RetrogeneDB ID: retro_dnov_1276

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17441:15054..15476(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000000282
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PAFAH1B3
• Ensembl ID: ENSDNOG00000002870
• Aliases: None
• Description: platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa) [Source:HGNC Symbol;Acc:8576]

Sequence

>retro_dnov_1276
AGACATGTTTTGTGGAGACTAAAGAATGGAGAACTAGAGAATATTAAACCTAAGGTCATTGTTGTCTGGGTAGGAACAAA
CAACCATGAAAATACAGCAGAAGAGGTAGCAGGTGGGATCGAGGCCATCGTACAACTTATCAACACAAGGCAGCCACAGG
CCAAAATCGTCGTATTGGGTTTGTTACCTCGAGGTGAGAAGCCCAACCCTTTGAGGCAAAAGAATGCCAAGGTGAACCAG
CTTCTCAAGGTTTCCCTGCCGGAGCTGCCAATGTTCAGCTCCTGGATACGGATGGGGGCTTTGTGCACTCGGACGGTGCC
ATCTCCTGCCACGACATGTTTGATTTTCTGCATCTCACAGGAGGGGGCTATGCAAAGATCTGCAAACCCCTCCATGAACT
GATCATGCAGTTGTTGGAGGAA

Alignment

ORF - retro_dnov_1276 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.38 %
• Parental protein coverage: 61.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QHVLWRLENGDHEHIRPKIVVVWVGTNNHGHTAEQVTGGIEAIVQLVNQRQPQARVVVLGLLPRGQHPNP
          .HVLWRL.NG..E.I.PK..VVWVGTNNH..TAE.V.GGIEAIVQL.N.RQPQA..VVLGLLPRG..PNP
Retrocopy RHVLWRLKNGELENIKPKVIVVWVGTNNHENTAEEVAGGIEAIVQLINTRQPQAKIVVLGLLPRGEKPNP

Parental  LREKNQQVNKLVRVAL-AGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLLLRLL
          LR.KN..VN.L..V.L.AG......LD.D.GFVHSDG.IS.HDM.D.LHL...GY...C..LH.L...LL
Retrocopy LRQKNAKVNQLLKVSL<AGAANVQLLDTDGGFVHSDGAISCHDMFDFLHLTGGGYAKICKPLHELIMQLL

Parental  AQ
          ..
Retrocopy EE

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	26.45 RPM	34.81 RPM
SRP012922_cerebellum	43.03 RPM	38.63 RPM
SRP012922_heart	6.73 RPM	4.18 RPM
SRP012922_kidney	8.21 RPM	32.31 RPM
SRP012922_liver	7.28 RPM	6.50 RPM
SRP012922_lung	23.83 RPM	37.11 RPM
SRP012922_quadricep_muscle	3.81 RPM	5.54 RPM
SRP012922_spleen	20.83 RPM	27.24 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_1276 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019787	1 retrocopy	retro_btau_547,
Canis familiaris	ENSCAFG00000004847	1 retrocopy	retro_cfam_610,
Dasypus novemcinctus	ENSDNOG00000002870	1 retrocopy	retro_dnov_1276 ,
Macaca mulatta	ENSMMUG00000012172	1 retrocopy	retro_mmul_18,
Mustela putorius furo	ENSMPUG00000007574	1 retrocopy	retro_mputfur_351,
Rattus norvegicus	ENSRNOG00000020481	1 retrocopy	retro_rnor_976,