RetrogeneDB ID: retro_dnov_2494

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_80066:3428..3943(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTDNEP1
• Ensembl ID: ENSDNOG00000013673
• Aliases: None
• Description: CTD nuclear envelope phosphatase 1 [Source:HGNC Symbol;Acc:19085]

Sequence

>retro_dnov_2494
CTTACCCATTCCCACCGCGATGGGGTCCTGAGGCCCACGGTTAGCCTGGAACACCTCCTGTCTTCATTCTCGAGGTGGTA
CTAGACAAGCACCCTGTCCGGTTTTTTGTACATAGGAGGCCCCATGTGGATTTCCTCTTAAAAGTGGTGAGCCAGTAGTA
CAAGCTGGTGGTGTTCACAGCAAGCATGAGATTTATGGCTCTGCTGTGACAAACTGGACAATAAATAGCACAAGCATTGT
CAAGAGAAGATACTATAGACAGCAGTGCACTTTGGAGTTGGGCAGTTACATCAAGGACCCCTCTGTGGTCCACAGTGACC
TCTCTAGAATTGTGATCCTGGATAGCTCCCAGGGGCTTAGAGGAGCCATCCAGACAACACCACCCCTATCAAGTCCTGGT
TCAGTTACCCAGTGACACAGCCCTTCTCAACCTGCTCCCAATGCTAGATGCCCTCAGGTTCACTGCTGATGTTCCTTCCG
TGCTGAGCCAAAACCTTCACCGACACAGGCCCTGG

Alignment

ORF - retro_dnov_2494 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.79 %
• Parental protein coverage: 70.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LIHSHHDGVLRPTVR-PGTPPDFILKVVIDKHPVRFFVHKRPHVDFFLEVVSQWYELVVFTASM-EIYDS
          L.HSH.DGVLRPTV..PGTPP.FIL.VV.DKHPVRFFVH.RPHVDF.L.VVSQ.Y.LVVFTASM.EIY.S
Retrocopy LTHSHRDGVLRPTVS<PGTPPVFILEVVLDKHPVRFFVHRRPHVDFLLKVVSQ*YKLVVFTASM<EIYGS

Parental  AVTDKLDNSRSILKRRYYRQHCTLELGSYIKDLSVVHSDLSSIVILDNS-PGAYRSHPDNAIPIKSWFSD
          AVT....NS.SI.KRRYYRQ.CTLELGSYIKD.SVVHSDLS.IVILD.S.PGA.RSHPDN..PIKSWFS.
Retrocopy AVTNWTINSTSIVKRRYYRQQCTLELGSYIKDPSVVHSDLSRIVILDSS<PGA*RSHPDNTTPIKSWFSY

Parental  -PSDTALLNLLPMLDALRFTADVRSVLSRNLHQHRLW
          .PSDTALLNLLPMLDALRFTADV.SVLS.NLH.HR.W
Retrocopy <PSDTALLNLLPMLDALRFTADVPSVLSQNLHRHRPW

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	41.42 RPM
SRP012922_cerebellum	0.00 RPM	42.20 RPM
SRP012922_heart	0.00 RPM	15.78 RPM
SRP012922_kidney	0.00 RPM	51.75 RPM
SRP012922_liver	0.00 RPM	13.78 RPM
SRP012922_lung	0.00 RPM	51.16 RPM
SRP012922_quadricep_muscle	0.00 RPM	90.52 RPM
SRP012922_spleen	0.00 RPM	53.80 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_2494 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019443	1 retrocopy	retro_btau_915,
Dasypus novemcinctus	ENSDNOG00000013673	2 retrocopies	retro_dnov_1802, retro_dnov_2494 ,
Echinops telfairi	ENSETEG00000004654	1 retrocopy	retro_etel_125,
Homo sapiens	ENSG00000175826	2 retrocopies	retro_hsap_2687, retro_hsap_3188,
Gorilla gorilla	ENSGGOG00000013777	2 retrocopies	retro_ggor_1338, retro_ggor_1874,
Macaca mulatta	ENSMMUG00000010547	1 retrocopy	retro_mmul_2011,
Mus musculus	ENSMUSG00000018559	1 retrocopy	retro_mmus_1023,
Otolemur garnettii	ENSOGAG00000004389	1 retrocopy	retro_ogar_1001,
Pongo abelii	ENSPPYG00000007902	2 retrocopies	retro_pabe_2294, retro_pabe_2645,
Pan troglodytes	ENSPTRG00000008668	2 retrocopies	retro_ptro_1814, retro_ptro_2256,
Drosophila melanogaster	FBgn0029067	1 retrocopy	retro_dmel_18,