RetrogeneDB ID:

retro_oniv_28

Retrocopy
location
Organism:Indian wild rice (Oryza nivara)
Coordinates:3:24022888..24024214(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ONIVA03G28340
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ONIVA03G37650
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_oniv_28
ATGGCGAGCTCGCCGATGGCCATGGACGCGGACAAGCTCAGCTACGAGATCTTCTCCCTGCTGGAGAGCAAGTTCCTCTT
CGGCGGCGGCGGCGGCGGGTGCCTGTCGTCGGGGCCGTGCACGCCGGCGAGGCCGTTTCTTGGCGGCGGTGGCGGCATGG
ACGGGCGGGTGCGGGTGCTGGCCATCGACGGGTGCGGCTCGTCGGGCGCCGGGGACGCGCTGCTCGCCGCGGCGGCGCTC
GCGCGGCTGGAGGCCGGGCTGCGGAAGCGAACCGGGGACTCCGACGCCCGCGTCGCGGATTTCTTCGACGTCGCGGCGGG
CGCCGGCGCCGGTGGGGTGCTCGCGGCGATGCTGTTCTTGAGGGGCCCCGACGGGAGGCCGAGGTACACGGCGGAGGAGG
CGCTTGAGTTCGTGGCTGCTAGCGTCGGGAGGGACTGGGCCGGCCGGCGCGGGCGGTGGGCGCGGCTGTTCCGCGGCGGC
GCGCGGGGGGCGGAGAGGTCGTTCCGGCGGGTGTTCGGCGACGCCACGCTCAAGGACACCGTCGCGCCGCTGCTCGTCCC
GTGCTACGACCTCGCCACCGCCGCGCCTTTCATGTTCTCGCGCGCCGACGCCGTCGAGAGCGACAGCTACGACTTCGCCC
TCCGCGACGTCTGCGCGGCCACCTGCGCCGCCGGGAGCACGGCCGCCGCCGTCAGGTCGGTGGACGGGCGCACCGCCATC
GCCGCGGCTTCCGGCGGCGTGGCGGCCATGGGCAACCCGGCCGCGGCGGCCATCACGCACGTGCTCCACAACAAGCAGGA
GTTCCCCCTCGCCACCACCGTCGACGACATCCTCGTCCTCTCCATCGGCACCGGCGCCTCCACCTCCGCCACCGCGACGC
CGATGCCCACGCGCTCCCCGTCGCCGCGCGAGATGGCGCGCGTCACCGCCGAGGGCGTGGCGGACATGGTCGACGAGTCC
GTCGCCATGGCGTTCGGCCACACGAGCGGGAGCAGCAGCAACTACGTGCGCATCCAGGCCAGCAAGGCGGCGACCGCGCT
CCACGGCGCCGCCGCCGCGGGCGCGATGCTGTCGCAGCGGAACGTGGAGTCCGTGCTGTTCCGCGGGCGGAGGATGTCGG
AGAGGACGAACGCCGAGAAGGTGGACGCCGCGGCGGCGGAGGTGGTGAAGGAGCACGAGCGGCGGCGGCGCAGCCCGCTG
CCGAACGTGGTGATCAAGCAGGTGGGCACGCCGCGGGTATCGTCGGCGACCACGGCGTCGTCGGGGACGGCGAGGACGGC
GGCGTCGACGTTGGCGTCGCCGGCGTCGTACGGCTCCCGCCAATAG

ORF - retro_oniv_28 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 54.17 %
Parental protein coverage: 76.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAAAAGQLDVDKLTYEIFSILESKFLFGYDDPKLVFSGGDEPQGAVKGTLARGPAVVERGKVCVLSIDGGG
A......D.DKL.YEIFS.LESKFLFG........SG...P.......L..G.....R..V......G..
RetrocopyASSPMAMDADKLSYEIFSLLESKFLFGGGGGGCLSSG---PCTPARPFLGGGGGMDGRVRVLAIDGCGSS
ParentalRAADGLLAGAALVSLEASLRRRTGDETARLADFFDVAAGSGAGGVLAAMLVARGGDGRPMFSAEDALAFL
.A.D.LLA.AAL..LEA.LR.RTGD..AR.ADFFDVAAG.GAGGVLAAML..RG.DGRP...AE.AL.F.
RetrocopyGAGDALLAAAALARLEAGLRKRTGDSDARVADFFDVAAGAGAGGVLAAMLFLRGPDGRPRYTAEEALEFV
ParentalMRSLRRGWSGGGGGGAAGGIRALFRRPGAAFRKVFGDLTLRDTVRPVLVPCYDLASAGPFLFSRADAVET
..S..R.W.G..G..A....R...R.....FR.VFGD.TL.DTV.P.LVPCYDLA.A.PF.FSRADAVE.
RetrocopyAASVGRDWAGRRGRWAR-LFRGGARGAERSFRRVFGDATLKDTVAPLLVPCYDLATAAPFMFSRADAVES
ParentalAAYDFRLRDVCAATCAGSDGSASAVEVRSSDGATRIAAVGGGL-ALGNPTAAAITHVLNNKREFPLAAGV
..YDF.LRDVCAATCA.......A..VRS.DG.T.IAA..GG..A.GNP.AAAITHVL.NK.EFPLA..V
RetrocopyDSYDFALRDVCAATCA---AGSTAAAVRSVDGRTAIAAASGGVAAMGNPAAAAITHVLHNKQEFPLATTV
ParentalEDLLVISIGSGECDN---RPTGGAAASTSEIVRIAAEGVADMVDQAVAMAFGH--NRTNNYIRIQAMGSP
.D.LV.SIG.G........P......S..E..R..AEGVADMVD..VAMAFGH......NY.RIQA....
RetrocopyDDILVLSIGTGASTSATATPMPTRSPSPREMARVTAEGVADMVDESVAMAFGHTSGSSSNYVRIQASKAA
ParentalRASRGGMRCG
.A..G....G
RetrocopyTALHGAAAAG

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_28 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 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Oryza sativa indicaBGIOSGA0097031 retrocopy
Oryza glumaepatula OGLUM03G361701 retrocopy
Oryza nivara ONIVA03G37650 1 retrocopy
retro_oniv_28 ,
Oryza rufipogon ORUFI03G379501 retrocopy



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