RetrogeneDB ID:

retro_osat_16

Retrocopy
location
Organism:Rice subsp. japonica (Oryza sativa japonica)
Coordinates:11:16510175..16512449(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:OS11G0475600
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OS02G0229400
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_osat_16
ATGAGAGGCGCCGTGTTGGTGGCCGTGGCGGCCGCCATCGGCAACTACCTGCAGGGATGGGACAACGCCACCATCGCCGG
CGCCGTGCTGTACATCAAGCGGGAGTTCGCCCTCGAGACCCAGCCCGCCGTGGAGGGCCTCGTCGTCGCCATGTCCCTCA
TCGGCGCCACCATCATCACCACCTTCTCCGGCCCCGTCTCCGACCTCGTCGGCCGCCGCCCCATGCTCATCGCCTCCTCC
CTCCTCTACTTCGCCGGCGGCCTCATCATGCTCTGGTCCCCCAACGTCTACGTCCTCCTCCTCGCCCGCCTCGTCGACGG
CTTCGGCGTCGGCCTCGCCGTCACCCTCGTCCCCGTCTACATCTCCGAGACCTCCCCGCCGGAGATCCGCGGCCGCCTCA
ACACGCTGCCGCAGTTCACCGGCTCCGGCGGCATGTTCATGTCCTACTGCATGATCTTCGCCATGACGCTCTCGCCCTCG
CCCAACTGGCGCATCATGCTCGGCGTCCTCTTCGTCCCCTCGCTGCTCTACCTGTTCGTCACCGTCTTCTACCTCCCGGA
GTCGCCGCGGTGGCTCGTCAGCAAGGGGCGCATGAAGGAGGCCAGGGTTGTGCTCGAGATGCTGCGCGGCCGCGAGGACG
TCTCCGGCGAGATGGCGCTGCTCGTCGAGGGCCTCGGCACCGGCGGCGACACCGAGATCGAGGACTACGTCGTCGGCCCG
TCCGAGGGCGACGCCGGCGAGAACGAGCAGGCGAGGGACACCGTCACGCTGTACGGGCCGGAGCAGGGGCTTTCGTGGGT
GGCGCAGCCGGTCGCCGGCGGCCGCGGCAGCATGCTGGGGAGCTCGCTGGGGCTGCAGGCGTCGCGCCATGGCAGCATGT
ACGAGCAGATGAAGGACCCCGTGGTGGCGCTTCTCGGGAGCGTCCACGAGCGGCTGCCGGAGTCCGGCGGCGGCGCCACC
GGCAGCATGAGGGGGAGCACGCTGTTCCCCAACCTCGGGAGCATGCTTAGCGTCAACGATAGGCCCGGCGGCAGCAGCTG
GGACGAGGAGAACGTGCAGCCTGGCGACGACGACCTCGACGAGGAGGAGGAGGAGTACCTCTCCGACGACGGCAAGGACG
ACGACGACGGCGGCGGCCTGCAGGCACCGCTGCTGTCGCGGCAGAGCACCGACGTGGAGACCAAGAACGAGCCCGCCTCC
GGCCAGGTGGCGATGCAGCGGCACAGCAGCATCGGCGGCGGCGGCGGCGTCGAGACGGCGAGCACCATGGGCATCGGCGG
CGGGTGGCAGCTGGCGTGGAAGTGGACGGAGAACGTGGGCCCCGACGGCGTCAAGCGCGGCGCGGTGAAGCGCATGTACC
TGCACGAGGAGTCCGAGGCCGCGCCCGGCGGTGACTCGGGCGCCGCCGGCGACGCGCAGTCCACGGCGTACGTCCACGCG
GCGGCGCTGGTGAGCCGGTCGATGCTGTACACCAAGGACGTCCTGATCGGGCAGAGCCCCACCGAGCCGGCGTTCGCGAA
CCCGCCGGAGGCGGTGGCGGCGGCGGCGTCGACGGGCCCGGCGTGGCGCGAGCTGCTCGAGCCGGGCGTCCGCCACGCCC
TCTTCTGCGGCGTCACCATCCAGATCCTCCAGCAATTCTCCGGCATCAACGGCGTGCTCTACTACACCCCGCAGATCCTC
GACCAGGCCGGCGTCAGCGTCCTCCTCGCCAGCCTCGGCCTCTCCGGCGACTCCACCTCCATCCTCATCAGCGGCCTCAC
CACGCTCCTCATGCTCCCGTCCATCGGCGTCGCCATGCGCCTCATGGACGCCTCGGGCCGCCGCGCCCTCCTCCTCTGGA
CGCTGCCCGTCCTCGTCGCGTCCCTCGCCGTGCTCGTGGTGGCGAACGTCGTGCCCATGGCGGCGACCGCGCACGCGGCG
CTGTCGACGGGGAGCGTCATCGTCTACTTCTGCTGCTTCGTCATGGGGTTCGGCCCCATCCCCAACATCCTCTGCGCCGA
GATCTTCCCGACGAGGGTGAGGGGACTCTGCATTGCCATCTGCTCGCTGACGTTCTGGCTCGGCGACATCGCCGTCACGT
ACAGCCTCCCCGTCATGCTCAGCTCCGTGGGGCTCGCCGGCGTGTTCTCCTTCTACGCCGCCGTGTGCTGCGTCGCGCTC
GTGTTCGTGGCGCTCAAGGTGCCCGAGACCAAGGGCCTCCCGCTCGAGGTCATCATCGAGTTCTTCAACGTCGGCGCCAA
GGCCGGCACGTTGCCTGACGAAGAGTTCCACTGA

ORF - retro_osat_16 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.34 %
Parental protein coverage: 61.39 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSGAALVAIAASIGNLLQGWDNATIAGAVLYIKKEFKLESEPTVEGLIVAMSLIGATIITTFSGPVSDWI
M.GA.LVA.AA.IGN.LQGWDNATIAGAVLYIK.EF.LE..P.VEGL.VAMSLIGATIITTFSGPVSD..
RetrocopyMRGAVLVAVAAAIGNYLQGWDNATIAGAVLYIKREFALETQPAVEGLVVAMSLIGATIITTFSGPVSDLV
ParentalGRRPMLILSSILYFLSSLIMLWSPNVYVLLLARLIDGFGIGLAVTLVPLYISETAPSEIRGLLNTLPQFS
GRRPMLI.SS.LYF...LIMLWSPNVYVLLLARL.DGFG.GLAVTLVP.YISET.P.EIRG.LNTLPQF.
RetrocopyGRRPMLIASSLLYFAGGLIMLWSPNVYVLLLARLVDGFGVGLAVTLVPVYISETSPPEIRGRLNTLPQFT
ParentalGSGGMFLSYCMVFGMSLLPSPDWRIMLGVLAIPSLFFFGLTIFYLPESPRWLVSKGRMAEAKKVLQKLRG
GSGGMF.SYCM.F.M.L.PSP.WRIMLGVL..PSL.....T.FYLPESPRWLVSKGRM.EA..VL..LRG
RetrocopyGSGGMFMSYCMIFAMTLSPSPNWRIMLGVLFVPSLLYLFVTVFYLPESPRWLVSKGRMKEARVVLEMLRG
ParentalREDVSGEMALLVEGLEVGADTSIEEYIIGPAIEPADEHVVDGDKDQITLYGPEEGQSWIARPSKG--PSI
REDVSGEMALLVEGL..G.DT.IE.Y..GP....A.E.......D..TLYGPE.G.SW.A.P..G...S.
RetrocopyREDVSGEMALLVEGLGTGGDTEIEDYVVGPSEGDAGEN--EQARDTVTLYGPEQGLSWVAQPVAGGRGSM
ParentalLGSVLSL-TSRHGSMVNQSVPLMDPIVTLFGSVHENMPHAGG----SMR-STLFPNFGSMFSVTDQHPKV
LGS.L.L..SRHGSM..Q.....DP.V.L.GSVHE..P..GG....SMR.STLFPN.GSM.SV.D..P..
RetrocopyLGSSLGLQASRHGSMYEQ---MKDPVVALLGSVHERLPESGGGATGSMRGSTLFPNLGSMLSVNDR-PGG
ParentalDQWDEENLHRDD---EEYASDGAGGDYEDNVHSPLLSRQTTSAEGKDIAHHAHRGSALSMRRRSLLEEGG
..WDEEN....D....E........D..D......L.....S....D........S......R.....GG
RetrocopySSWDEENVQPGDDDLDEEEEEYLSDDGKDDDDGGGLQAPLLSRQSTDVETKNEPASGQVAMQRHSSIGGG
ParentalEAVSSTGIGG---GWQLAWKWSEREGEDGKKEGGFKRIYLHQEE--VPGSRRGS
..V......G...GWQLAWKW.E..G.DG.K.G..KR.YLH.E....PG...G.
RetrocopyGGVETASTMGIGGGWQLAWKWTENVGPDGVKRGAVKRMYLHEESEAAPGGDSGA

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






Oryza sativa japonica was not studied using RNA-Seq expression data.
Oryza sativa japonica was not studied using ChIP-Seq data.
Oryza sativa japonica was not studied using EST data.
Oryza sativa japonica was not studied using FANTOM5 data.
retro_osat_16 was not experimentally validated.

Retrocopy orthology:
Oryza sativa japonica 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 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Oryza punctata OPUNC02G085901 retrocopy
Oryza rufipogon ORUFI02G096101 retrocopy
Oryza sativa japonicaOS02G0229400 1 retrocopy
retro_osat_16 ,



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