RetrogeneDB ID:

retro_oniv_10

Retrocopy
location
Organism:Indian wild rice (Oryza nivara)
Coordinates:8:3712506..3714066(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ONIVA08G04580
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ONIVA01G47760
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_oniv_10
ATGGCGGGCGGCGCGATGGTCCAGACGGTGGGTGGCAAGACGTACCCGGGGAAGATGACCGCGTTCGTGTTCTTCACCTG
CCTCGTCGCCTCCTCCGGCGGCCTCATCTTCGGCTACGACATCGGCATCTCCGGCGGCGTCACCTCCATGGACTCCTTCC
TCAGCGAGTTCTTCCCGTCGGTGTACGCGCAGGCGAAGGCGAGCAAGGACACCAACCAGTACTGCAAGTTCGACAGCCAG
CTGCTGACGCTCTTCACCTCGTCGCTGTACCTGGCGGCGCTGGCGACGTCGTTCGTGGCGGCGTGGGTCACCCGGGTGTT
CGGCCGGAAGTGGTCCATGTTCTGCGGCGGCGTCACCTTCCTCGCCGGCTCGGCGCTCAACGGCGCCGCCACCGACGTCA
TGATGCTCATCCTCGGCCGCATCCTCCTCGGCATCGGCGTCGGCTTCGCCAACCAGTCCGTGCCGCTCTACCTGTCGGAG
ATGGCGCCGGCGAACCTCCGCGGGATGCTCAACATCGGCTTCCAGCTCATGACCACCATCGGCATCCTCTCCGCCAACCT
CATCAACTACGCGACGTCGAGCATCGAGGGCGGGTGGGGGTGGCGCATCGGCCTCGGCCTCGCCGGCGTGCCCGCGCTCA
TCATCACGCTCGGCGCGCTCGTCCTCCCGGACACCCCAAACTCCCTCATCGCCCGCGGCTACGCCGGCGACGCCAAGCGC
GTCCTCGTCAAGATCCGCGGCACGGACGACGTCCACGACGAGTACGACGACATGGTAGCGGCAAGCGAAGAAGCCGCCTC
GATCGAGCACCCATGGCGGAACATCCTCCATCGCAAGTACCGCCCGCAGCTCACCATCGCCATCCTCATCCCGTGCTTCC
AACAGCTCACCGGCATCAACGTGATCATGTTCTACGCGCCGGTGCTCTTCCTCACCATCGGCTTCGCCGGCGACGCGTCG
CTCATGTCCGCCGTGATCACGGGCCTCGTCAACATGTTCGCCACCGTCGTCTCGATCATCTCCGTGGACCGCCTCGGCCG
CCGAGTGCTGTTCCTCCAGGGCGGCACGCAGATGTTCATCTCCCAGGTGGTGGTCGGGACGCTGATCGCGCTCCAGTTCG
GCGTCGCGGGCGTCGGCGAGATGTCGCGGTCGTACGCCATCTTGCTCGTGCTGTTCATCTGCATGTACGTGGCCGGGTTC
GCGTGGTCGTGGGGGCCCCTGGGGTGGCTGGTGCCGAGCGAGGTGTTCGCGCTGGAGATCAGGTCGGCGGGGCAGAGCAT
CGCGGTGTGCGTCAACATGATGCTGACGTTCGTCATCGGGCAGGCGTTCCTCACCATGCTGTGCCACCTCAAGTTCGGCC
TCTTCTACTTCTTCGCCGGGTGGATGCTGGTCATGACCACCTTCGTCGCGCTCTTCCTGCCGGAGACGAAGGGGGTGCCC
ATCGAGGAGATGAACCACGTCTGGAGCCGGCACTGGTTCTGGGGCAGCTACGTCACCGCCCACGACGTCGCCGCCGCCGG
CGCCGGAGGAGGAGGAAACCGCAGAAGCCACAACGTCTAG

ORF - retro_oniv_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.21 %
Parental protein coverage: 97.3 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAGGAVVSTGAGKDYPGKLTLFVFFTCVVAATGGLIFGYDIGISGGVTSMDPFLKKFFPEVYRKKQMADK
MAGGA.V.T..GK.YPGK.T.FVFFTC.VA..GGLIFGYDIGISGGVTSMD.FL..FFP.VY........
RetrocopyMAGGAMVQTVGGKTYPGKMTAFVFFTCLVASSGGLIFGYDIGISGGVTSMDSFLSEFFPSVYAQAKASKD
ParentalNNQYCKYDNQLLQTFTSSLYLAALVSSFFAATVTRVLGRKWSMFAGGLTFLIGAALNGAAENVAMLIVGR
.NQYCK.D.QLL..FTSSLYLAAL..SF.AA.VTRV.GRKWSMF.GG.TFL.G.ALNGAA..V.MLI.GR
RetrocopyTNQYCKFDSQLLTLFTSSLYLAALATSFVAAWVTRVFGRKWSMFCGGVTFLAGSALNGAATDVMMLILGR
ParentalILLGVGVGFANQSVPVYLSEMAPARLRGMLNIGFQLMITIGILAAELINYGTAKIKAGWGWRVSLALAAV
ILLG.GVGFANQSVP.YLSEMAPA.LRGMLNIGFQLM.TIGIL.A.LINY.T..I..GWGWR..L.LA.V
RetrocopyILLGIGVGFANQSVPLYLSEMAPANLRGMLNIGFQLMTTIGILSANLINYATSSIEGGWGWRIGLGLAGV
ParentalPAAIITLGSLFLPDTPNSLIDRGHPEAAERMLRRIRGSDVDVSEEYADLVAASEESKLVQHPWRNIIRRK
PA.IITLG.L.LPDTPNSLI.RG....A.R.L..IRG.D.DV..EY.D.VAASEE.....HPWRNI..RK
RetrocopyPALIITLGALVLPDTPNSLIARGYAGDAKRVLVKIRGTD-DVHDEYDDMVAASEEAASIEHPWRNILHRK
ParentalYRAQLTMAICIPFFQQLTGINVIMFYAPVLFDTLGFKSDASLMSAVITGLVNVFATLVSIFTVDRLGRRK
YR.QLT.AI.IP.FQQLTGINVIMFYAPVLF.T.GF..DASLMSAVITGLVN.FAT.VSI..VDRLGRR.
RetrocopyYRPQLTIAILIPCFQQLTGINVIMFYAPVLFLTIGFAGDASLMSAVITGLVNMFATVVSIISVDRLGRRV
ParentalLFLQGGAQMVVCQVVVGTLIAVKFGTSGIGDIPKGYAAVVVLFICMYVAGFAWSWGPLGWLVPSEIFPLE
LFLQGG.QM...QVVVGTLIA..FG..G.G.....YA...VLFICMYVAGFAWSWGPLGWLVPSE.F.LE
RetrocopyLFLQGGTQMFISQVVVGTLIALQFGVAGVGEMSRSYAILLVLFICMYVAGFAWSWGPLGWLVPSEVFALE
ParentalIRPAGQSINVSVNMLFTFVIAQAFLTMLCHMKFGLFYFFAGWVVIMTVFIALFLPETKNVPIEEMVLVWK
IR.AGQSI.V.VNM..TFVI.QAFLTMLCH.KFGLFYFFAGW...MT.F.ALFLPETK.VPIEEM..VW.
RetrocopyIRSAGQSIAVCVNMMLTFVIGQAFLTMLCHLKFGLFYFFAGWMLVMTTFVALFLPETKGVPIEEMNHVWS
ParentalSHWFWRRFIGDHDV
.HWFW......HDV
RetrocopyRHWFWGSYVTAHDV

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Oryza nivara was not studied using ChIP-Seq data.

EST - click to see more details

Oryza nivara was not studied using EST data.

TSS - click to see more details

Oryza nivara was not studied using FANTOM5 data.

Lab - click to see more details

retro_oniv_10 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 ONIVA01G47760 1 retrocopy
retro_oniv_10 ,


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