RetrogeneDB ID:

retro_dnov_172

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_2305:299185..299721(+)
Located in intron of:ENSDNOG00000013535
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLA2G12A
Ensembl ID:ENSDNOG00000016573
Aliases:None
Description:phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]


Retrocopy-Parental alignment summary:






>retro_dnov_172
TCACTGAGGCTCCTCCTCCTGGCTGTAGCTCTCAGGTGACAGGAGGAGGCCAAACCATCCACTGGAGGGCCACCTTTAAG
ACTATTTGGAACAGACCTCACAAGACAGACACATACCTGAATGCCACCTTGGACCTCCAGGGAGAGAGGATGGGCTGTGC
CCGTACAAGAGCAGTGTTGGATTTAAGTCCTTGCCACATTATGTTTATAAACCCTTGCCACAAAATGGATATGTCCTCTG
CTGTTTGGTGTTCTCACCTTAACACTGGCATCCCTTCCCTAAAAAAGTGCTGCAACCAACATGACAGGTGCTATGAGACC
TGTGGCAAAAGCAAGAATAACTGCGATGAGGAGTTCCAGTACTGCCACTCCAAGATCTGCCGAGATGCGCAGAAAACATT
AGGACTAGCTCAGCATGTTCAGGCATGTGAAACAATAGTAGAGCTCTTGTTTGACACTGTTACACATTTAAGCTGTAAAC
CATATTTGGATAGCCAAAGAGCCACATGCAGGTGTTGTTATGAGGAAAAACTGGAT

ORF - retro_dnov_172 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.53 %
Parental protein coverage: 95.72 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalALALLLLAAALSCQGEA-QTTDWRTTLKTIRNGVHKIDTYLNAALDLLGG-EDGLCQYKCSDGSKPFPHY
.L.LLLLA.AL..Q.EA.QT..WR.T.KTI.N..HK.DTYLNA.LDL.G..EDGLC.YK.S.G.K..PHY
RetrocopySLRLLLLAVALR*QEEA<QTIHWRATFKTIWNRPHKTDTYLNATLDLQGE<EDGLCPYKSSVGFKSLPHY
ParentalDYKPSPPNG-CGSPMFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRNVQKTLGLA
.YKP.P.NG...S.....HLN.GIPSL.KCCNQHDRCYETCGKSKN.CDEEFQYC.SKICR..QKTLGLA
RetrocopyVYKPLPQNG>MSSAVWCSHLNTGIPSLKKCCNQHDRCYETCGKSKNNCDEEFQYCHSKICRDAQKTLGLA
ParentalQHVQACETTVELLFGSVIHLGCKPYLDSQRAACRCRYEEKTD
QHVQACET.VELLF..V.HL.CKPYLDSQRA.CRC.YEEK.D
RetrocopyQHVQACETIVELLFDTVTHLSCKPYLDSQRATCRCCYEEKLD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP012922_ascending_colon 0 .00 RPM 14 .59 RPM
SRP012922_cerebellum 0 .00 RPM 14 .30 RPM
SRP012922_heart 0 .00 RPM 3 .94 RPM
SRP012922_kidney 0 .00 RPM 12 .87 RPM
SRP012922_liver 0 .15 RPM 18 .73 RPM
SRP012922_lung 0 .00 RPM 9 .77 RPM
SRP012922_quadricep_muscle 0 .00 RPM 10 .56 RPM
SRP012922_spleen 0 .00 RPM 13 .39 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_172 was not experimentally validated.

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.

Parental genes homology:
Parental genes homology involve 14 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000152301 retrocopy
Callithrix jacchus ENSCJAG000000161692 retrocopies
Dasypus novemcinctus ENSDNOG00000016573 7 retrocopies
Homo sapiens ENSG000001237391 retrocopy
Gorilla gorilla ENSGGOG000000010822 retrocopies
Loxodonta africana ENSLAFG000000008522 retrocopies
Mustela putorius furoENSMPUG000000086371 retrocopy
Mus musculus ENSMUSG000000279991 retrocopy
Otolemur garnettii ENSOGAG000000046861 retrocopy
Ochotona princeps ENSOPRG000000145052 retrocopies
Pan troglodytes ENSPTRG000000163621 retrocopy
Sus scrofa ENSSSCG000000091393 retrocopies
Tarsius syrichta ENSTSYG000000047564 retrocopies
Vicugna pacos ENSVPAG000000098421 retrocopy



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