RetrogeneDB ID: retro_dnov_1218

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_164967:179..587(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLT1D1
• Ensembl ID: ENSDNOG00000017272
• Aliases: None
• Description: glycosyltransferase 1 domain containing 1 [Source:HGNC Symbol;Acc:26483]

Sequence

>retro_dnov_1218
GTTAATTCTGTGTGTGTAAGGGAGTAAACGCCAAAGTGAGAAGGAAGCTGGGGGGTGCCTGATAGCAGAGATGTCTCGGG
AAGACTTCCATGCTGTGGTGAAAAATTGCTTTGTGGTCATGAGTAGTTCCATTTCTGTAGGCTTGTCAAGTGCAATTCTG
GAGGCAATGAATTTGGAATTTCCAGTGTTGGCGAGGATTACTCCTGGAAATGCTGCTATGGTGAGACATGAGGCAACGGG
ATTATTGTTTTCAGATCCTCAGGCATTTGTTCAGCTGGCAAGGAGACTGCTCATTGATCCTGCATTAGAGAAATAGATTG
TGGCCAGTGGAAGGGAGTATGTGAGCAGGCATATTCCTGATGCTCTGAAGGAGACATCTATGGAAACTTTGTCTGGAGAC
TTGAAGGG

Alignment

ORF - retro_dnov_1218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.57 %
• Parental protein coverage: 56.38 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VDPVFTRE-VKAKVGRS-AGVRLRAEMPRGDLHAAVKSCFAVVNSSVSEGMSAAILEAMDLEVPVLARNI
          V..V..RE.V.AKV.R..AG..L.AEM.R.D.HA.VK.CF.V..SS.S.G.S.AILEAM.LE.PVLAR..
Retrocopy VNSVCVRE<VNAKVRRK<AGGCLIAEMSREDFHAVVKNCFVVMSSSISVGLSSAILEAMNLEFPVLARIT

Parental  PGNAAVVRHGATGLLFSDPQEFVRLAKRLLRDPALERRIVAGGRAYVGAH-HSWRSERDTYGRLVQSLAG
          PGNAA.VRH.ATGLLFSDPQ.FV.LA.RLL.DPALE..IVA.GR.YV..H..S..SE.D.YG..V..L.G
Retrocopy PGNAAMVRHEATGLLFSDPQAFVQLARRLLIDPALEK*IVASGREYVSRH<YS*CSEGDIYGNFVWRLEG

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	13.61 RPM
SRP012922_cerebellum	0.00 RPM	2.20 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	8.20 RPM
SRP012922_lung	0.00 RPM	2.14 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	1.49 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_1218 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000025870	1 retrocopy	retro_acar_76,
Dasypus novemcinctus	ENSDNOG00000017272	2 retrocopies	retro_dnov_1218 , retro_dnov_2540,