RetrogeneDB ID: retro_dnov_1575

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_238691:11..705(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000015893
• Aliases: None
• Description: None

Sequence

>retro_dnov_1575
CCCGAGCTGCAGGAGGCGCGGCCGCGCAGCCAGAGCACAGGCCGCAGGAGCTGCGGCGCCTCTGCCAGAACCCGCCACCG
CCGCGGCCCGGCTCCACAAAGCCCGAGCGTGTCACAGCCAGGACTTCCTCTCCAGGTCCCCTTCCAAAATGCAGCCACCG
CCGTCACCAGTCTCTGCAAAGAAAGCGTGGATACCCGTCAGCGAAGTTTTGATATTGGAATTCAGATTGGCTATCAGCGT
CGCAGTAAGGATGTGTTGGCTTGGGTTAAAAAACGCAGAAGAACTGTACGTAGAGAAGATTTGATCAGCTTCCTGTGTGG
AAAAGCTCCTCCACCTGGGAACTCTAGAGCTCCCCCAGGACTGACTGCAGTGCCCCCTAACGGAGCACTTCAGCGGAAGC
TAGCTCATCTGTAGAGGCTGGTTTGCAACCCTTCCGGGAAGCCGCGGCTCTGCACGGGCTTAGTGGTGCGATGGCCAGCA
TAGCGCGCTCCAGTCCCCAGGCTCTCCTCCACGGGTAAGCAGCGGATCGAATGCTCGTCGTCGGAGAAGTGGACTCCACG
ATGTCGATGTGAACACTTTCACATCAGAAGAAACGGCACTCCACTTGGACAATGGTGGAGCTAGAAAGCGTACCTCAGCC
CAATGGGGCGATGTCTTTACAGACTCAACAACCCATAAACGCAGCAGAATGATC

Alignment

ORF - retro_dnov_1575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 86.84 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  PELQEA-AAAQPEHKPRELRRLCQNP-ATAAARLHKDRVCQ-QPGLSLWVPFQNAATAVTNLYKESVDTH
          PELQEA.AAAQPEH.P.ELRRLCQNP.ATAAARLHK.R.C..QPGL.L.VPFQNAATAVT.L.KESVDT.
Retrocopy PELQEA<AAAQPEHRPQELRRLCQNP<ATAAARLHKARACH<QPGLPLQVPFQNAATAVTSLCKESVDTR

Parental  QRSFDIGIQIGYQRRNKDVLAWV-KRRRTIRREDLISFLCGKAPPPRNSRAPPRLTVESPN-RATSTETS
          QRSFDIGIQIGYQRR.KDVLAWV.KRRRT.RREDLISFLCGKAPPP.NSRAPP.LT...PN.R.TS.E.S
Retrocopy QRSFDIGIQIGYQRRSKDVLAWVKKRRRTVRREDLISFLCGKAPPPGNSRAPPGLTAVPPN<RSTSAEAS

Parental  SSVETDVQPFPETVALHGLSGAMASIARSSPGS-PPRVSSGSNARSRR-SGLHDVDVNTFTSEEMALHLD
          SSVE...QPF.E..ALHGLSGAMASIARSSP....P...S......RR.SGLHDVDVNTFTSEE.ALHLD
Retrocopy SSVEAGLQPFREAAALHGLSGAMASIARSSPQA<SPPRVSSGSNARRRRSGLHDVDVNTFTSEETALHLD

Parental  NGGARKRTSAQWGDVFTDSTTHKRNRMI
          NGGARKRTSAQWGDVFTDSTTHKR.RMI
Retrocopy NGGARKRTSAQWGDVFTDSTTHKRSRMI

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	7.78 RPM
SRP012922_cerebellum	0.14 RPM	5.36 RPM
SRP012922_heart	0.00 RPM	5.34 RPM
SRP012922_kidney	0.55 RPM	3.56 RPM
SRP012922_liver	0.00 RPM	4.64 RPM
SRP012922_lung	0.15 RPM	10.23 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.27 RPM
SRP012922_spleen	0.23 RPM	8.70 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_1575 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 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575 , retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,