RetrogeneDB ID: retro_dnov_321

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3596:214933..215482(+)
• Located in intron of: ENSDNOG00000005803

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBX3
• Ensembl ID: ENSDNOG00000006250
• Aliases: None
• Description: chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]

Sequence

>retro_dnov_321
ATGGCCTCCAATAAAACTACATTGCAAAAAATGGGAAAGAAGCAGAATGGAAAGAGTAAAAAAGTTGAAGAGGCAGAGCC
TGAAGAATTTGTGGTGGAGAAAGTACTGGATCGACGTGTAGTGAACGGGAAAGTGGAATATTTCCTAAAGTGGAAGGGAT
TTACCAATGCTGGCAATACTTGGGAGCCTGAAGAAAATTTAGATTGCCCAGAGTTAATTGAAGCATTTCTTAATTCTCAA
AAAGCTGGTAAAGAAAAAGATGGTACAAAAAGAAAATCTTTATCTGACAGTGAATCTGATGACAGCAAATCAAAGAAGAA
AAGAGATGCTGCTGACAAACAAAGAGGCTTTGCTAGAGGTCTTGATCCTGAACGCATAATTGGTGCCACAGACAGCAGTG
GAGAGCTCATGTTTCTTATGAAATGGAAAGATCCAGATGAGGCAGACTTGGTGCTGGCAAAAGAGGCAAACATGAAGTGT
CCTCAGATTGTAATTGCTTTTTATGAAGAGAGACTAACTTGGCATTCTTGTCCAGAAGATGAAGCTCAA

Alignment

ORF - retro_dnov_321 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.71 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCP
          MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFT.A.NTWEPEENLDCP
Retrocopy MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTNAGNTWEPEENLDCP

Parental  ELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPRGFARGLDPERIIGATDSSGELMFLM
          ELIEAFLNS.............SLSDSESDDSKSKKKRDAADK.RGFARGLDPERIIGATDSSGELMFLM
Retrocopy ELIEAFLNSXXXXXXXXXXXXXSLSDSESDDSKSKKKRDAADKQRGFARGLDPERIIGATDSSGELMFLM

Parental  KWKDSDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
          KWKD.DEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ
Retrocopy KWKDPDEADLVLAKEANMKCPQIVIAFYEERLTWHSCPEDEAQ

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	4.47 RPM	32.48 RPM
SRP012922_cerebellum	6.32 RPM	44.68 RPM
SRP012922_heart	3.71 RPM	30.16 RPM
SRP012922_kidney	6.02 RPM	21.08 RPM
SRP012922_liver	7.28 RPM	38.08 RPM
SRP012922_lung	6.57 RPM	57.88 RPM
SRP012922_quadricep_muscle	2.25 RPM	23.71 RPM
SRP012922_spleen	9.39 RPM	65.13 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_321 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 6 parental genes, and 50 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006250	19 retrocopies	retro_dnov_1136, retro_dnov_1174, retro_dnov_1208, retro_dnov_1270, retro_dnov_1605, retro_dnov_2306, retro_dnov_2307, retro_dnov_2397, retro_dnov_2543, retro_dnov_2605, retro_dnov_2633, retro_dnov_321 , retro_dnov_359, retro_dnov_385, retro_dnov_445, retro_dnov_772, retro_dnov_794, retro_dnov_833, retro_dnov_844,
Felis catus	ENSFCAG00000015224	6 retrocopies	retro_fcat_1005, retro_fcat_1103, retro_fcat_1485, retro_fcat_1519, retro_fcat_336, retro_fcat_473,
Microcebus murinus	ENSMICG00000006998	11 retrocopies	retro_mmur_1015, retro_mmur_1030, retro_mmur_1076, retro_mmur_1178, retro_mmur_1497, retro_mmur_1500, retro_mmur_1548, retro_mmur_386, retro_mmur_421, retro_mmur_68, retro_mmur_685,
Ochotona princeps	ENSOPRG00000011713	9 retrocopies	retro_opri_103, retro_opri_159, retro_opri_209, retro_opri_300, retro_opri_429, retro_opri_569, retro_opri_598, retro_opri_728, retro_opri_733,
Sarcophilus harrisii	ENSSHAG00000017913	1 retrocopy	retro_shar_153,
Sus scrofa	ENSSSCG00000016711	4 retrocopies	retro_sscr_1031, retro_sscr_204, retro_sscr_420, retro_sscr_755,