RetrogeneDB ID: retro_dnov_2500

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_80669:2985..3446(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000003421
• Aliases: None
• Description: None

Sequence

>retro_dnov_2500
ATCAATAACCTGGTCTCAGTAGGATATCAAGTCTGCAAAAGAGATGTGCTTTCCCAACTGGACAAGGAAAAGTGTTGATA
GAAGGAATAGGATTTCCTGAATACCACAGTTCAGGGAGGAAAAGTGCCTTGAAAACATATGATATGATAGAAATGATAGA
CTATCAACCTACCTTTAGGAAAAACACTTCTAAAATCATGGGATTGCAGAGATCTCACACCCAAAAGAATTTCTTTAAAT
ATAATTATTTACAAGAAGATTCCTTTCACACATCAATAGTGAAAAAACATGCATTAATTCACAGAAGAAAGAATTCCTAT
TTCAAGAAACCACCTCCAACAATCCACGGTGATCATTCATCTTTCAATCAATGTAAGCATATTCTCCCTAGAAGTAAATC
ATATGAATGTTCCCAAAGGGCTAAAAATTGTATGCAGTGCTCTGACCTCAGACAATACAGT

Alignment

ORF - retro_dnov_2500 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.69 %
• Parental protein coverage: 51.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INNLVSVETGYQVCKRDVLSQLEQEE-VSREGIVFPQYQNPGRQYAFKTWEMIEMIFSQPTCRKDTSKTM
          INNLVSV..GYQVCKRDVLSQL..E..V..EGI.FP.Y...GR..A.KT..MIEMI..QPT.RK.TSK.M
Retrocopy INNLVSV--GYQVCKRDVLSQLDKEK<VLIEGIGFPEYHSSGRKSALKTYDMIEMIDYQPTFRKNTSKIM

Parental  SLHRSHTRKNSFKCNSLQEESSHTSIVNQYALIHLTKKSYFRKPPPAVLSDYSYVKQHKHLHHTSKSYEC
          .L.RSHT.KN.FK.N.LQE.S.HTSIV...ALIH..K.SYF.KPPP....D.S...Q.KH....SKSYEC
Retrocopy GLQRSHTQKNFFKYNYLQEDSFHTSIVKKHALIHRRKNSYFKKPPPTIHGDHSSFNQCKHILPRSKSYEC

Parental  YQSDKNCIQCSDIRQYN
          .Q..KNC.QCSD.RQY.
Retrocopy SQRAKNCMQCSDLRQYS

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	1.75 RPM	1.17 RPM
SRP012922_cerebellum	2.20 RPM	0.96 RPM
SRP012922_heart	0.93 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	0.27 RPM
SRP012922_liver	0.00 RPM	0.31 RPM
SRP012922_lung	1.07 RPM	0.76 RPM
SRP012922_quadricep_muscle	1.38 RPM	0.17 RPM
SRP012922_spleen	0.69 RPM	0.57 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_2500 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003421	1 retrocopy	retro_dnov_2500 ,
Homo sapiens	ENSG00000196946	1 retrocopy	retro_hsap_2965,