RetrogeneDB ID:

retro_dnov_106

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_1614:247706..248239(-)
Located in intron of:ENSDNOG00000018889
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RCE1
Ensembl ID:ENSDNOG00000004274
Aliases:None
Description:RCE1 homolog, prenyl protein protease (S. cerevisiae) [Source:HGNC Symbol;Acc:13721]


Retrocopy-Parental alignment summary:






>retro_dnov_106
CCCCACTCGTAGGCCTGCTGCCTCACAGGTATTTGCTGGCTGCGGAACCAAGTGACTGTGCCCCTAACAGAGGAGCTGCT
GTTCTGGCCCTACGTGCTGCCCATGTTAGTGCCATGTGTGGGTATGGGCCCTGCTGTATTCACCTGCCCACTCTTCTTTG
GAGTTGCCCATTTTCACCACATTATTGAGCAGCTGTGGTTCTGCCAGAATAGTGTGGGGAGTATCTTCTTGTCTGCAGTG
TTCCAATTCTCCTACACAGCTGTCTTCGATGCTTACACTGCTTTCCTCTTCATCTGCACAGGACACCTGATTGGGCCCAT
TCACTGCCACTCTTTCTGCAATTACATGGGCTTCTTTGCTGTATGTGTGGCCCTGGAGTATCCACAGAGGCGGCCCTTGC
TGGCTGGCTATGCCTGGGTATGGGACTCTTCCTGCTTCTATTCCAGCCCCTCACAGACCCCAAGCTCTAGAGCAGCCTTC
CCCTTCATGTGCTTTTGGAGCGGGCAGGAGACTCAGAGGCTCCCCTGTGCTCC

ORF - retro_dnov_106 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.01 %
Parental protein coverage: 54.43 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPRSWAHCLTDMRWLRNQVIAPLTEELVFRGCMLPMLAPCMGLGPAVFTCPLFFGVAHFHHIIEQLRFRQS
P.S.A.CLT...WLRNQV..PLTEEL.F....LPML.PC.G.GPAVFTCPLFFGVAHFHHIIEQL.F.Q.
RetrocopyPHS*ACCLTGICWLRNQVTVPLTEELLFWPYVLPMLVPCVGMGPAVFTCPLFFGVAHFHHIIEQLWFCQN
ParentalSVGSIFLSAAFQFSYTAVFGAYTAFLFIRTGHLIGPVLCHSFCNYMGFPAVCAALEHPQRWPLLAGYA-L
SVGSIFLSA.FQFSYTAVF.AYTAFLFI.TGHLIGP..CHSFCNYMGF.AVC.ALE.PQR.PLLAGYA.L
RetrocopySVGSIFLSAVFQFSYTAVFDAYTAFLFICTGHLIGPIHCHSFCNYMGFFAVCVALEYPQRRPLLAGYA<L
ParentalGVGLFLLLLQPLTDPKLYGSLPLCVLLERAGDSEAPLCS
G.GLFLLL.QPLTDPKL..SLPL.VLLERAGDSEAPLCS
RetrocopyGMGLFLLLFQPLTDPKL*SSLPLHVLLERAGDSEAPLCS

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 13 .03 RPM
SRP012922_cerebellum 0 .00 RPM 18 .42 RPM
SRP012922_heart 0 .00 RPM 5 .10 RPM
SRP012922_kidney 0 .00 RPM 11 .50 RPM
SRP012922_liver 0 .00 RPM 5 .73 RPM
SRP012922_lung 0 .00 RPM 18 .79 RPM
SRP012922_quadricep_muscle 0 .00 RPM 5 .19 RPM
SRP012922_spleen 0 .00 RPM 19 .80 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_106 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 2 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG00000004274 2 retrocopies
retro_dnov_106 , retro_dnov_1957,
Oryctolagus cuniculus ENSOCUG000000098211 retrocopy



Copyright © RetrogeneDB 2014-2017