RetrogeneDB ID: retro_dnov_116

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1762:43001..43370(-)
• Located in intron of: ENSDNOG00000000905

Retrocopy information

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

Parental gene information

• Parental gene symbol: GSTZ1
• Ensembl ID: ENSDNOG00000017287
• Aliases: None
• Description: glutathione S-transferase zeta 1 [Source:HGNC Symbol;Acc:4643]

Sequence

>retro_dnov_116
AAGGAGACTCAGAAGAGGGCCAGCGTGCGCATGATTTCCAACCTCATCGCTGGTGACATCCAACCTCTATAGAACTTGTC
TGTCCTGAAGCAAGTGAGTCAGGAGAATCAGCTGACCTGGGCCCAGAATGCCATCAGTTCTGCTTTAACGCTCTGGCACA
TCCTGCAGAGCATAGCAGGGAATGTGGAAGATGAGGTTTCCATGGCTGATTTGTGTCTAGTCCCTCAGGTGGCAAAAGCC
AAAAGTTTCAAGGTGGATCTCACTCCCTACCCCACCACTGGCCTCATCAACAGACACTGTTGGCCTTAAGAGGCCTTCCA
ACTGTCTCACCCTTGCCGGCAGCCAGATAAATGCCCTGAGTTGAGGGCT

Alignment

ORF - retro_dnov_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.44 %
• Parental protein coverage: 59.52 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QDPKKRASVRMISDLITGGIQPLQNLSVLKQLSQENQLTWAQNAICSGFNALEQILQSTAGKYCVEDEF-
          ....KRASVRMIS.LI.G.IQPL.NLSVLKQ.SQENQLTWAQNAI.S....L..ILQS.AG...VEDE..
Retrocopy KETQKRASVRMISNLIAGDIQPL*NLSVLKQVSQENQLTWAQNAISSALT-LWHILQSIAGN--VEDEVS

Parental  MTDLCLVPQVANAERFKVDLTPYPTISRINK-TLLAL-EAFQLSHPCRQPDTPPELRA
          M.DLCLVPQVA.A..FKVDLTPYPT...IN..TLLAL.EAFQLSHPCRQPD..PELRA
Retrocopy MADLCLVPQVAKAKSFKVDLTPYPTTGLINR<TLLAL>EAFQLSHPCRQPDKCPELRA

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	10.89 RPM
SRP012922_cerebellum	0.00 RPM	3.30 RPM
SRP012922_heart	0.00 RPM	6.50 RPM
SRP012922_kidney	0.00 RPM	52.57 RPM
SRP012922_liver	0.46 RPM	150.63 RPM
SRP012922_lung	0.31 RPM	7.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	12.81 RPM
SRP012922_spleen	0.00 RPM	9.50 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_116 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000017287	1 retrocopy	retro_dnov_116 ,
Monodelphis domestica	ENSMODG00000005427	1 retrocopy	retro_mdom_1030,
Xenopus tropicalis	ENSXETG00000011079	1 retrocopy	retro_xtro_38,