RetrogeneDB ID: retro_dnov_2243

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_57985:3948..4575(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000011999
• Aliases: None
• Description: None

Sequence

>retro_dnov_2243
AACTTTTGGCAGAGCTCCCACTATTTGCAATGGATTTTGGATAAACAATATCTGTTGAAGGAGTGTCAAAAGGACTTAGA
GTTTCTATCAGAAGAAGAATATTGGAAAATACAACTATTTTTTACAAACGTTATTCAAGCACTAGGTGAACATCTTAAAT
TCAGACAAGTTATTGCCACAGCTACAGTCTATTTCAAGAGATTCTATGCCAGGTATTCTCTGAAAAGTATAGATCCTTTA
TTAATGGCTCCTACGTGTGTGTTTTTGGCATCCAAAGTAGAGAAATTTGGAGTAGTCTCAAAGATAAGACTGATTACTGC
TGCTATTTCTGTAGTATAAACAAGATTTTCATATGCCTTTCTAAAGGAATTTCCTTATAGGATGAACCGTATATTAGAAT
GTGAATTCTGTCTTTTAGAACTAATGGATTGTTGCTTGATAGTGTATCATCCTTATAGACCTTTGCTCCAGTATGTGCAG
GACATGGGCCAACAAGACATGTTGCTTCCCCTTACATGAAGGATAGTGAATGATACCTACAGAATGGATCTTTGCCTACT
ATATCCTCCTTTCATGATAGCTTTAGCTTGCCTCCATGTAGCCTGTGTTGTACAGCAGAAAGATGCC

Alignment

ORF - retro_dnov_2243 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.05 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEHLKLRQQVIATATVYFKRFY
          NFWQSSHYLQWILDKQ.LLKE.QKDL.FLSEEEYWK.Q.FFTNVIQALGEHLK.RQ.VIATATVYFKRFY
Retrocopy NFWQSSHYLQWILDKQYLLKECQKDLEFLSEEEYWKIQLFFTNVIQALGEHLKFRQ-VIATATVYFKRFY

Parental  ARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLTAAATSVLKTRFSYAFPKEFPYRMNHILECEFYLL
          ARYSLKSIDP.LMAPTCVFLASKVE.FGVVS..RL..AA.SV..TRFSYAF.KEFPYRMN.ILECEF.LL
Retrocopy ARYSLKSIDPLLMAPTCVFLASKVEKFGVVSKIRLITAAISVV*TRFSYAFLKEFPYRMNRILECEFCLL

Parental  ELMDCCLIVYHPYRPLLQYVQDMGQEDMLLPLAWRIVNDTYRTDLCLLYPPFMIALACLHVACVVQQKDA
          ELMDCCLIVYHPYRPLLQYVQDMGQ.DMLLPL..RIVNDTYR.DLCLLYPPFMIALACLHVACVVQQKDA
Retrocopy ELMDCCLIVYHPYRPLLQYVQDMGQQDMLLPLT*RIVNDTYRMDLCLLYPPFMIALACLHVACVVQQKDA

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	5.06 RPM	11.67 RPM
SRP012922_cerebellum	2.61 RPM	9.21 RPM
SRP012922_heart	2.09 RPM	4.18 RPM
SRP012922_kidney	1.92 RPM	5.75 RPM
SRP012922_liver	1.86 RPM	3.41 RPM
SRP012922_lung	2.75 RPM	7.64 RPM
SRP012922_quadricep_muscle	0.87 RPM	5.19 RPM
SRP012922_spleen	2.17 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_2243 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Bos taurus	ENSBTAG00000015744	3 retrocopies	retro_btau_1206, retro_btau_1536, retro_btau_1836,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774,
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216, retro_dnov_2243 ,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Echinops telfairi	ENSETEG00000002643	1 retrocopy	retro_etel_1441,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888,
Otolemur garnettii	ENSOGAG00000001116	1 retrocopy	retro_ogar_2123,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026, retro_opri_151,
Sorex araneus	ENSSARG00000004726	2 retrocopies	retro_sara_141, retro_sara_583,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,