RetrogeneDB ID: retro_dnov_2525

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_82850:908..1733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP5A1
• Ensembl ID: ENSDNOG00000006331
• Aliases: None
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1, cardiac muscle [Source:HGNC Symbol;Acc:823]

Sequence

>retro_dnov_2525
CCAATTGGTCGTGGTCAGCATGAGCTTATTATTGGTGACTGACAGACTGGCAAAACTTCAATTGCTATTGACACAATCAT
TAACCAGAAACATTTCAATGATGGAACTGATGAAAAGAAGCTATACAGTATATATGTTGCTATTGGTCAAAAGAGATCCA
CTGTTGCCCAGTTAGTGAAGAGACTTACAGATGCAGATGCCATGAAGTACACCATTGTGGTTTCTGCTATGACTTCTGAT
GCTGCCCCACTTCAGTACCTGGCTCCTTATTCTGGCTGTTCCATGGGAGAATATTTTGGGGATAACAGCAAACACGCTTT
GATTATCTATGATGACTTATCCAAACAAGCTGTTGCTTACCGTCAGATGTCTCTATTGCTCCACCGACCCCCTGGTTGTG
AGGCTTATCCTGGTGATGTGTTCTGCCTACACCCCCACCTGCTAGAGAGAGCAGCCAAGATGAATGATTCTTTTGGTGGT
GGTTCCTTGACTGCTTTACCAGTCATAGAAACACAAGCTGGTGATGTGTCTGCTTACATTCCAACAAATGTCATCTCCAT
CACTGATGGACAGATCTTCCTGGAAACAGAATTGTTCTCCAAAGGTATTCGCCCAGCCATTAATGTTGGTTTGTCTGTGT
CTCGTGTCGGGTCTGCTGCCCAAACCAGAGCCGTGAAACAGGTGGCAGGTACCATGAAGCTGGAATTAGCTCAGTATCGT
GAGGTTGCTGCTTTTGCCCAGTTTGGTTCTGACCTTGATGCTGCTACACAGCAACTCTTGAGTCATGGTGTGCATCTGAC
TGAGTTGCTGAAAGAGGGACAGTAT

Alignment

ORF - retro_dnov_2525 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.12 %
• Parental protein coverage: 58.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PIGRGQRELIIGDRQTGKTSIAIDTIINQKRFNDGTDEKKKLYCIYVAIGQKRSTVAQLVKRLTDADAMK
          PIGRGQ.ELIIGD.QTGKTSIAIDTIINQK.FNDGTDEKK.LY.IYVAIGQKRSTVAQLVKRLTDADAMK
Retrocopy PIGRGQHELIIGD*QTGKTSIAIDTIINQKHFNDGTDEKK-LYSIYVAIGQKRSTVAQLVKRLTDADAMK

Parental  YTIVVSATASDAAPLQYLAPYSGCSMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGD
          YTIVVSA..SDAAPLQYLAPYSGCSMGEYF.DN.KHALIIYDDLSKQAVAYRQMSLLL.RPPG.EAYPGD
Retrocopy YTIVVSAMTSDAAPLQYLAPYSGCSMGEYFGDNSKHALIIYDDLSKQAVAYRQMSLLLHRPPGCEAYPGD

Parental  VFYLHSRLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINV
          VF.LH..LLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELF.KGIRPAINV
Retrocopy VFCLHPHLLERAAKMNDSFGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFSKGIRPAINV

Parental  GLSVSRVGSAAQTRAMKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSRGVRLTELLKQGQY
          GLSVSRVGSAAQTRA.KQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLS.GV.LTELLK.GQY
Retrocopy GLSVSRVGSAAQTRAVKQVAGTMKLELAQYREVAAFAQFGSDLDAATQQLLSHGVHLTELLKEGQY

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	902.33 RPM
SRP012922_cerebellum	0.00 RPM	306.97 RPM
SRP012922_heart	0.00 RPM	720.46 RPM
SRP012922_kidney	0.00 RPM	585.65 RPM
SRP012922_liver	0.00 RPM	333.14 RPM
SRP012922_lung	0.00 RPM	126.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	842.57 RPM
SRP012922_spleen	0.00 RPM	204.31 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_2525 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 18 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002507	2 retrocopies	retro_btau_1380, retro_btau_1426,
Canis familiaris	ENSCAFG00000017648	2 retrocopies	retro_cfam_1483, retro_cfam_516,
Dasypus novemcinctus	ENSDNOG00000006331	2 retrocopies	retro_dnov_1740, retro_dnov_2525 ,
Equus caballus	ENSECAG00000021561	1 retrocopy	retro_ecab_788,
Homo sapiens	ENSG00000152234	1 retrocopy	retro_hsap_1702,
Gorilla gorilla	ENSGGOG00000016560	1 retrocopy	retro_ggor_1275,
Meleagris gallopavo	ENSMGAG00000009963	1 retrocopy	retro_mgal_14,
Microcebus murinus	ENSMICG00000017500	1 retrocopy	retro_mmur_1210,
Myotis lucifugus	ENSMLUG00000009856	1 retrocopy	retro_mluc_1198,
Macaca mulatta	ENSMMUG00000003570	1 retrocopy	retro_mmul_1208,
Mustela putorius furo	ENSMPUG00000000923	1 retrocopy	retro_mputfur_601,
Nomascus leucogenys	ENSNLEG00000010973	1 retrocopy	retro_nleu_1334,
Oryctolagus cuniculus	ENSOCUG00000003967	1 retrocopy	retro_ocun_1235,
Pongo abelii	ENSPPYG00000009130	1 retrocopy	retro_pabe_1363,
Pan troglodytes	ENSPTRG00000009991	1 retrocopy	retro_ptro_1151,
Sarcophilus harrisii	ENSSHAG00000017177	1 retrocopy	retro_shar_109,
Tarsius syrichta	ENSTSYG00000007804	1 retrocopy	retro_tsyr_1186,
Tursiops truncatus	ENSTTRG00000005118	1 retrocopy	retro_ttru_159,