RetrogeneDB ID: retro_dnov_410

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_4470:161357..161651(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIPIN
• Ensembl ID: ENSDNOG00000003177
• Aliases: None
• Description: TIMELESS interacting protein [Source:HGNC Symbol;Acc:30750]

Sequence

>retro_dnov_410
AGAGCAATTAAAAGGAATATAACCAATTTGGATGCTCAGAGATTAATTTCAGAGAGAGAGTTTCCAATATTAAGGCATGT
GTTTGACACAGCAAAATTCAAAGGTGGCGTCATGAGGCTGACAACTTAAAGATACTGATAAGACACATAGAGCCCTGGGC
ACATAGACTATTCCCTAAATTGTAATTTGAGGACTTTATTAACCACCCAGGAAACAAAAAGGAAGTTCAGACCTGTTTAA
AATGAATTCAACTTGGATCTTCCTGTTTTGCATGAACATTTTATTAGCAATAAT

Alignment

ORF - retro_dnov_410 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 63.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RTVKRNIPKLDAQRLISERGLPALRHVFDKAKFKGR-GHEAEDLKTLIRHMEHWAHRLFPKLQFEDFINR
          R..KRNI..LDAQRLISER..P.LRHVFD.AKFKG...HEA..LK.LIRH.E.WAHRLFPKL.FEDFIN.
Retrocopy RAIKRNITNLDAQRLISEREFPILRHVFDTAKFKGG<RHEADNLKILIRHIEPWAHRLFPKL*FEDFIN-

Parental  VEYLGNKKEVQTCLKRIR-LDLPVLHDDFISNN
          ....GNKKEVQTCLK.I..LDLPVLH..FISNN
Retrocopy --HPGNKKEVQTCLK*IQ>LDLPVLHEHFISNN

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	2.92 RPM
SRP012922_cerebellum	0.00 RPM	8.25 RPM
SRP012922_heart	0.00 RPM	3.94 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.00 RPM	2.17 RPM
SRP012922_lung	0.00 RPM	5.96 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.38 RPM
SRP012922_spleen	0.00 RPM	7.33 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_410 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 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004860	1 retrocopy	retro_chof_223,
Dasypus novemcinctus	ENSDNOG00000003177	3 retrocopies	retro_dnov_1334, retro_dnov_1481, retro_dnov_410 ,
Homo sapiens	ENSG00000075131	1 retrocopy	retro_hsap_4837,
Gorilla gorilla	ENSGGOG00000000061	3 retrocopies	retro_ggor_1268, retro_ggor_2907, retro_ggor_3016,
Loxodonta africana	ENSLAFG00000026016	1 retrocopy	retro_lafr_1104,
Microcebus murinus	ENSMICG00000004386	2 retrocopies	retro_mmur_155, retro_mmur_255,
Macaca mulatta	ENSMMUG00000003695	1 retrocopy	retro_mmul_1582,
Nomascus leucogenys	ENSNLEG00000012909	1 retrocopy	retro_nleu_1336,
Pan troglodytes	ENSPTRG00000007192	2 retrocopies	retro_ptro_1145, retro_ptro_3220,
Rattus norvegicus	ENSRNOG00000043068	1 retrocopy	retro_rnor_364,