RetrogeneDB ID: retro_dnov_747

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_104147:3531..4150(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DEPTOR
• Ensembl ID: ENSDNOG00000015660
• Aliases: None
• Description: DEP domain containing MTOR-interacting protein [Source:HGNC Symbol;Acc:22953]

Sequence

>retro_dnov_747
TGTGGTGAGCATAAGGAGTTCAAGGATGTCAAACTCTTCTGCTGCTTTATAAAGGATGATAGCATCTTCCCATTGGACAT
TGAGAATAAAGGCCTTCATGAGAAGATAGAGGCTCTATGAGATGATGATAAGCCCTGAAAATGCACTCCTGCAGCCCAGG
GAGGAGAAAAGGTTCAAATATGAGTACACTTTCAAGGCATCTGAATTCATGGACTGGTTGGTTCAAGAAGGTGAGGTCAC
CACAAGGAAAGAGGCAGTGCAGCTTTGCCATTAAAAGGAAAAGGGAAGCTGGAGCATGACATCACACAGTATGTGTCCAA
TAAACACAAATCTTCTTTACCAGTTCAGAATGAACTCCCTTCGGACTCAGAAACTAATGAAGCTGCTCAATGAAAAGTCC
CCCTCTTTCCTGGAAACTCATGATAGTCCTTTCTGCTTCAGAAAGCAAAACCATGACAATCAGAAATCTGCCAGTTTTAT
GTCAGTCAGTCCCAGCTAGGAACTCAAGATTGTGTCTGTGGTGAGGAGGAGCAGCATGGTCAACTGTGGCAGCAATGGCT
ACTTCAGCAGGAGCCCCACACTCAGCTGCAGCTTCCCTGTGCTCTGCAACCTCAAGTCT

Alignment

ORF - retro_dnov_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.67 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CDEHKEFKDVKLFYRFRKDDGTFPLDNE-VKAFMRGQRLYEKLMSPENTLLQPREEEGIKYERTFMASEF
          C.EHKEFKDVKLF..F.KDD..FPLD.E..KAFMR..RLYE...SPEN.LLQPREE...KYE.TF.ASEF
Retrocopy CGEHKEFKDVKLFCCFIKDDSIFPLDIE>IKAFMRR*RLYEMMISPENALLQPREEKRFKYEYTFKASEF

Parental  LDWLVQEGEATTRKEAEQLCHRLMEHGIIQHVSNKHPFLDSNLLYQFRMNFRRRRRLMELLNEKSPSSQE
          .DWLVQEGE.TTRKEA.QLCH...E.G.....S........NLLYQFRMN..R...LM.LLNEKSPS..E
Retrocopy MDWLVQEGEVTTRKEAVQLCH*-KEKGSWSMTSHSMCPINTNLLYQFRMNSLRTQKLMKLLNEKSPSFLE

Parental  THDSPFCLRKQSHDNRKSTSFMSVSPSKEIKIVSVVRRSSMSSCGSSGYFSSSPTLSSSPPVLCNPKS
          THDSPFC.RKQ.HDN.KS.SFMSVSPS.E.KIVSVVRRSSM..CGS.GYFS.SPTLS.S.PVLCN.KS
Retrocopy THDSPFCFRKQNHDNQKSASFMSVSPS*ELKIVSVVRRSSMVNCGSNGYFSRSPTLSCSFPVLCNLKS

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	30.34 RPM
SRP012922_cerebellum	0.00 RPM	4.26 RPM
SRP012922_heart	0.00 RPM	2.55 RPM
SRP012922_kidney	0.00 RPM	2.19 RPM
SRP012922_liver	0.00 RPM	7.74 RPM
SRP012922_lung	0.00 RPM	2.90 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.98 RPM
SRP012922_spleen	0.00 RPM	5.61 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_747 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
Callithrix jacchus	ENSCJAG00000005497	1 retrocopy	retro_cjac_1898,
Dasypus novemcinctus	ENSDNOG00000015660	1 retrocopy	retro_dnov_747 ,
Ictidomys tridecemlineatus	ENSSTOG00000013845	1 retrocopy	retro_itri_669,