RetrogeneDB ID:

retro_dnov_359

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_397:145063..145581(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CBX3
Ensembl ID:ENSDNOG00000006250
Aliases:None
Description:chromobox homolog 3 [Source:HGNC Symbol;Acc:1553]


Retrocopy-Parental alignment summary:






>retro_dnov_359
ATGTGAAAGAAGCAGAATGAAAAGAGTAAAAAAGCTGAGGAGGCAGAGCCTGAAAAATCTGTGGTGGAAAAAGTACTGGA
TCGACGGGTAGTGAATGGGAAGGTAGAATATTTTCCTAAAGTGGAGGGGATTTACAGATGCTGACAATATTTGGAAGCCT
GAAGAAAACTTAGATTGCCCAGAGTTATCAGAAGCTTTTCTCAATTCTCGAAAAGCTGATAAAGAAAAAGATGGTACAAA
AAGAAAATCTTTATCTGGCAGTGAATCTGATGACAGCAAATCAGAAAAGGAAAGAGATGCTGTAGAAACCAAGAGGCGTT
GCCACAGGGCTTGATCCTGAAGGCATCACTGGTGCCACTGACAGTGGTGGGGAGCGAATGTTTTTAAGAACTGGGAAGAT
TCAGAAGAGGCAGACTTGGTGCTGGGAAAAGAGGCAAACACAAAGGGTCCTCAGATTGTAATCACTTTTTACGAAGAGAG
ACTTAACTTGGCATTCTAGTCCAGAAGATGAAGCGCAA

ORF - retro_dnov_359 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.53 %
Parental protein coverage: 94.54 %
Number of stop codons detected: 1
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMGKKQNGKSKKVEEAEPEEFVVEKVLDRRVVNGKVEYF-LKWKGFTDADNTWEPEENLDCPELIEAFLNS
M.KKQN.KSKK.EEAEPE..VVEKVLDRRVVNGKVEYF.LKW.GFTDADN.W.PEENLDCPEL.EAFLNS
RetrocopyM*KKQNEKSKKAEEAEPEKSVVEKVLDRRVVNGKVEYF>LKWRGFTDADNIWKPEENLDCPELSEAFLNS
ParentalQKAGKEKDGTKRKSLSDSESDDSKSKKKRDAADKPR-GFARGL-DPERIIGATDSSGELMFL-MKWKDSD
.KA.KEKDGTKRKSLS.SESDDSKS.K.RDA....R.....GL.DPE.I.GATDS.GE.MFL...W.DS.
RetrocopyRKADKEKDGTKRKSLSGSESDDSKSEKERDAVETKR<ALPQGL<DPEGITGATDSGGERMFL<KNWEDSE
ParentalEADLVLAKEANMKCPQIVIAFYEER-LTWHSCPEDEAQ
EADLVL.KEAN.K.PQIVI.FYEER.LTWHS.PEDEAQ
RetrocopyEADLVLGKEANTKGPQIVITFYEER>LTWHSSPEDEAQ

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 32 .48 RPM
SRP012922_cerebellum 0 .00 RPM 44 .68 RPM
SRP012922_heart 0 .00 RPM 30 .16 RPM
SRP012922_kidney 0 .00 RPM 21 .08 RPM
SRP012922_liver 0 .00 RPM 38 .08 RPM
SRP012922_lung 0 .00 RPM 57 .88 RPM
SRP012922_quadricep_muscle 0 .00 RPM 23 .71 RPM
SRP012922_spleen 0 .00 RPM 65 .13 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_359 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 6 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000006250 19 retrocopies
Felis catus ENSFCAG000000152246 retrocopies
Microcebus murinus ENSMICG0000000699811 retrocopies
Ochotona princeps ENSOPRG000000117139 retrocopies
Sarcophilus harrisii ENSSHAG000000179131 retrocopy
Sus scrofa ENSSSCG000000167114 retrocopies



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