RetrogeneDB ID: retro_dnov_1933

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_37649:42598..43175(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX11
• Ensembl ID: ENSDNOG00000014862
• Aliases: None
• Description: cytochrome c oxidase assembly homolog 11 (yeast) [Source:HGNC Symbol;Acc:2261]

Sequence

>retro_dnov_1933
CAGGAGGGGGACTGGAGGTGGCCAAGTAAGTCGTTGAGTCACCTAAGAGGCCGCAGCTGCAGTGGGCCTGCCATTTGCCT
CCTATGCCCTGTCCCCCACAATCAGTGCTATTGCCAGACTGTTGGACCTGGAGGATCTGCAGTTGCGCATCAAGTATTAG
AACAGATTGAAGCCACGGTGCCTGTTAAGGATGTCATCATAAAGTTACCTTTAATGCAAGTGTGTCTGCAAGTCTCCAGT
GGAAACTTGACCTCCACAAACAGAAATATATGTTCACCAGGAAAGACTGCCCTAGTCTTTTATAAAGCTAAAAATCCTAC
TGACAAACTAGTAATTCAGAATTTCTGCATACAGTCTTGTGCCATTTGAAGCTGGACAGTATTTCAATAAAATACAGTGT
GTCTGTTTTGAAGAACAAAGGCTTAATTCACAAGAGGAAGTAGAAATGCCAGCATTTTTTCTACATTGTTCCTGATTTTG
CCAAAGATCTAAGTATGGTGAATGTTGATCTCATCACTCTTTCTTATACTTTTTTTTTAAGCAAAAGAAAGTCACAATTT
TGCCAGCTCAAAGCTAT

Alignment

ORF - retro_dnov_1933 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.17 %
• Parental protein coverage: 70.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 9

Retrocopy - Parental Gene Alignment:

Parental  QEEDWRRRNKTV-LTYVAAAAVGMLGASYAA-VPLYRLYCQTTGLGGSAVAGHASDQIEAMRPVKDRIIK
          QE.DWR...K....T..AAAAVG...ASYA..VP....YCQT.G.GGSAVA.....QIEA..PVKD.IIK
Retrocopy QEGDWRWPSKSL>VT*EAAAAVGLPFASYAL<VPHNQCYCQTVGPGGSAVAHQVLEQIEATVPVKDVIIK

Parental  -VTFNADVHASLQWNFR-PQQTEIYV-VPGETALAFYKAKNPTDKPVIG-ISTYNVVPFEAGQYFNKIQC
          .VTFNA.V.ASLQW....P.QTEIYV..PG.TAL.FYKAKNPTDK.VI..IS.Y..VPFEAGQYFNKIQC
Retrocopy <VTFNASVSASLQWKLD<PPQTEIYV<SPGKTALVFYKAKNPTDKLVIQ>ISAYSLVPFEAGQYFNKIQC

Parental  FCFEEQRLNPQEEVDMPV-FFYIDPEFAEDPRMVNVDLITLSY-TFFEAKEGHK-LPVPGY
          .CFEEQRLN.QEEV.MP..FFYI.P.FA.D..MVNVDLITLSY.....AKE.H..LP...Y
Retrocopy VCFEEQRLNSQEEVEMPA>FFYIVPDFAKDLSMVNVDLITLSY>XXXXAKESHN>LPAQSY

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	30.34 RPM
SRP012922_cerebellum	0.00 RPM	19.93 RPM
SRP012922_heart	0.00 RPM	18.33 RPM
SRP012922_kidney	0.00 RPM	29.30 RPM
SRP012922_liver	0.15 RPM	21.98 RPM
SRP012922_lung	0.00 RPM	28.41 RPM
SRP012922_quadricep_muscle	0.00 RPM	21.81 RPM
SRP012922_spleen	0.00 RPM	21.75 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_1933 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008482	1 retrocopy	retro_cpor_1340,
Dasypus novemcinctus	ENSDNOG00000014862	1 retrocopy	retro_dnov_1933 ,
Dipodomys ordii	ENSDORG00000001207	1 retrocopy	retro_dord_180,
Homo sapiens	ENSG00000166260	1 retrocopy	retro_hsap_3442,
Microcebus murinus	ENSMICG00000005225	1 retrocopy	retro_mmur_1119,
Monodelphis domestica	ENSMODG00000014855	1 retrocopy	retro_mdom_952,
Mus musculus	ENSMUSG00000020544	4 retrocopies	retro_mmus_1318, retro_mmus_2318, retro_mmus_2714, retro_mmus_986,
Nomascus leucogenys	ENSNLEG00000007990	1 retrocopy	retro_nleu_2297,
Ochotona princeps	ENSOPRG00000004138	1 retrocopy	retro_opri_441,
Pongo abelii	ENSPPYG00000008259	2 retrocopies	retro_pabe_156, retro_pabe_2847,
Pan troglodytes	ENSPTRG00000009422	1 retrocopy	retro_ptro_2335,
Rattus norvegicus	ENSRNOG00000046318	1 retrocopy	retro_rnor_1515,