RetrogeneDB ID: retro_dnov_175

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2332:453193..453813(-)
• Located in intron of: ENSDNOG00000016335

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPPL3
• Ensembl ID: ENSDNOG00000016589
• Aliases: None
• Description: signal peptide peptidase like 3 [Source:HGNC Symbol;Acc:30424]

Sequence

>retro_dnov_175
CTCTCTGTCACTATGATCGCCTTTGTCTGCCTGCCAAGCCTCAAGGTCTCCTGCCTGCTTCTCTCAGGACTTCTCATCTA
TGATGTCTTTGGGTGTTTTTCTCAGCCTTCATCTTCAATAGCAACATCATGGTGAAGTTTGTCCTGCAGTGGGCTGACAA
TCCCCTTGATGGTCTATCCCGGAAGCTCCACCTGGGGCCCAATGTTGGGCACGATGTTCCTCACCTGACTCTGCCAGGAA
AACTGGTCTTGCCAAGCTCCACAGGCAGTCACTGCTCTATGCTGGGCAGTGGAGACATTGTGACGCCCAGTCTCCTGTTG
TGCTTTGTCCTTCCTTATGACAACTACAAAAAACAAGCCAGCGGTGACTCCTGTGGTGCCTCTGGACTCGCCAACATCTC
TGGGCATGTGAAGAAGGTCTCCTACTTCCACCACACCCTCACGGGATATTTTGTAGGTCTGCTAACTGTGGCATCCCACA
CTCACTGAGCAGCCCAGACTGCCCTTATCTATTTGGTGCCATTTACCTTATTGCCACTCCTCATGATGCCCTATTTAAAG
GGTGACCTAGAGCAGATGTGGTCCAAACCATTCTACTCCAAGTCCAGCAGCTCCCATTTC

Alignment

ORF - retro_dnov_175 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.71 %
• Parental protein coverage: 54.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LCVAMIAFVRLPSLKVSCLLLSGLLIYDVF-WVFFSAYIFNSNVMVKVATQPADNPLDVLSRKLHLGPNV
          L.V.MIAFV.LPSLKVSCLLLSGLLIYDVF.WVFFSA.IFNSN.MVK...Q.ADNPLD.LSRKLHLGPNV
Retrocopy LSVTMIAFVCLPSLKVSCLLLSGLLIYDVF<WVFFSAFIFNSNIMVKFVLQWADNPLDGLSRKLHLGPNV

Parental  GRDVPRLSLPGKLVFPSSTGSHFSMLGIGDIVMPGLLLCFVLRYDNYKKQASGDSCGASGPANISGRMQK
          G.DVP.L.LPGKLV.PSSTGSH.SMLG.GDIV.P.LLLCFVL.YDNYKKQASGDSCGASG.ANISG...K
Retrocopy GHDVPHLTLPGKLVLPSSTGSHCSMLGSGDIVTPSLLLCFVLPYDNYKKQASGDSCGASGLANISGHVKK

Parental  VSYFHCTLIGYFVGLLKSTVASRIHRAAQPXXXXXXXXXXXPLLTMAYL-GDLRRMWSEPFHSKSSSSRF
          VSYFH.TL.GYFVGLL..TVAS..H.AAQ............PLL.M.YL.GDL..MWS.PF.SKSSSS.F
Retrocopy VSYFHHTLTGYFVGLL--TVASHTH*AAQTALIYLVPFTLLPLLMMPYLKGDLEQMWSKPFYSKSSSSHF

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	19.84 RPM
SRP012922_cerebellum	0.00 RPM	14.43 RPM
SRP012922_heart	0.00 RPM	5.34 RPM
SRP012922_kidney	0.00 RPM	9.58 RPM
SRP012922_liver	0.00 RPM	5.42 RPM
SRP012922_lung	0.00 RPM	13.75 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.33 RPM
SRP012922_spleen	0.00 RPM	19.00 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_175 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016589	1 retrocopy	retro_dnov_175 ,
Homo sapiens	ENSG00000157837	1 retrocopy	retro_hsap_1898,
Gorilla gorilla	ENSGGOG00000016245	1 retrocopy	retro_ggor_1392,
Myotis lucifugus	ENSMLUG00000012754	1 retrocopy	retro_mluc_672,
Macaca mulatta	ENSMMUG00000020650	1 retrocopy	retro_mmul_1359,
Pongo abelii	ENSPPYG00000005041	2 retrocopies	retro_pabe_1578, retro_pabe_1579,
Pan troglodytes	ENSPTRG00000005548	1 retrocopy	retro_ptro_1275,
Rattus norvegicus	ENSRNOG00000001178	1 retrocopy	retro_rnor_2157,
Sarcophilus harrisii	ENSSHAG00000015326	1 retrocopy	retro_shar_660,