RetrogeneDB ID: retro_dnov_348

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3883:70893..71331(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000017212
• Aliases: None
• Description: None

Sequence

>retro_dnov_348
CAGCAATGGCAGGCAGCACCTAAAGCAACTTCAAAGCAGAGAGAGATGCTCATGGAAGATACCAGCAGTGAGGAAGGACA
AGAAGAGGTGATGCGCTATTGCAGGAGAAATATTCTGGCAGTGATGAAGATTTCCTAATGGAAGAGGATGACGGTGACTA
CGGCAGTTCAAAAAAGAAAAACAAAAAGACGGTTAAGAAGGCCACACCTGAGAGAAAAGAAAAGAAAATGCCCAAACCCA
GGCTACAGGCCACCATGCTGCCAAGTCCAGTGAAAGGCAAAGGGAAAGTGGGCCATCCACAGCGTCAAAGGAAAAGACTC
CTTTCCCCCAAGAAGAGGATGAACCAGAAGTCCTCCAGAAAAGAAAGCATCTGCAAGCCCTCCACCCGAAAAATCTGGGG
TTGAAGGGTCTGAAGATGAGGCTCAGTCTGGGGAAGAT

Alignment

ORF - retro_dnov_348 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.36 %
• Parental protein coverage: 57.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QQRQAASKAASKQREMLMEDVGSEEEQEEE-DEAPFQEKDSGSDEDFLMEDDDDSDYGSSKKKNKKMVKK
          QQ.QAA.KA.SKQREMLMED..SEE.Q.EE...A..QEK.SGSDEDFLME.DD..DYGS........VKK
Retrocopy QQWQAAPKATSKQREMLMEDTSSEEGQ-EE<GDALLQEKYSGSDEDFLMEEDD-GDYGSXXXXXXXTVKK

Parental  AKPERKEKKMPKPRLKATVTPSPVKGKGKVGRP-TASKASKEKTPSPKEDDDEPE-SPPEKKTSASPPPE
          A.PERKEKKMPKPRL.AT..PSPVKGKGKVG.P.TASK...EKTP.P.E..DEPE.SPPEKK.SASPPPE
Retrocopy ATPERKEKKMPKPRLQATMLPSPVKGKGKVGHP<TASK---EKTPFPQE-EDEPE<SPPEKKASASPPPE

Parental  KSGDEGSEDEAQSGED
          KSG.EGSEDEAQSGED
Retrocopy KSGVEGSEDEAQSGED

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	81.68 RPM
SRP012922_cerebellum	0.00 RPM	105.85 RPM
SRP012922_heart	0.00 RPM	52.67 RPM
SRP012922_kidney	0.00 RPM	145.11 RPM
SRP012922_liver	0.00 RPM	56.66 RPM
SRP012922_lung	0.00 RPM	136.99 RPM
SRP012922_quadricep_muscle	0.00 RPM	59.19 RPM
SRP012922_spleen	0.00 RPM	151.09 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_348 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012950	1 retrocopy	retro_amel_339,
Bos taurus	ENSBTAG00000008001	1 retrocopy	retro_btau_541,
Choloepus hoffmanni	ENSCHOG00000001855	1 retrocopy	retro_chof_437,
Dasypus novemcinctus	ENSDNOG00000017212	2 retrocopies	retro_dnov_348 , retro_dnov_6,
Dipodomys ordii	ENSDORG00000003183	1 retrocopy	retro_dord_688,
Homo sapiens	ENSG00000069275	1 retrocopy	retro_hsap_521,
Gorilla gorilla	ENSGGOG00000026655	1 retrocopy	retro_ggor_480,
Macropus eugenii	ENSMEUG00000007829	2 retrocopies	retro_meug_2015, retro_meug_372,
Macaca mulatta	ENSMMUG00000005645	1 retrocopy	retro_mmul_422,
Monodelphis domestica	ENSMODG00000001832	1 retrocopy	retro_mdom_980,
Nomascus leucogenys	ENSNLEG00000014564	1 retrocopy	retro_nleu_2576,
Pan troglodytes	ENSPTRG00000001904	1 retrocopy	retro_ptro_389,
Rattus norvegicus	ENSRNOG00000047287	2 retrocopies	retro_rnor_2337, retro_rnor_2338,
Tupaia belangeri	ENSTBEG00000015641	1 retrocopy	retro_tbel_2591,
Tarsius syrichta	ENSTSYG00000000910	1 retrocopy	retro_tsyr_987,
Vicugna pacos	ENSVPAG00000003751	1 retrocopy	retro_vpac_313,