RetrogeneDB ID: retro_dnov_1630

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_249801:137..965(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000014786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000024041
• Aliases: None
• Description: None

Sequence

>retro_dnov_1630
GTGGCCGAGTGTGTGGAGCGGCTGCAGCAGCGGGTGCAGGCCCTGGAGCAGCAGCTGGCCGAGCAGAGGAGCCGGCGGGC
TGTGGGGGGCGCCCACGGAGGGGTCGACCGGCCCTGCGTGGAGCAGATGAGCTCGGAAGTGGTGAACTCCAACCCCTACA
GCCGCCTGATGGCATTGAAGCGAATGGGAATTGTAAATGATGAGAAAATCCGTACTTTTGCTGTAGCAATAGTAGGTATT
GGAGTTGGTAGTGTGACTGCTGAAATGCTGACAAGATGTGGCATTGGTAAGTTGCTGCTCTTTGACTATCACAAGGTGGA
ACTGGCCAGTATGAATAGACTTTTCTTCCAATCTCATCAAGCAGGATTAAGTAAAGTTCAAGCAGCTGAACATACTTTGA
GAAACATTAATCCTGATGTTCTTTTTGAGGTACACAACTACAATATCACCACAGTGGAAAACTTTCAACATTTCATGGAG
AGAATAAGTAATGGTGGGTTAGAAGAAGGAAAACCTTTTGACCTAGTTCTTAGCCGTGTGGACAGTTTTGAAGCTCGAAT
GACAATAAATACGGCTTGTAGTGAACTTGGACAAACACGGATGGAGTCTAGGGTCAGTGAAAATGCAATTTCAGGACATA
CACAGTTCATAATTCCTGGAGAATCTGCTTGTTTTGCGTGTGCTCCACCACTTGTCGTTGCTGCAAATATTGATGAAAAT
ACTCTGGAACGGAAAGGTGTTTGTGCAGCCAGCCTTCCTACTATGATGGGAGTGGTGGCTGGAATCTTAGTACAAAATGT
GTTAAAGGTTCTGTTAGGTTTTGGTAGT

Alignment

ORF - retro_dnov_1630 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.53 %
• Parental protein coverage: 68.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAECVERLKQELQDLERHLVEENSRQAVGGARGGVVRPGVAHMSSEVVDSNPYSRLMALKRMGIVNDYEK
          VAECVERL.Q..Q.LE..L.E..SR.AVGGA.GGV.RP.V..MSSEVV.SNPYSRLMALKRMGIVND.EK
Retrocopy VAECVERLQQRVQALEQQLAEQRSRRAVGGAHGGVDRPCVEQMSSEVVNSNPYSRLMALKRMGIVND-EK

Parental  IRTCAVAIVGVGGVGSVSAEMLTRCGIGKLLLFDYDKVELANMNRLFFQPHQAGLSKVQAAEHTLRHINP
          IRT.AVAIVG.G.VGSV.AEMLTRCGIGKLLLFDY.KVELA.MNRLFFQ.HQAGLSKVQAAEHTLR.INP
Retrocopy IRTFAVAIVGIG-VGSVTAEMLTRCGIGKLLLFDYHKVELASMNRLFFQSHQAGLSKVQAAEHTLRNINP

Parental  DVLFEVHNYNITTVENFQHFMERTSNGGLEEGKPVDLVLSCVDTFEARMTINTACNELGQTWMASGVSEN
          DVLFEVHNYNITTVENFQHFMER.SNGGLEEGKP.DLVLS.VD.FEARMTINTAC.ELGQT.M.S.VSEN
Retrocopy DVLFEVHNYNITTVENFQHFMERISNGGLEEGKPFDLVLSRVDSFEARMTINTACSELGQTRMESRVSEN

Parental  AVSGHIQLIIPGESACFACAPPLVVAANIDEKTLKWEGVCAASLPTTMGVVAGILVQNVLKFLLGFGT
          A.SGH.Q.IIPGESACFACAPPLVVAANIDE.TL...GVCAASLPT.MGVVAGILVQNVLK.LLGFG.
Retrocopy AISGHTQFIIPGESACFACAPPLVVAANIDENTLERKGVCAASLPTMMGVVAGILVQNVLKVLLGFGS

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	0.78 RPM	1.75 RPM
SRP012922_cerebellum	1.10 RPM	2.61 RPM
SRP012922_heart	0.46 RPM	0.23 RPM
SRP012922_kidney	0.55 RPM	0.82 RPM
SRP012922_liver	0.62 RPM	0.77 RPM
SRP012922_lung	2.14 RPM	1.53 RPM
SRP012922_quadricep_muscle	0.35 RPM	0.87 RPM
SRP012922_spleen	1.26 RPM	1.49 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_1630 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006654	1 retrocopy	retro_dnov_882,
Dasypus novemcinctus	ENSDNOG00000024041	2 retrocopies	retro_dnov_1630 , retro_dnov_2468,
Tarsius syrichta	ENSTSYG00000003103	1 retrocopy	retro_tsyr_1365,