RetrogeneDB ID:

retro_oniv_33

Retrocopy
location
Organism:Indian wild rice (Oryza nivara)
Coordinates:1:27599634..27600666(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ONIVA01G31640
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ONIVA08G17800
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_oniv_33
ATGAGGCGACCCATGGCTCGCGATTTTACGGCGACGTTTCTTCTGCTGTTCAGCGTCGCGTCGCTGCTGGTGATCTCGCC
GTGCGCGGCCCAGCAGATCAAGACCACCGACACGCGGTGGAGCTACCACCTCCCGCTTCCCGACGGCGTCAGCGGCGCCG
AGAGCCTCGCCTTCGACGGCAAGGACGGCCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGAGGCAGCGCC
GCCGGCTGGACCACGTTCGCGTACAATGCGAACTACCGGAAAATCCCTCTCTGCTCGTCGTCCGAGGTGCCACCGGAGGA
GAGGGAGAGCATCTGCGGGCGCCCGCTGGGGATCCGGTTGTTCAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACA
AGGGGCTGATGAAGGTCGGGCCCGACGGCGGCGAGGCCCAGGTGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTC
CTCAATGGCCTTGACGTCGACCAAGCTACGGGTGATGCCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAA
CGGGGAGATCACGATGAACGCCGACGCGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGA
AGACCGACCTGCCGTACCCGAACGGCGTCGCCGTCAGCCGAGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGC
CAGGCGTTCCGGTACTGGCTGCGGGGCACCAAAGCCGGCGAGTATGAGCTCTTCGCCGACCTCCCGGGCTACCCCGACAA
CGTGAGGCGCGACACCAAGGGAGGCTACTGGGTGGCGCTCAACCAGGAGAGGATGCGGCTGGGCGCGGCGCCCGCAGCCA
AGCACCTGGTCGGCGTACGGCTCAACCCCGACGGCGTGGAGGTGGAGGAGTTGACGGCTGCCAAGGGCGTCACGCTCAGC
GAGGTGGCGGAGCAGAAGGGCAAGCTGTGGTTGGGCTCCGTCGAACTCGATTACATTGGCATGTTTGCTTGA

ORF - retro_oniv_33 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.91 %
Parental protein coverage: 75.35 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPCTASSQVKTTPTNRASHVRLPEGVTGAESLAFDSSNRGPFTGVSDGRVLKWGGDSAGWTTFAYSPNYRS
PC.A..Q.KTT.T....H..LP.GV.GAESLAFD....G..TGVSDGRVLKWGG..AGWTTFAY..NYR.
RetrocopyPC-AAQQIKTTDTRWSYHLPLPDGVSGAESLAFDGKD-GLYTGVSDGRVLKWGGSAAGWTTFAYNANYRK
ParentalSPTCAASS---EETESTCGRPLGLAFHLKTGILYFADAYKGLMRVGPRGGQADVLATEADGVPFNYLNGV
.P.C..S....EE.ES.CGRPLG.....KTG.LY.ADAYKGLM.VGP.GG.A.V.ATEADGVPF..LNG.
RetrocopyIPLCSSSEVPPEERESICGRPLGIRLFRKTGELYIADAYKGLMKVGPDGGEAQVVATEADGVPFHFLNGL
ParentalDVDQDTGDVYFTDSSTTITRRYQENIMRNRDATARLMKYDAKTKQVTVLKDRLPYANGVAVSHDGRYLVV
DVDQ.TGD.YFTDSS.T.TRR....I..N.DAT.RL.KYDA.T..VTVLK..LPY.NGVAVS.D...LVV
RetrocopyDVDQATGDAYFTDSSSTYTRRFNGEITMNADATGRLLKYDARTRRVTVLKTDLPYPNGVAVSRDRTHLVV
ParentalAHTGPAQVFRYWLKGAKAGQYELFADLPGYPDNVRRDAKGGYWVGLNREKITFNVPAAA
AHT.P.Q.FRYWL.G.KAG.YELFADLPGYPDNVRRD.KGGYWV.LN.E........AA
RetrocopyAHTVPCQAFRYWLRGTKAGEYELFADLPGYPDNVRRDTKGGYWVALNQERMRLGAAPAA

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






Oryza nivara was not studied using RNA-Seq expression data.
Oryza nivara was not studied using ChIP-Seq data.
Oryza nivara was not studied using EST data.
Oryza nivara was not studied using FANTOM5 data.
retro_oniv_33 was not experimentally validated.

Retrocopy orthology:
Oryza nivara 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 nivara ONIVA08G17800 1 retrocopy
retro_oniv_33 ,



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