RetrogeneDB ID:

retro_opun_33

Retrocopy
location
Organism:Red rice (Oryza punctata)
Coordinates:1:27193702..27195982(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:OPUNC01G23690
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OPUNC04G21280
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opun_33
ATGGGCTCGGGCGAGCTCGTCGACGTCGAGCGCGGCCTCCGCGGGATGGTCGGTGAGGAGGAGGTAGACGACGACGCCTC
GCCGATCGAGGAGGTCCGGCTGACGGTTCCGGTCACTGATGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACAC
TCGGGCTGCTCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACAGAGCCGCTCATCGTCACCCAG
ATCACCGTGCAGGTGGCCTCGCTACCGCTGGGCCACCTCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGC
CCTGCTCGGCGGCGGGGAGTGGAGCCTGAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCA
ACGCCGGCTGCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACCGGCGGTCC
ATTTCCTTCTTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTA
CGTGGTGGAGCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCCAGGCGCTGCACGGGAAGGAGG
AGCAGGAGGAGAAGACGGAGGGCGGCAGCGGCGGCGGCGGAATGTCTCAGGCTAAGTTCTTCCTGATTGCGCTCGCCTGC
AGCTTCGTGTGGTACGCCGTGCCGGGCTACCTATTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAA
GTCCGTCACCGCGCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGTCTTCACCCTCGATTGGACGGCCGTAT
CAGCCTTCCTGTACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTAC
GTGATTGTGCCGGTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCAC
GGCCAGCGGCAGGACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGCGTACCAGCAGATGG
GGCGGATCAACATGAGCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTG
GCGCTGTTCCACGGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGAT
GAAGAGCTACCGCGACGTGCCGAACTGGTGGTTCTACGCGATGCTCGCGCTCTCCGTGGCCGTCTCGCTCGTGCTCTGCA
CCGTCCTCAGGACGGCGGTGCAGCTCCCGTGGTGGGGACTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCG
ATCAGCATCATCACGGCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCC
GGGCAAGCCCATCGCTAATGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACT
TCAAGCTCGGCCACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTCGTCGGCACGGTGGTCGCCGCCACG
GTCAACCTCGTGGTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCAGACAGCCC
GTGGACGTGCCCGAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGACCGCGCCGCATCTTTGGTC
CCCTCGGCAACTACGGCGCGCTCAACTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATCGTGTACTTGCTCCACAGG
GCGTTCCCCAGCAAAACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCGAC
GGCTCTGAACTACAACTCGTGGCTGATCATCGGGATCGTCTTCAACTTCTTCGTGTTCCGGTACAGGAAGCTGTGGTGGA
AGAGGTACAATTACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCG
ATGGAGAACCGGAGCATCAGCTGGTGGGGGACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGAT
AAACTTGGGCCCTGATAGCGTCTGCCCTGTTGTATTATAA

ORF - retro_opun_33 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.41 %
Parental protein coverage: 71.2 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMTRAKFFLIALICSAAWYVVPGYLFPTVGAVSWLCWAFPRSVTMQQIGSGMSGLGVGAFTLDWATVVSFL
M..AKFFLIAL.CS..WY.VPGYLFPT...VSW.CW.F..SVT.QQ.GSGM.GLG.G.FTLDW..V..FL
RetrocopyMSQAKFFLIALACSFVWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMKGLGLGVFTLDWTAVSAFL
ParentalGSPLVYPFFAIVNVWVGFVLLVYVMLPIAYWVLNLYQASTFPFFSASLFDHAGQEYRIREIVNDRFELDT
.SPL..PFFA..N...G.VLL.YV..P..YW.L.LY.A..FP.FS..LF...G..Y.I..IVNDRFE.D.
RetrocopyYSPLISPFFATANILAGYVLLMYVIVPVSYWGLDLYNARRFPIFSSHLFTASGRTYDITAIVNDRFEIDM
ParentalDAYARQGKIHLSLFFATSYGLGFATIAATLSHVTLFYGTEMYRRFRQAAREKPDVHTRLMRRYDDIPNWW
DAY...G.I..S.FFA.SYGLGFATIAAT..HV.LF.G.E.YRRFR...R.KPDVHTRLM..Y.D.PNWW
RetrocopyDAYQQMGRINMSTFFALSYGLGFATIAATVTHVALFHGKEIYRRFRASQRDKPDVHTRLMKSYRDVPNWW
ParentalFYGMLALAMAGALVLCIVFKDEVQLPWWALLCAMAVAFFFTLPISVITATTNTTPGLNIITEYVMGLIMP
FY.MLAL..A..LVLC.V....VQLPWW.LL.A.A.AF.FTLPIS.ITATTN.TPGLNIITEYV.GL..P
RetrocopyFYAMLALSVAVSLVLCTVLRTAVQLPWWGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLP
ParentalGKPIANVCFKVYGYISMNQAVSFLTDFKLGHYMKIPPRSMFLVQFIGTIVAGTVNMSVAWWLLSTVPHIC
GKPIANVCFK.YGY.SM.QAVSFL.DFKLGHYMKIPP.SMFLVQF.GT.VA.TVN..VA.WLL...P.IC
RetrocopyGKPIANVCFKAYGYMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQFVGTVVAATVNLVVAYWLLGSIPNIC
ParentalDKKHLPDGSPWTCPGSRVFFDASVIWGLVGPRRIFGPLGYYGALNWFFLGGLAGPAVVWLLAWALPRHAS
....LP..SPWTCP..RVFFDASVIWGLVGPRRIFGPLG.YGALNWFFL.G..GP..V.LL..A.P....
RetrocopyQDALLPADSPWTCPNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFP-SKT
ParentalWIRLIHLPVLLGATANMPPASTLNYTAWCSVGAVFNYLVFRRRKAWWQRYNYVLSAAMDAGVAIMGVLIF
WI..I.LPVL.GAT..MPPA..LNY..W...G.VFN..VFR.RK.WW.RYNY.LSAA.DAGVA.M.VL..
RetrocopyWIPMINLPVLIGATSYMPPATALNYNSWLIIGIVFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLY
ParentalFCLSSRGITPDWWGTSAINIDHCDLSTCPTAKGV
F.LS.......WWGT......HC.L..CPTAKG.
RetrocopyFSLSMENRSISWWGTAG---EHCPLASCPTAKGI

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






RNA-Seq - click to see more details

Oryza punctata was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Oryza punctata was not studied using ChIP-Seq data.

EST - click to see more details

Oryza punctata was not studied using EST data.

TSS - click to see more details

Oryza punctata was not studied using FANTOM5 data.

Lab - click to see more details

retro_opun_33 was not experimentally validated.

Retrocopy orthology:
Oryza punctata 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Oryza punctata OPUNC04G21280 1 retrocopy
retro_opun_33 ,


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