RetrogeneDB ID: retro_dnov_1114

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_149415:1460..1875(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GCA
• Ensembl ID: ENSDNOG00000012124
• Aliases: None
• Description: grancalcin, EF-hand calcium binding protein [Source:HGNC Symbol;Acc:15990]

Sequence

>retro_dnov_1114
GATCCACTCTATGGTTACTTTCCTGCTGTAGCTGGGCAGGATGGGCAAATAGACACTGATGAATTGCAGAGTTGTCTCAC
ACAGTCACACATTGCCGGAGGATATAAACCTTTTAACCTGGAGACTTGTTGTCTTATGGTTTCAATACCGGATAGAGACA
TGCCAGGAACAATGGGTTTCAAATGAATTTAAAGAACTCTGGGCTGTACTGAATGCCTGGAGGCAACACTTCATCAGTTT
TGACAGTGATAGAAATGGAACAGTGGCTCCTAAAGAATTGCAGAAGGCCTGGACAACAAGGGGATTTAGGATGAGTCCTC
AGGCTGTGAATTCTCTTGCCAAATGGTTCAGCACCAATGGAAAAATTACCTTTGATGACTCCATTGCCTGCTGTGTCAAA
CTGAGGGCCCTCACA

Alignment

ORF - retro_dnov_1114 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 75.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DSMWTYFNAVAGQDGEVDAEELQRCLTQSGISGTYSPFSLETCRIMIALLDRDYTGKMGF-NEFKELWAA
          D....YF.AVAGQDG..D..ELQ.CLTQS.I.G.Y.PF.LETC..M....DRD..G.MGF.NEFKELWA.
Retrocopy DPLYGYFPAVAGQDGQIDTDELQSCLTQSHIAGGYKPFNLETCCLMVSIPDRDMPGTMGF>NEFKELWAV

Parental  LNAWKQNFMTIDRDQSGTVEHHELSQAIAAMGYRLSPQTLTAIVKRYSKNGRIFFDDYVACCVKLRALT
          LNAW.Q.F...D.D..GTV...EL..A....G.R.SPQ......K..S.NG.I.FDD..ACCVKLRALT
Retrocopy LNAWRQHFISFDSDRNGTVAPKELQKAWTTRGFRMSPQAVNSLAKWFSTNGKITFDDSIACCVKLRALT

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	47.06 RPM	5.45 RPM
SRP012922_cerebellum	8.11 RPM	0.96 RPM
SRP012922_heart	3.02 RPM	0.70 RPM
SRP012922_kidney	4.11 RPM	2.74 RPM
SRP012922_liver	2.63 RPM	1.55 RPM
SRP012922_lung	9.32 RPM	2.75 RPM
SRP012922_quadricep_muscle	1.21 RPM	1.21 RPM
SRP012922_spleen	9.84 RPM	1.72 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_1114 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006229	2 retrocopies	retro_chof_2009, retro_chof_34,
Dasypus novemcinctus	ENSDNOG00000012124	1 retrocopy	retro_dnov_1114 ,
Oryctolagus cuniculus	ENSOCUG00000002868	2 retrocopies	retro_ocun_1786, retro_ocun_741,