RetrogeneDB ID: retro_dnov_2171

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_52571:7717..8143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDO1
• Ensembl ID: ENSDNOG00000009577
• Aliases: None
• Description: cysteine dioxygenase type 1 [Source:HGNC Symbol;Acc:1795]

Sequence

>retro_dnov_2171
TATGCCAAGTTCGACCAGGACAGGTATACATGAAATCTTGTGGATCAAGGAAATGGGAAATTTAATCTGATGATTCTGTG
TTGGGGTGAAGGCCATGGCAGCAGTATCCACAATCCCACTGACTCCCACTGCTTTATGAAGAGGCTGCAGAGAAATCTAA
AGGAGACACTATTTGCCTCGCCAGATAAAAAACCCAATGAGATGATCAAGAAGTCTGAAAGAATCTTGAGGGGAAACCAG
CGTCCCTACCTCAATGATTCCATTGGTTTGCATCCGGTAGAGACTATCAGCCACATGGAACCTGCTGTGAGCCTTCGCTT
GTACAGTCCACCTTTGGATACATGCCACGCCTTTGATCAAAGAACAGGACATAAAAACCAAGTCACCATGACATTCCACA
GCAAATTTTGAATCAGGACTCCATTC

Alignment

ORF - retro_dnov_2171 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.92 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YAKFDQYRYTRNLVDQGNGKFNLMILCWGEGHGSSIHDHTDSHCFLKMLQGNLKETLFAWPDKKSNEMIK
          YAKFDQ.RYT.NLVDQGNGKFNLMILCWGEGHGSSIH..TDSHCF.K.LQ.NLKETLFA.PDKK.NEMIK
Retrocopy YAKFDQDRYT*NLVDQGNGKFNLMILCWGEGHGSSIHNPTDSHCFMKRLQRNLKETLFASPDKKPNEMIK

Parental  KSERILRENQGAYINDSIGLHRVENISHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTMTFHSKFGIRT
          KSERILR.NQ..Y.NDSIGLH.VE.ISH.EPAVSL.LYSPP.DTCHAFDQRTGHKN.VTMTFHSKF.IRT
Retrocopy KSERILRGNQRPYLNDSIGLHPVETISHMEPAVSLRLYSPPLDTCHAFDQRTGHKNQVTMTFHSKF*IRT

Parental  PF
          PF
Retrocopy PF

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	1.56 RPM
SRP012922_cerebellum	0.00 RPM	20.48 RPM
SRP012922_heart	0.00 RPM	16.94 RPM
SRP012922_kidney	0.00 RPM	7.39 RPM
SRP012922_liver	0.00 RPM	887.82 RPM
SRP012922_lung	0.00 RPM	31.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.12 RPM
SRP012922_spleen	0.00 RPM	1.14 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_2171 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009577	1 retrocopy	retro_dnov_2171 ,
Microcebus murinus	ENSMICG00000009005	1 retrocopy	retro_mmur_1405,
Otolemur garnettii	ENSOGAG00000009306	1 retrocopy	retro_ogar_660,
Tupaia belangeri	ENSTBEG00000003937	2 retrocopies	retro_tbel_3406, retro_tbel_4269,