RetrogeneDB ID: retro_dnov_215

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2697:14565..14811(+)
• Located in intron of: ENSDNOG00000004841

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2A
• Ensembl ID: ENSDNOG00000007060
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2A [Source:HGNC Symbol;Acc:12472]

Sequence

>retro_dnov_215
TCTGCAAACAACATCATGCAGTGGAATGCATTTATATTTGGACCAGAAGGGACACCCTTTGAAGATGGTACTTTAAAATT
CATAATAGAATTTTCTGAAGAATATCCAGATAAACTGTCAACTGTAAGGTTTTTATCCAAAATGCTTCATCCAAATGTGT
ATGCTGATGATACCATATGTTGAGATATCCTTCAGAACAGATGGAGCCCAACAGATGATGTATCTTCTATCTTCACATCA
ATTCAG

Alignment

ORF - retro_dnov_215 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.07 %
• Parental protein coverage: 53.64 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SENNIMVWNAVIFGXXXXXXXXXTFKLTIEFTEEYPNKPPTVRFVSKMF-PNVYADGSICLDILQNRWSP
          S.NNIM.WNA.IFG.........T.K..IEF.EEYP.K..TVRF.SKM..PNVYAD..IC.DILQNRWSP
Retrocopy SANNIMQWNAFIFGPEGTPFEDGTLKFIIEFSEEYPDKLSTVRFLSKMLHPNVYADDTIC*DILQNRWSP

Parental  TYDVSSILTSIQ
          T.DVSSI.TSIQ
Retrocopy TDDVSSIFTSIQ

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	16.92 RPM
SRP012922_cerebellum	0.14 RPM	22.82 RPM
SRP012922_heart	0.46 RPM	12.99 RPM
SRP012922_kidney	0.00 RPM	11.77 RPM
SRP012922_liver	0.00 RPM	11.92 RPM
SRP012922_lung	0.15 RPM	20.16 RPM
SRP012922_quadricep_muscle	0.52 RPM	23.54 RPM
SRP012922_spleen	0.23 RPM	14.88 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_215 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 11 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001079	1 retrocopy	retro_chof_1316,
Callithrix jacchus	ENSCJAG00000005098	2 retrocopies	retro_cjac_1180, retro_cjac_3862,
Cavia porcellus	ENSCPOG00000011908	1 retrocopy	retro_cpor_489,
Dasypus novemcinctus	ENSDNOG00000007060	1 retrocopy	retro_dnov_215 ,
Macropus eugenii	ENSMEUG00000003026	1 retrocopy	retro_meug_2180,
Monodelphis domestica	ENSMODG00000010209	1 retrocopy	retro_mdom_341,
Oryctolagus cuniculus	ENSOCUG00000016739	1 retrocopy	retro_ocun_183,
Otolemur garnettii	ENSOGAG00000024335	1 retrocopy	retro_ogar_3203,
Procavia capensis	ENSPCAG00000005045	1 retrocopy	retro_pcap_222,
Sus scrofa	ENSSSCG00000012621	1 retrocopy	retro_sscr_29,
Tarsius syrichta	ENSTSYG00000000888	1 retrocopy	retro_tsyr_676,