RetrogeneDB ID: retro_dnov_4

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_140846:3..549(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000446
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000010231
• Aliases: None
• Description: None

Sequence

>retro_dnov_4
TTCCTGGGCCCCAAAGACCTCTTCCCTTATGAGGAGTTCAAGGAGAAGTTTGGCAAACCCAACAAGAGGAAAGGGTTCAG
CGAGGGGCTATGGGAGATTGAGAACAACCCTACTGTCAAGGCTTCCGGCTACCAGTCTTCCCAGAAAAAAAGCTGCATGG
AAGAGCCTGAGGCCGAGGCCACAGAAGGTGATGGTGATAAGAAGGGGAATGCAGAGGGCAGCAGTGATGAGGAGGGCAAG
CTGGTCATCGATGAGCCAACCAAGGAGAAAAATGAGAAGGGGGCGCTGAAGAGGAGAGCAGGGGACCTGCTGGAGGATTC
CCCCAAATGTCCCAAGGAGGCTGAGGACCCTGAAAGGGAGGAGAAGGAGGCAGCCACCTTGGAGGGTGAGAGGCCCATCC
CTGTGGAGGTGGAGAAGAACAATACCCCCTCCGAGCCTGGCTCTGGCCGGGGACCTCCTCAGGAAGAGGAGGGTGATGAC
GAGGAGGAAGAGGCTACCAAGGAAGATGCTGAGGCCTCAGGTGTCAGAGATCATGAGAGCCTGTAG

Alignment

ORF - retro_dnov_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.24 %
• Parental protein coverage: 86.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FLGPKDLFPYEESKEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCMEEPEAEA-EGDGDKKGN
          FLGPKDLFPYEE.KEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCMEEPEAEA.EGDGDKKGN
Retrocopy FLGPKDLFPYEEFKEKFGKPNKRKGFSEGLWEIENNPTVKASGYQSSQKKSCMEEPEAEATEGDGDKKGN

Parental  AEGSSDEEGKLVIDEPTKEKNEKGALKRRAGDLLEDSPKRPKEAEDPEREEKEAATLEGERPIPVEVEKN
          AEGSSDEEGKLVIDEPTKEKNEKGALKRRAGDLLEDSPK.PKEAEDPEREEKEAATLEGERPIPVEVEKN
Retrocopy AEGSSDEEGKLVIDEPTKEKNEKGALKRRAGDLLEDSPKCPKEAEDPEREEKEAATLEGERPIPVEVEKN

Parental  STPSEPGSGRGPPQEEEDDDEEEEATKEDAEASGVRDHESL
          .TPSEPGSGRGPPQEEE.DDEEEEATKEDAEASGVRDHESL
Retrocopy NTPSEPGSGRGPPQEEEGDDEEEEATKEDAEASGVRDHESL

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	41.81 RPM	48.23 RPM
SRP012922_cerebellum	29.01 RPM	32.44 RPM
SRP012922_heart	12.76 RPM	12.53 RPM
SRP012922_kidney	35.59 RPM	44.90 RPM
SRP012922_liver	31.89 RPM	31.74 RPM
SRP012922_lung	26.88 RPM	29.32 RPM
SRP012922_quadricep_muscle	32.02 RPM	28.73 RPM
SRP012922_spleen	55.28 RPM	60.09 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_4 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000039793	1 retrocopy	retro_btau_216,
Callithrix jacchus	ENSCJAG00000006157	2 retrocopies	retro_cjac_338, retro_cjac_4022,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Dasypus novemcinctus	ENSDNOG00000010231	1 retrocopy	retro_dnov_4 ,
Equus caballus	ENSECAG00000011178	1 retrocopy	retro_ecab_5,
Echinops telfairi	ENSETEG00000005243	1 retrocopy	retro_etel_1899,
Homo sapiens	ENSG00000143321	1 retrocopy	retro_hsap_33,
Myotis lucifugus	ENSMLUG00000010413	1 retrocopy	retro_mluc_257,
Mus musculus	ENSMUSG00000004897	1 retrocopy	retro_mmus_3647,
Pongo abelii	ENSPPYG00000000703	1 retrocopy	retro_pabe_6,
Pan troglodytes	ENSPTRG00000001474	1 retrocopy	retro_ptro_1,
Sus scrofa	ENSSSCG00000006468	1 retrocopy	retro_sscr_65,