RetrogeneDB ID:

retro_dnov_1912

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_36269:6203..6509(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2D3
Ensembl ID:ENSDNOG00000009320
Aliases:None
Description:ubiquitin-conjugating enzyme E2D 3 [Source:HGNC Symbol;Acc:12476]


Retrocopy-Parental alignment summary:






>retro_dnov_1912
GCCCGGGACCCCAGCCCACGTCCTGCAGGGCCGGGTGGGGGGAAATGCTCCACTGCAAGTCACCAGCAGGGGACCTAGTG
ACAGCCCATCTCCAGGCGGTGAATTCTTTTGGACAGTTCATTTTCCTCCAGACCAGCCCTTCAGCCAGCTAAGGTGGCCT
TTACCAGGAGAGTTTATCATCCAAGTATTAACAGCGATGGCAGCGTTTGGCGCCATAAAAGATGACAGTGCTCTCCTGCT
TGAGCTATTTCGAAAGTTCTTTGATGCATTTCTTCACAGCTATGTGAGCTGAACCCAGATGATCCC

ORF - retro_dnov_1912 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.41 %
Parental protein coverage: 75.54 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalARDPPAQCSAGPVGD-DMFHW-QATIMGPNDSPYQGGVFFLTIHFPTDYPF-KPPKVAFTTRIYHPNINS
ARDP.....AGP.G...M.H..Q.T..GP.DSP..GG.FF.T.HFP.D.PF..P.KVAFT.R.YHP.INS
RetrocopyARDPSPR-PAGPGGG<EMLHC<QVTSRGPSDSPSPGGEFFWTVHFPPDQPF<QPAKVAFTRRVYHPSINS
ParentalNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDP
.GS......R.Q.SPA..ISKVL..I.S.LC..NPDDP
RetrocopyDGSVWRH-KR*QCSPA*AISKVL*CISSQLCELNPDDP

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 44 .92 RPM
SRP012922_cerebellum 0 .00 RPM 32 .86 RPM
SRP012922_heart 0 .00 RPM 30 .16 RPM
SRP012922_kidney 0 .00 RPM 28 .75 RPM
SRP012922_liver 0 .00 RPM 33 .28 RPM
SRP012922_lung 0 .00 RPM 42 .15 RPM
SRP012922_quadricep_muscle 0 .00 RPM 52 .27 RPM
SRP012922_spleen 0 .00 RPM 60 .89 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_1912 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 16 parental genes, and 80 retrocopies.

Species Parental gene accession Retrocopies number
Ciona intestinalis ENSCING000000187112 retrocopies
Ciona savignyi ENSCSAVG000000061361 retrocopy
Dasypus novemcinctus ENSDNOG000000054487 retrocopies
Dasypus novemcinctus ENSDNOG00000009320 30 retrocopies
Dasypus novemcinctus ENSDNOG000000138211 retrocopy
Erinaceus europaeus ENSEEUG000000146583 retrocopies
Echinops telfairi ENSETEG000000012913 retrocopies
Gorilla gorilla ENSGGOG000000013682 retrocopies
Ornithorhynchus anatinus ENSOANG000000054151 retrocopy
Ochotona princeps ENSOPRG000000116959 retrocopies
Pongo abelii ENSPPYG000000149671 retrocopy
Pteropus vampyrus ENSPVAG000000154381 retrocopy
Rattus norvegicus ENSRNOG000000137419 retrocopies
Sus scrofa ENSSSCG000000243061 retrocopy
Sus scrofa ENSSSCG000000298224 retrocopies
Tupaia belangeri ENSTBEG000000002705 retrocopies



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