RetrogeneDB ID: retro_dnov_827

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_11150:127715..128473(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000398
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_dnov_827
CCCGAGCACTGGTTCTCCGAGTGGAGGGCAGCGCCTGGCCGAGGCCGCGCAGGCCGAGCAGCTGCCCCCGAGCTGCAGGA
GGCGGCGGCCGCGCAGCCCGAGCACAAGCCGCAGGAGCTGCGGCGCCTCTGCCAGAACCCGGCCACCGCCGCGGCCCGGC
TCCACAAAGCCCGAGCGTGTCACAGCCAGGACTTCCTCTCCAGGTCCCCTTCCAAAATGCAGCCACCGCCGTCACCAGTC
TCTGCAAAGAAAGCGTGGATACCCGTCAGCGAAGTTTTGATATTGGAATTCAGATTGGCTATCAGCGTCGCAGTAAGGAT
GTGTTGGCTTGGGTTAAAAAACGCAGAAGAACTGTAGAGAAGATTTGATCAGCTTCCTGTGTGGAAAAGTTCCTCCACCT
GGGAACTCTAGAGCTCCCCCAGGACTGACTGTAGTGCCCCCTAACGGAGCACTTCAGCGGAAGCTAGCTCATCTGTAGAG
GCTGGTTTGCAGCCCTTCCGGGAAGCCGCGGCTCTGCACGGGCTTAGTGGTGCGATGGCCAGCATAGCGCGCTCCAGTCC
CCAGGCTCTCCTCCACGGGTAAGCAGCGGATCGAATGCTCGTCGTCGGAGAAGTGGACTCCACGATGTCGATGTGAACAC
TTTCACATCAGAAGAAATGGCACTCCACTTGGACAATGGTGGAGCTAGAAAGCGTACCTCAGCCCAATGGGGCGATGTCT
TTACAGACTCAACAACCCATAAACGCAGCAGAATGATC

Alignment

ORF - retro_dnov_827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.13 %
• Parental protein coverage: 94.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PEHWFSEWQRLAEAAQAEQL--PELQEAAAAQPEHKPRELRRLCQNPATAAARLHKDRVCQ-QPGLSLWV
          PEHWFSEW........A.....PELQEAAAAQPEHKP.ELRRLCQNPATAAARLHK.R.C..QPGL.L.V
Retrocopy PEHWFSEWRAAPGRGRAGRAAAPELQEAAAAQPEHKPQELRRLCQNPATAAARLHKARACH<QPGLPLQV

Parental  PFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKRRRTI-RREDLISFLCGKAPPPRNSR
          PFQNAATAVT.L.KESVDT.QRSFDIGIQIGYQRR.KDVLAWVK.RR....REDLISFLCGK.PPP.NSR
Retrocopy PFQNAATAVTSLCKESVDTRQRSFDIGIQIGYQRRSKDVLAWVKKRRRT<CREDLISFLCGKVPPPGNSR

Parental  APPRLTVESPN-RATSTETSSSVETDVQPFPETVALHGLSGAMASIARSSPGS-PPRVSSGSNARSRR-S
          APP.LTV..PN.R.TS.E.SSSVE...QPF.E..ALHGLSGAMASIARSSP....P...S......RR.S
Retrocopy APPGLTVVPPN<RSTSAEASSSVEAGLQPFREAAALHGLSGAMASIARSSPQA<SPPRVSSGSNARRRRS

Parental  GLHDVDVNTFTSEEMALHLDNGGARKRTSAQWGDVFTDSTTHKRNRMI
          GLHDVDVNTFTSEEMALHLDNGGARKRTSAQWGDVFTDSTTHKR.RMI
Retrocopy GLHDVDVNTFTSEEMALHLDNGGARKRTSAQWGDVFTDSTTHKRSRMI

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	0.00 RPM	5.36 RPM
SRP012922_heart	0.00 RPM	5.34 RPM
SRP012922_kidney	0.00 RPM	3.56 RPM
SRP012922_liver	0.00 RPM	4.64 RPM
SRP012922_lung	0.00 RPM	10.23 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.27 RPM
SRP012922_spleen	0.00 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_827 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,