGAGCAAAAAGAGGTTGATTACAGCAGTTTCCAAGTTCAGGTAATGCAATTAAATGA
AAGGAAAAAAGATGAGAATGAAAAGAGAGAAGATCCAGGTGATAACTGGGAAGAAAGTAGAGGTGGTGGTGGTGGTGGTG
TCGAAAAATCTTCGGATCCCTAGAATAAAACGGTTCTGGTACAAGTACCTCCTGCTCCAGTGATTGTTACAGAAATCCCA
GAAGTAGCAATGACTACTGGTGTGAATGGGCTTCCTGGGGCCTACAACAAGGAAAACACCACAAGGACCACC

Alignment

ORF - retro_dnov_460 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.76 %
• Parental protein coverage: 57.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEDEWKEFEQKEVDYSGLRVQAMQISSEKEEDDNEKREDPGDNWEEG-GGGGGGVEKSSGPWNKTAVVQA
          DEDEWKEFEQKEVDYS...VQ.MQ...E...D.NEKREDPGDNWEE.........EKSS.P.NKT..VQ.
Retrocopy DEDEWKEFEQKEVDYSSFQVQVMQL-NERKKDENEKREDPGDNWEESRXXXXXXXEKSSDP*NKTVLVQV

Parental  PPAPVIVTETPEPAMTSGVYRPPGA--RLTTTRKT
          PPAPVIVTE.PE.AMT.GV...PGA.....TTR.T
Retrocopy PPAPVIVTEIPEVAMTTGVNGLPGAYNKENTTRTT

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	0.19 RPM	26.64 RPM
SRP012922_cerebellum	0.00 RPM	13.47 RPM
SRP012922_heart	0.00 RPM	38.29 RPM
SRP012922_kidney	0.00 RPM	30.67 RPM
SRP012922_liver	0.00 RPM	20.28 RPM
SRP012922_lung	0.00 RPM	23.67 RPM
SRP012922_quadricep_muscle	0.00 RPM	48.46 RPM
SRP012922_spleen	0.00 RPM	33.88 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_460 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 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000035556	1 retrocopy	retro_btau_253,
Choloepus hoffmanni	ENSCHOG00000008963	5 retrocopies	retro_chof_1355, retro_chof_1701, retro_chof_1763, retro_chof_2308, retro_chof_818,
Callithrix jacchus	ENSCJAG00000002998	1 retrocopy	retro_cjac_2928,
Dasypus novemcinctus	ENSDNOG00000010208	5 retrocopies	retro_dnov_2359, retro_dnov_2616, retro_dnov_460 , retro_dnov_496, retro_dnov_656,
Equus caballus	ENSECAG00000015689	2 retrocopies	retro_ecab_444, retro_ecab_636,
Homo sapiens	ENSG00000091527	1 retrocopy	retro_hsap_2678,
Gorilla gorilla	ENSGGOG00000027821	1 retrocopy	retro_ggor_1869,
Myotis lucifugus	ENSMLUG00000009864	1 retrocopy	retro_mluc_1296,
Mus musculus	ENSMUSG00000032803	10 retrocopies	retro_mmus_1266, retro_mmus_2405, retro_mmus_2408, retro_mmus_2411, retro_mmus_2412, retro_mmus_2416, retro_mmus_2418, retro_mmus_2422, retro_mmus_2423, retro_mmus_2534,
Nomascus leucogenys	ENSNLEG00000003470	1 retrocopy	retro_nleu_1181,
Oryctolagus cuniculus	ENSOCUG00000012748	1 retrocopy	retro_ocun_1106,
Ochotona princeps	ENSOPRG00000003600	3 retrocopies	retro_opri_1017, retro_opri_739, retro_opri_740,
Pongo abelii	ENSPPYG00000025898	1 retrocopy	retro_pabe_2301,
Pan troglodytes	ENSPTRG00000015409	1 retrocopy	retro_ptro_1805,
Sus scrofa	ENSSSCG00000011637	1 retrocopy	retro_sscr_701,
Tupaia belangeri	ENSTBEG00000014910	5 retrocopies	retro_tbel_2284, retro_tbel_2443, retro_tbel_4022, retro_tbel_4157, retro_tbel_4378,
Tarsius syrichta	ENSTSYG00000011401	2 retrocopies	retro_tsyr_1381, retro_tsyr_1759,