RetrogeneDB ID: retro_dnov_150

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_212:208397..209020(-)
• Located in intron of: ENSDNOG00000007549

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUPT3H
• Ensembl ID: ENSDNOG00000011043
• Aliases: None
• Description: suppressor of Ty 3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:11466]

Sequence

>retro_dnov_150
CTCAATCTGTTACAGCAAGCTGCTGAAGTTTCTCAGCTACGTGGAGCAAGAGTAATTTCTGCTGAAGATCTTCTGTTTTT
GATGCGCAAAGATAAGAAAAACTTAGAAGACTGCTAAAATACATGTTTTTCCGAGATTACAAATCAAAGATTGTTAAAGG
GATAGATGAGGATGATCTTCTGGAAGACAAATTGAGTGGCAGCAGTAACACAAAAAAAAGACAAAAAATTGCTCAAGACT
TCCTCAACTCTATTGACCAGACAGGAGAACTCTTGGCAATGTTTGAAGATGATGAAATTGATGAAGTTAAACAACAGAGA
ATGGAGAGAGCAGAAAGACAAACTCAAATGATGGATTCAGCACAATATGCAGAATTTTGTGAAAGTTGACAATTAAGTTT
TTCTAAAAAAGCCTCCAAATTTCAAGACTGGTTGGACTGCAACAGTATGGAGATAAAACCTAATGCTGTCGCTATGGAAA
TTTTAGCATACTTAGCGTATGAAACTGTGGCACAGTTAGTGGATCTGGCTCTTCTTGTGAGGCAGGACATGGTAACCAAG
GCAGGGGATCCCTTCGGCCATGTCATTTCTGCAACCTTCATTCAGTATCACAACTCTGCTGAA

Alignment

ORF - retro_dnov_150 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.3 %
• Parental protein coverage: 66.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  INLLQQAAEVSQLRGARVISAEDLLFLMRKDKK-KLRRLLKYMFFRDYKSKIVKGIDEDDLLEDKLSGSS
          .NLLQQAAEVSQLRGARVISAEDLLFLMRKDKK.KLRRLLKYMFFRDYKSKIVKGIDEDDLLEDKLSGSS
Retrocopy LNLLQQAAEVSQLRGARVISAEDLLFLMRKDKK<KLRRLLKYMFFRDYKSKIVKGIDEDDLLEDKLSGSS

Parental  NTNKRQKIAQDFLNSIDQTGELLAMFEDDEIDEVKQERMERAERQTRMMDSAQYAEFCESRQLSFSKKAS
          N.......AQDFLNSIDQTGELLAMFEDDEIDEVKQ.RMERAERQT.MMDSAQYAEFCES.QLSFSKKAS
Retrocopy NXXXXXXXAQDFLNSIDQTGELLAMFEDDEIDEVKQQRMERAERQTQMMDSAQYAEFCES*QLSFSKKAS

Parental  KFRDWLDCNSMEIKPNAVAMEILAYLAYETVAQLVDLALLVRQDMVTKAGDPFSHVISATFIQYHNSAE
          KF.DWLDCNSMEIKPNAVAMEILAYLAYETVAQLVDLALLVRQDMVTKAGDPF.HVISATFIQYHNSAE
Retrocopy KFQDWLDCNSMEIKPNAVAMEILAYLAYETVAQLVDLALLVRQDMVTKAGDPFGHVISATFIQYHNSAE

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	1.36 RPM	5.64 RPM
SRP012922_cerebellum	0.41 RPM	5.09 RPM
SRP012922_heart	0.70 RPM	0.93 RPM
SRP012922_kidney	0.55 RPM	6.57 RPM
SRP012922_liver	0.15 RPM	0.93 RPM
SRP012922_lung	0.61 RPM	5.04 RPM
SRP012922_quadricep_muscle	0.35 RPM	3.98 RPM
SRP012922_spleen	1.83 RPM	6.87 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_150 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000024037	1 retrocopy	retro_cpor_1320,
Dasypus novemcinctus	ENSDNOG00000011043	1 retrocopy	retro_dnov_150 ,
Echinops telfairi	ENSETEG00000004704	1 retrocopy	retro_etel_1029,
Myotis lucifugus	ENSMLUG00000016339	1 retrocopy	retro_mluc_2262,
Oryctolagus cuniculus	ENSOCUG00000014574	1 retrocopy	retro_ocun_1724,