RetrogeneDB ID: retro_dnov_2306

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_62661:7302..7709(+)
• Located in intron of: None

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_2306
ATGGTCTCCAACAAAACTGCATTGCAGAACATGGGAAAGTAGTAGAATGGAAAGAGTGAAAATGTTGAAGAGGAAGAGCG
TGAAGGATTTGTGGTGGAAACATGTGTAGTGAATTAGAAGATGGAGTATTTCCTGAAGTGGAAGAGATTTCCAGATCCTG
ACAGTACTTTTGAGCCTGAAGAAAATTTCAATCGCTCAGAGTAACCTAAAGTATTTCTTAAGTTTCCAAACCTGGGAAAG
AAAAAGATGTACAAAAGAAAATCTTTGTCTGGCAGTGAATATGATGGCAGTAAATAAAAAAGAAAACCGAATCTGCTGAC
AAACCCAGAGGCTCTGCTGGAGATCTTGACACTGAATGAACAACAGGGGCCCCAGAGAGCAGCAGAGATCAAATATTTCT
TACTAAA

Alignment

ORF - retro_dnov_2306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.93 %
• Parental protein coverage: 77.05 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASNKTTLQKMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCP
          M.SNKT.LQ.MGK..NGKS..VEE.E.E.F....V....VVN.K.EYFLKWK.F.D.D.T.EPEEN....
Retrocopy MVSNKTALQNMGK**NGKSENVEEEEREGF----VVETCVVN*KMEYFLKWKRFPDPDSTFEPEENFNRS

Parental  ELIEAFLNSQKAGKEKDGTKRKSLSDSESDDSK-SKKKRDAADKPRGFARGLDPERIIGATDSSGELMFL
          E....FL.....GK.K...KRKSLS.SE.D.SK..KKK...ADKPRG.A..LD.E...GA..SS....FL
Retrocopy E*PKVFLKFPNLGKKK-MYKRKSLSGSEYDGSK<IKKKTESADKPRGSAGDLDTE*TTGAPESSRDQIFL

Parental  MK
          .K
Retrocopy TK

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	32.48 RPM
SRP012922_cerebellum	0.00 RPM	44.68 RPM
SRP012922_heart	0.00 RPM	30.16 RPM
SRP012922_kidney	0.00 RPM	21.08 RPM
SRP012922_liver	0.00 RPM	38.08 RPM
SRP012922_lung	0.00 RPM	57.88 RPM
SRP012922_quadricep_muscle	0.00 RPM	23.71 RPM
SRP012922_spleen	0.00 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_2306 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,