RetrogeneDB ID: retro_dnov_1310

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17984:12716..13149(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPA1
• Ensembl ID: ENSDNOG00000014861
• Aliases: None
• Description: pyrophosphatase (inorganic) 1 [Source:HGNC Symbol;Acc:9226]

Sequence

>retro_dnov_1310
CAAGGAATATCTCCATTGCATGATATTCCAATTTATGCAGATAAGGATGTGTTCCACATGGTAGTTGAAGTACCATGCTG
GCCTAATGCAAAAATGGAGATTGCTACAAAGGACCCTTTAAACCCAATTAAACAAGATGAGAAAAAAAGGAAAACTCCGT
TATGTTGCAAATTTGTTCCCTTATAAAGGATATATCTGGAACTATGGTGCCATCCCTCAGACTTGGGAAGACCCAGGACA
CAATGACAAACATACTGGCTGTTGTGGTGACAATGACCTGATTGATGTGTGTGAAACTGGAGGCAAGGTATGTGCAAGAG
GTGAAATAATTGGGGTGAAAGTTTTGGGCATTTTGGCTATGATTGATGAAGGGGAAACTGACTGGAAAGTCATCGCCATT
AATGTGGAAGATTCTGATGCAGCCAACTATAAT

Alignment

ORF - retro_dnov_1310 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.38 %
• Parental protein coverage: 51.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QYISPFHDIPIYADKXXXXXXXXXXXXXXXXXXIATKDPLNPIKQDV-KKGKLRYVANLFPYKGYIWNYG
          Q.ISP.HDIPIYADK..................IATKDPLNPIKQD..KKGKLRYVANLFPYKGYIWNYG
Retrocopy QGISPLHDIPIYADKDVFHMVVEVPCWPNAKMEIATKDPLNPIKQDE>KKGKLRYVANLFPYKGYIWNYG

Parental  AIPQTWEDPGHNDKHTGCSGDNDPIDVCEIGSKVCARGEIIGVKVLGILAMIDEGETDWKVIAINVEDPD
          AIPQTWEDPGHNDKHTGC.GDND.IDVCE.G.KVCARGEIIGVKVLGILAMIDEGETDWKVIAINVED.D
Retrocopy AIPQTWEDPGHNDKHTGCCGDNDLIDVCETGGKVCARGEIIGVKVLGILAMIDEGETDWKVIAINVEDSD

Parental  AANYN
          AANYN
Retrocopy AANYN

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	29.17 RPM	62.04 RPM
SRP012922_cerebellum	7.15 RPM	11.96 RPM
SRP012922_heart	4.64 RPM	4.64 RPM
SRP012922_kidney	5.20 RPM	4.65 RPM
SRP012922_liver	59.91 RPM	116.41 RPM
SRP012922_lung	12.22 RPM	22.15 RPM
SRP012922_quadricep_muscle	11.60 RPM	14.19 RPM
SRP012922_spleen	5.84 RPM	9.84 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_1310 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000014033	1 retrocopy	retro_cfam_1040,
Dasypus novemcinctus	ENSDNOG00000014861	1 retrocopy	retro_dnov_1310 ,
Equus caballus	ENSECAG00000018686	1 retrocopy	retro_ecab_691,
Loxodonta africana	ENSLAFG00000004048	1 retrocopy	retro_lafr_990,
Nomascus leucogenys	ENSNLEG00000016098	1 retrocopy	retro_nleu_7,
Procavia capensis	ENSPCAG00000006788	1 retrocopy	retro_pcap_247,
Pongo abelii	ENSPPYG00000029405	1 retrocopy	retro_pabe_37,