RetrogeneDB ID: retro_dnov_1659

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_258211:812..1109(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM47
• Ensembl ID: ENSDNOG00000006509
• Aliases: None
• Description: transmembrane protein 47 [Source:HGNC Symbol;Acc:18515]

Sequence

>retro_dnov_1659
GTCACGACCGTCCACCAGTATTACTGTCCCTGGGGGAGTCCTGCCGGAAACCCGCCAGCTGGACATCTGTCCTGCCAGTC
CACGCTCAGCAGCGATTGGAAGATTGCTATGCTGGCTTTATTCTTGGGCGGTGCTGCCATCATTCTCATTGCCTTCCTGG
TGGGTTTGATTTCCATCTGCGTGGGGTCTCGAAGGCCCTTCTACCGACCTGTTGTTGTCATGATTTTTGCAGCAGTTGTT
TTACAGATATGTCGCCTGGTCCTTTACCCAATGAAGTTCATTGAAACTGTTGGGGTT

Alignment

ORF - retro_dnov_1659 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.58 %
• Parental protein coverage: 55.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VTADHQYY-LSLWESCRKPAS-LDIW-HCESTLSSDWQIATLALLLGGAAIILIAFLVGLISICVGSRRR
          VT..HQYY.LSL.ESCRKPAS.LDI...C.STLSSDW.IA.LAL.LGGAAIILIAFLVGLISICVGSRR.
Retrocopy VTTVHQYY<LSLGESCRKPAS<LDIC<SCQSTLSSDWKIAMLALFLGGAAIILIAFLVGLISICVGSRRP

Parental  FYRPVAVMLFAAVVLQVCSLVLYPIKFIETVSL
          FYRPV.VM.FAAVVLQ.C.LVLYP.KFIETV..
Retrocopy FYRPVVVMIFAAVVLQICRLVLYPMKFIETVGV

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	5.45 RPM
SRP012922_cerebellum	0.00 RPM	11.82 RPM
SRP012922_heart	0.00 RPM	1.39 RPM
SRP012922_kidney	0.00 RPM	1.92 RPM
SRP012922_liver	0.15 RPM	2.32 RPM
SRP012922_lung	0.00 RPM	7.03 RPM
SRP012922_quadricep_muscle	0.00 RPM	7.79 RPM
SRP012922_spleen	0.00 RPM	8.47 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_1659 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006509	1 retrocopy	retro_dnov_1659 ,
Macaca mulatta	ENSMMUG00000004530	1 retrocopy	retro_mmul_1399,
Ictidomys tridecemlineatus	ENSSTOG00000019440	1 retrocopy	retro_itri_1673,