RetrogeneDB ID: retro_dnov_2495

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_80315:9984..10303(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARPC5
• Ensembl ID: ENSDNOG00000010375
• Aliases: None
• Description: actin related protein 2/3 complex, subunit 5, 16kDa [Source:HGNC Symbol;Acc:708]

Sequence

>retro_dnov_2495
GAGAACACCGTGTCGTCGGCCTCGTTCTGGAAGGTGGACATGGGTGAGTACAACAAGAACAAGTTCATGGACGAGGAAGA
TGGAGGCGACGGCCAGGCTGGGCCCAAGGAAGGCTGAGGTGGGCTCCTGTATGCGGCAAAAACACACGACAGCTGCTCCG
CAAGCCGCGCTGGAAAAGCCCCCAGTCAACACCAAGAGTCAGGCCATGCAGGCCCAAGCAGGCAGCAGTGTCCTGAAGGT
GCTCATCTCTCTTAAAGTCAATGATGTTGAAAAGGCAATTCAACCTCTGGACCAGAAGGGTGTGGATCTGCTAACACGT

Alignment

ORF - retro_dnov_2495 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.27 %
• Parental protein coverage: 81.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KNTVSSARFRKVDVDEYDENKFVDEEDGGDGQAGPDEG-EVDSCLRHSVTGNMTAALQAALKNPPINTKS
          .NTVSSA.F.KVD..EY..NKF.DEEDGGDGQAGP.EG.EV.SC.R...T...TAA.QAAL..PP.NTKS
Retrocopy ENTVSSASFWKVDMGEYNKNKFMDEEDGGDGQAGPKEG>EVGSCMRQKHT---TAAPQAALEKPPVNTKS

Parental  QAVKDRAGSIVLKVLISFKANDIEKAVQSLDKNGVDLLMK
          QA....AGS.VLKVLIS.K.ND.EKA.Q.LD..GVDLL..
Retrocopy QAMQAQAGSSVLKVLISLKVNDVEKAIQPLDQKGVDLLTR

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	0.58 RPM	102.87 RPM
SRP012922_cerebellum	0.00 RPM	25.71 RPM
SRP012922_heart	0.00 RPM	10.91 RPM
SRP012922_kidney	0.55 RPM	21.36 RPM
SRP012922_liver	0.00 RPM	40.25 RPM
SRP012922_lung	0.15 RPM	71.63 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.23 RPM
SRP012922_spleen	0.80 RPM	121.44 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_2495 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000560	2 retrocopies	retro_chof_1502, retro_chof_783,
Dasypus novemcinctus	ENSDNOG00000010375	3 retrocopies	retro_dnov_1277, retro_dnov_199, retro_dnov_2495 ,
Echinops telfairi	ENSETEG00000014969	1 retrocopy	retro_etel_1922,
Monodelphis domestica	ENSMODG00000007194	1 retrocopy	retro_mdom_968,
Mus musculus	ENSMUSG00000008475	1 retrocopy	retro_mmus_281,
Rattus norvegicus	ENSRNOG00000028062	1 retrocopy	retro_rnor_1873,