RetrogeneDB ID: retro_dnov_546

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_598:233093..233762(+)
• Located in intron of: ENSDNOG00000007641

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPOPL
• Ensembl ID: ENSDNOG00000014763
• Aliases: None
• Description: speckle-type POZ protein-like [Source:HGNC Symbol;Acc:27934]

Sequence

>retro_dnov_546
TCAATAAATAACTTTAGCCTTTACCAGACGGAAGTGGGTGAAGTCATTAAAAGTTCAACCTTTTCACCAGGAGCCAATAA
TAAACTGAAATGGTGTTTGCAAGTAAACCCAAAAGTGCTTGATGAAGAAAGAAAAGATTATCTGTCATTTCACCTGTTAC
TGGTCAGCTGTCCAAAGGGTGAAGTTTGGGCAAAATTTAAATTCCCTATCCTGAATGCCAAGGAAGAAGAAACCAAAGCA
ATGGAGTGTCAACAGGCATACAGGTTTGTGCAAGGCAAGAACTGGGGACTCAAAACATTCATCTGTAGAGATTTTCTCTT
GGAAGAGGCCAGAGGCTTCTCCCTGATGGCAAGCTTACTCTGTTCTGTAAGGTGAGTGTGGGCAAGACTCTGTCAACATT
TCTCACCAGAATACTATGAATAAGGTGAAAGTCCCTGAATGCCGGTTGGCAGATGCCTTAGGAGGACTGTGGGAGAATTC
CCTGTTCACAGACATCTATTCGTATGTTGCTGGCTGGGAATTCCAGGCTCACAAAGCTATCTTAGCAGTTCCTTCTCCAG
ATTTAGTGCCTTGTTTGAACTTGAAATGGAGAAGAGCAAAAAAATTGGGTTGAAATCAATGATGTGGAGCCTGAAGTTTT
TAAGGATATGATGTGGCTTCATTTGCACA

Alignment

ORF - retro_dnov_546 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.43 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  TINNFSFCREEMGEVLKSSTFSSGPNDKMKWCLRVNPKGLDDESKDYLSLYLLLVSCPKSEVRAKFKFSL
          .INNFS....E.GEV.KSSTFS.G.N.K.KWCL.VNPK.LD.E.KDYLS..LLLVSCPK.EV.AKFKF..
Retrocopy SINNFSLYQTEVGEVIKSSTFSPGANNKLKWCLQVNPKVLDEERKDYLSFHLLLVSCPKGEVWAKFKFPI

Parental  LNAKREETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANG-LLPDDKLTLFCEVSV-VQDSVNISGHT
          LNAK.EETKAME.Q.AYRFVQGK.WG.K.FI.RDFLL.EA.G.LLPD.KLTLFC.VSV..QDSVNIS...
Retrocopy LNAKEEETKAMECQQAYRFVQGKNWGLKTFICRDFLLEEARG<LLPDGKLTLFCKVSV<GQDSVNISHQN

Parental  NTNTLKVPECRLAEDLGNLWENTRFTDCSFFVRGQEFKAHKSVLAARSP-VFNAMFEHEMEESK-KNQVE
          ..N..KVPECRLA..LG.LWEN..FTD....V.G.EF.AHK..LA..SP..F.A.FE.EME.SK.KN.VE
Retrocopy TMNKVKVPECRLADALGGLWENSLFTDIYSYVAGWEFQAHKAILAVPSP<RFSALFELEMEKSK<KNWVE

Parental  INDVDPEVFKEMM-GFIYT
          INDV.PEVFK.MM.GFI.T
Retrocopy INDVEPEVFKDMM>GFICT

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	15.17 RPM
SRP012922_cerebellum	0.00 RPM	7.56 RPM
SRP012922_heart	0.00 RPM	1.16 RPM
SRP012922_kidney	0.00 RPM	5.75 RPM
SRP012922_liver	0.00 RPM	5.26 RPM
SRP012922_lung	0.00 RPM	7.79 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.73 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_546 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014763	1 retrocopy	retro_dnov_546 ,
Homo sapiens	ENSG00000144228	2 retrocopies	retro_hsap_2943, retro_hsap_3048,
Gorilla gorilla	ENSGGOG00000016285	1 retrocopy	retro_ggor_2040,
Macaca mulatta	ENSMMUG00000002560	2 retrocopies	retro_mmul_1884, retro_mmul_1885,
Nomascus leucogenys	ENSNLEG00000013800	1 retrocopy	retro_nleu_1629,
Oryctolagus cuniculus	ENSOCUG00000006944	1 retrocopy	retro_ocun_1842,
Pongo abelii	ENSPPYG00000012825	4 retrocopies	retro_pabe_2438, retro_pabe_2439, retro_pabe_2440, retro_pabe_2599,
Pan troglodytes	ENSPTRG00000012504	2 retrocopies	retro_ptro_1991, retro_ptro_2054,