RetrogeneDB ID:

retro_obar_6

Retrocopy
location
Organism:Oryza barthii
Coordinates:7:23903885..23905649(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:OBART07G27290
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OBART03G13620
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_obar_6
ATGGAGAGCAACGGCGGAGGAGGAGGATCTCCCAAGGAGGCAGCGGTGGTGGTGCCGTCCTCCGGCGACGCCACACTGGG
CGGGCACCTGGCGCGGCGCCTCGTGCAGGTGGGCGTGAGCGACGTGTTCGCCGTGCCGGGGGACTTCAACCTGACGCTTC
TGGACCACCTGATCGCCGAGCCCGGGCTCCGCGTGGTGGGCTGCTGCAACGAGCTGAACGCCGGATACGCGGCCGACGGG
TACGCGCGGGCCCGTGGCGTGGGCGCCTGCGCCGTGACCTTCACCGTGGGCGGGCTGAGCGTGCTGAACGCCATCGGCGG
CGCGTACAGCGAGAACCTGCCGCTGATCTGCATCGTGGGGGGCCCAAACTCCAACGACTACGGCACCAACCGCATCCTCC
ACCACACCATCGGCCTCCCGGACTTCTCCCAGGAGCTCCGCTGCTTCCAGCCCCTCACCTGCTACCAGGCCGTCGTCAAC
AACCTCGACGACGCCCACGACCAGATCGACCGCGCCATCTCCACCGCCATCAGGGAGAGCAAGCCCGTCTACATCAGCGT
CAGCTGCAACCTCCCCGCCGTCCCCCACCCCACCTTCTCCCGCGACCCGGTGCCCTACTTCCTCTCCCCGAGGCTCTCCA
ACCAGGCCAGCCTCCACGCCGCGCTCGACGCCACCCTCGCCTTCCTCGACAAGGCCGTCAAGCCCGTCCTCGTCGCGGGG
CCCAAGCTCCGCGTCGCCAAGTCCGGAGGGGCCTTCGTGGACCTCGCCGACGCCAGCGGCTACGCGGTGGCCGCCATGCC
GTCCGCCAAGGGGCTGGTGCCGGAGACGCTGCCGCGCTTCATCGGGACCTACTGGGGCGCGGTCAGCACGGCCTTCTGCG
CGGAGATCGTGGAGTCCGCGGACGCCTACCTGTTCGCGGGGCCCATCTTCAACGACTACAGCTCCGTGGGGTACTCGTGC
CTGCTGAAGAAGGAGAAGGCGGTGGTGGTGCAGCCCGACCGCGTGACCATCGGCAATGGCCCCGCGTTCGGGTGCGTGAT
GATGAGGGACTTCCTGTCGGAGCTGGCCAAGCGCGTCCGGAAGAACACGACGGCGTTCGACAACTACAAGAGGATCTTCG
TGCCGGAGGGGCAGCTGCCGGAGTGCGAGGCCGGGGAGGCGCTGCGGGTGAACGTGCTGTTCAAGCACATACAGAGGATG
ATCGGTGGCGCGGAGATCGGGGCGGTGATGGCGGAGACGGGGGACTCGTGGTTCAACTGCCAGAAGCTGCGGCTGCCCGA
GGGTTGCGGGTACGAGTTCCAGATGCAGTACGGCTCCATCGGGTGGTCGGTGGGGGCGCTGCTGGGCTACGCGCAGGCTG
TCCAAAAACGGGTGGTGGCTTGCATCGGCGACGGCAGCTTCCAGGTGACGGCGCAGGACGTGTCGACGATGCTGCGTTGC
GGGCAGCGGAGCATCATCTTCCTCATCAACAACGGCGGGTACACCATCGAGGTGGAGATCCACGACGGGCCGTACAACGT
GATCAAGAACTGGGACTACGTGGGCCTCGTCAACGCCATCCACAACGGCGAGGGGCGGTGCTGGGCCACCCGGGTGCGGT
GCGAGGAGGAGCTGGAGGCGGCCATCGCGACGGCCACGGGGGACAAGGCGGACAGCCTCTGCTTCATCGAGGTGGTGGCG
CACAAGGACGACACCAGCAAGGAGCTCCTCGAATGGGGCTCCAGAGTCTCCGCCGCCAACTCCAGGCCGCCCAACCCGCA
GTAG

ORF - retro_obar_6 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.62 %
Parental protein coverage: 95.54 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalGCPMTSARPAPVSAGEASLGRHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRLVGCCNELNAGYA
G.P...A...P.S.G.A.LG.HLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLR.VGCCNELNAGYA
RetrocopyGSPKEAAVVVP-SSGDATLGGHLARRLVQVGVSDVFAVPGDFNLTLLDHLIAEPGLRVVGCCNELNAGYA
ParentalADGYARARGVGACAVTFTVGGLSVLNAIAGAYSENLPVICIAGGPNSNDYGTNRILHHTIGLPDFSQELR
ADGYARARGVGACAVTFTVGGLSVLNAI.GAYSENLP.ICI.GGPNSNDYGTNRILHHTIGLPDFSQELR
RetrocopyADGYARARGVGACAVTFTVGGLSVLNAIGGAYSENLPLICIVGGPNSNDYGTNRILHHTIGLPDFSQELR
ParentalCFQTVTCHQAVVTNLEDAHEQIDTAIATALRESKPVYLSISCNLPGLPHPTFSRDPVPFFLAPRLSNKMG
CFQ..TC.QAVV.NL.DAH.QID.AI.TA.RESKPVY.S.SCNLP..PHPTFSRDPVP.FL.PRLSN...
RetrocopyCFQPLTCYQAVVNNLDDAHDQIDRAISTAIRESKPVYISVSCNLPAVPHPTFSRDPVPYFLSPRLSNQAS
ParentalLEAAVEATVEFLNKAVKPVLVGGPKLRVAKAGKAFVDLVDASGYAYAVMPSAKGLVPETHPHFIGTYWGA
L.AA..AT..FL.KAVKPVLV.GPKLRVAK.G.AFVDL.DASGYA.A.MPSAKGLVPET.P.FIGTYWGA
RetrocopyLHAALDATLAFLDKAVKPVLVAGPKLRVAKSGGAFVDLADASGYAVAAMPSAKGLVPETLPRFIGTYWGA
ParentalVSTAFCAEIVESADAYLFAGPIFNDYSSVGYSFLLKKDKAIIVQPERVIVGNGPAFGCVMMKEFLSELAK
VSTAFCAEIVESADAYLFAGPIFNDYSSVGYS.LLKK.KA..VQP.RV..GNGPAFGCVMM..FLSELAK
RetrocopyVSTAFCAEIVESADAYLFAGPIFNDYSSVGYSCLLKKEKAVVVQPDRVTIGNGPAFGCVMMRDFLSELAK
ParentalRVNKNTTAYENYKRIFVPEGQPLESEPNEPLRVNVLFKHVQKMLNSD--SAVIAETGDSWFNCQKLKLPE
RV.KNTTA..NYKRIFVPEGQ..E.E..E.LRVNVLFKH.Q.M.......AV.AETGDSWFNCQKL.LPE
RetrocopyRVRKNTTAFDNYKRIFVPEGQLPECEAGEALRVNVLFKHIQRMIGGAEIGAVMAETGDSWFNCQKLRLPE
ParentalGCGYEFQMQYGSIGWSVGALLGYAQGAKDKRVIACIGDGSFQVTAQDVSTMIRCAQNSIIFLINNGGYTI
GCGYEFQMQYGSIGWSVGALLGYAQ.A..KRV.ACIGDGSFQVTAQDVSTM.RC.Q.SIIFLINNGGYTI
RetrocopyGCGYEFQMQYGSIGWSVGALLGYAQ-AVQKRVVACIGDGSFQVTAQDVSTMLRCGQRSIIFLINNGGYTI
ParentalEVEIHDGPYNVIKNWNYTGLVDAIHNGEGKCWTSKVKCEEELTEAIGMALGEKKDCLCFIEVIAHKDDTS
EVEIHDGPYNVIKNW.Y.GLV.AIHNGEG.CW...V.CEEEL..AI..A.G.K.D.LCFIEV.AHKDDTS
RetrocopyEVEIHDGPYNVIKNWDYVGLVNAIHNGEGRCWATRVRCEEELEAAIATATGDKADSLCFIEVVAHKDDTS
ParentalKELLEWGSRVSAANSRPPNPQ
KELLEWGSRVSAANSRPPNPQ
RetrocopyKELLEWGSRVSAANSRPPNPQ

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






Oryza barthii was not studied using RNA-Seq expression data.
Oryza barthii was not studied using ChIP-Seq data.
Oryza barthii was not studied using EST data.
Oryza barthii was not studied using FANTOM5 data.
retro_obar_6 was not experimentally validated.

Retrocopy orthology:
Oryza barthii 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 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Zea mays GRMZM2G0871861 retrocopy
Oryza barthii OBART03G13620 1 retrocopy
retro_obar_6 ,
Oryza glumaepatula OGLUM03G137201 retrocopy
Oryza meridionalis OMERI02G336901 retrocopy
Oryza punctata OPUNC03G131301 retrocopy
Oryza rufipogon ORUFI03G142801 retrocopy



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