RetrogeneDB ID:

retro_dnov_935

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_123449:1089..1505(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:STMN4
Ensembl ID:ENSDNOG00000003756
Aliases:None
Description:stathmin-like 4 [Source:HGNC Symbol;Acc:16078]


Retrocopy-Parental alignment summary:






>retro_dnov_935
GATATCCAGGTGAAAGAAATGGAGAAGTGTACCTCAGGCCAAGTCTTTGAGATGACACTCAGCCCTCTGTCGAAAGACTA
TGTCCCAGAATTTCCCCTTCCCCTCCAAAGAAGAAGGATCTCTCCCTGAAGGAAATTCAAATGAAGTTAGAAGCTGTAGA
AGAAAGATGCAAGTTCCATGAAGCTAAGGTCTTAAAGCAGCTTATTGAGAAATAAGAGGATGAAAAAGAAGTGCCTCAGA
AAATAACAGAAGAGAATAACAACTTCAGTAAAATGGCAGAAAAGTAACTGATACACAAAATGGAAGCCAACAAGGAGAAT
CGAGAGGCACAAATGGCTGCCAAAGTGGAGCATTTGCAAGAAAAGGACAAGCATATTGAACAAGTATGGAAGAAGAAAGA
GTCCAACGATCCTGCT

ORF - retro_dnov_935 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.86 %
Parental protein coverage: 63.85 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDMEVIELNKCTSGQSFEVILKPPSFDGVPEFNASLPRRR-DPSLEEIQKKLEAAEERRKYQEAELLKHLA
D..V.E..KCTSGQ.FE..L.P.S.D.VPEF...L.RRR.D.SL.EIQ.KLEA.EER.K..EA..LK.L.
RetrocopyDIQVKEMEKCTSGQVFEMTLSPLSKDYVPEFPLPLQRRR<DLSLKEIQMKLEAVEERCKFHEAKVLKQLI
ParentalEKREHEREVIQKAIEENNNFIKMANEKLAQKMES--KEREAHLAAMLERLQ-KDKHAEEVRKNKELKEEA
EK.E.E.EV.QK..EENNNF.KMA...L..KME.....REA..AA..E.LQ.KDKH.E.V.K.KE....A
RetrocopyEK*EDEKEVPQKITEENNNFSKMAEK*LIHKMEANKENREAQMAAKVEHLQEKDKHIEQVWKKKESNDPA

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 .19 RPM 0 .97 RPM
SRP012922_cerebellum 0 .27 RPM 86 .88 RPM
SRP012922_heart 0 .00 RPM 0 .23 RPM
SRP012922_kidney 0 .00 RPM 0 .00 RPM
SRP012922_liver 0 .00 RPM 0 .46 RPM
SRP012922_lung 0 .00 RPM 0 .61 RPM
SRP012922_quadricep_muscle 0 .00 RPM 0 .00 RPM
SRP012922_spleen 0 .00 RPM 0 .00 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_935 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 4 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000033733 retrocopies
Dasypus novemcinctus ENSDNOG00000003756 1 retrocopy
retro_dnov_935 ,
Macropus eugenii ENSMEUG000000060131 retrocopy
Tupaia belangeri ENSTBEG000000072901 retrocopy



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