RetrogeneDB ID: retro_dnov_134

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1977:137188..137530(-)
• Located in intron of: ENSDNOG00000019818

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLA2
• Ensembl ID: ENSDNOG00000011285
• Aliases: None
• Description: lysophospholipase II [Source:HGNC Symbol;Acc:6738]

Sequence

>retro_dnov_134
ATGTGCCGCAACAGCTTGTCAGCCCCACTTCCCACCATCATGCCCGCTTCCCACAAGGCCACTGCAGTGGTTATTTTTCT
TCACAGACTGGGAGATACAGGGCATGGATGGGTAGAAGCCTTTATAGGTATCAGAAGTTCACATATCAAATATATCTGCC
TGCATGTGCCAATTAGGTCTGTTAAATTAAACATGAACATGAGTATGCCTTCTTGGTTTGATATTATTGGGCTTTTGCAT
GATTTGAAGGAGGACGAACCTGAAATCAAGCAAGCAGAAGAAAATGTCAAAACTTTGATAGACCAAGAGGTGAAAAATGG
AATTCCTTATAACAGGATTATT

Alignment

ORF - retro_dnov_134 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.26 %
• Parental protein coverage: 50.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCGNTMSVPLLTDAATVSGAERETAAVIFLHGLGDTGHSWADALSTIRLSHVKYICLHAPRIPVTLNMKM
          MC.N..S.PL.T...........TA.VIFLH.LGDTGH.W..A...IR.SH.KYICLH.P...V.LNM.M
Retrocopy MCRNSLSAPLPT---IMPASHKATAVVIFLHRLGDTGHGWVEAFIGIRSSHIKYICLHVPIRSVKLNMNM

Parental  VMPSWFDLMGLSPDAPEDEAGIKKAAENIKALIEHERKNGIPANRIV
          .MPSWFD..GL..D..EDE..IK.A.EN.K.LI..E.KNGIP.NRI.
Retrocopy SMPSWFDIIGLLHDLKEDEPEIKQAEENVKTLIDQEVKNGIPYNRII

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	0.58 RPM	48.03 RPM
SRP012922_cerebellum	0.69 RPM	23.64 RPM
SRP012922_heart	0.70 RPM	9.75 RPM
SRP012922_kidney	1.10 RPM	24.92 RPM
SRP012922_liver	0.62 RPM	10.37 RPM
SRP012922_lung	0.76 RPM	33.90 RPM
SRP012922_quadricep_muscle	0.35 RPM	7.62 RPM
SRP012922_spleen	0.92 RPM	39.83 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_134 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011625	1 retrocopy	retro_btau_1605,
Callithrix jacchus	ENSCJAG00000020914	1 retrocopy	retro_cjac_2585,
Dasypus novemcinctus	ENSDNOG00000001461	1 retrocopy	retro_dnov_786,
Dasypus novemcinctus	ENSDNOG00000011285	2 retrocopies	retro_dnov_1186, retro_dnov_134 ,
Homo sapiens	ENSG00000011009	3 retrocopies	retro_hsap_2023, retro_hsap_3577, retro_hsap_4180,
Gorilla gorilla	ENSGGOG00000004330	3 retrocopies	retro_ggor_2114, retro_ggor_2413, retro_ggor_2626,
Macropus eugenii	ENSMEUG00000004768	2 retrocopies	retro_meug_1134, retro_meug_1526,
Microcebus murinus	ENSMICG00000005841	1 retrocopy	retro_mmur_1166,
Nomascus leucogenys	ENSNLEG00000008646	1 retrocopy	retro_nleu_2958,
Otolemur garnettii	ENSOGAG00000032260	1 retrocopy	retro_ogar_2866,
Pongo abelii	ENSPPYG00000001733	1 retrocopy	retro_pabe_142,
Tursiops truncatus	ENSTTRG00000016127	1 retrocopy	retro_ttru_1522,