RetrogeneDB ID:

retro_ogla_2

Retrocopy
location
Organism:African rice (Oryza glaberrima)
Coordinates:1:17932438..17934706(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ORGLA01G0190900
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ORGLA03G0313900
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ogla_2
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAGGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATCAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCCTC
TTCCCCGCATGGCTCCTCATCACTACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGAAGG
AGGAGAATAAGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGG
TACGCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACCGC
GCAGCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGT
ACAGCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCG
GTGTCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAG
CACATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACA
TGAGCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCAC
GGGAAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCG
CGACGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCGCTCTTTCTCTGCACCGTCCTCAGGT
CGGCGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATC
ACGGCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCAT
CGCCAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCC
ACTACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTG
GTGGCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCC
GAACGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGCAACT
ACGGCGCGCTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGC
AAGACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCAACGGCCGTGAACTA
CAACTCCTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACT
ACATCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACCGG
AGCATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGC
TGATAGCGTCTGCCCTGTTGTGTTATAA

ORF - retro_ogla_2 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.48 %
Parental protein coverage: 96.7 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEGERCPVEEVALVVPETDDPTTPVMTFRAWTLGLASCVVLIFLNTFFTYRTQPLTISGILAQILVLPAGQ
.....P.EEV.L.VP.TDDP..PV.TFR.WTLGL.SCV...FLN.FF.YRT.PL....I..Q...LP.G.
RetrocopyDDDASPIEEVRLTVPVTDDPSLPVWTFRMWTLGLLSCVLISFLNQFFSYRTEPLIVTQITVQVASLPLGH
ParentalFMAAVLPSREVR---LLGGRLGSFNLNPGPFNIKEHVIITIFANCGVSYGGGDAYSIGAITVMKAYYKQS
..A.VLP.R......LLGG..G...LNPGPFN.KEHV...IFAN.G...G.G.AY.........A.Y..S
RetrocopyILARVLPRRKFKAPALLGG--GECSLNPGPFNMKEHVLVSIFANAGCAFGSGSAYAVMIVDIIRAFYGRS
ParentalLSFLCALLIVLTTQILGYGWAGMLRRYLVDPADMWWPSNLAQVSLFRALHEK-EGGDGGKGSSSRGPTRM
.S...A.L...TTQ.LGYGWAG..R.Y.V.PA.MWWP..L.QVSLFRALH.K.E.....K..S..G....
RetrocopyISLFPAWLLITTTQVLGYGWAGLMRKYVVEPAQMWWPGTLVQVSLFRALHGKGEEKEENKEGSGGGMSQA
ParentalRFFLIFFFASFAYYALPGYLLPILTFFSWACWAWPHSITAQQVGSGYHGLGVGAFTLDWAGISAYHGSPL
.FFLI....SF..YA.PGYL.P.LT..SW.CW....S.TAQQ.GSG..GLG.GAFTLDW...SA...SPL
RetrocopyKFFLIALACSFLWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMKGLGLGAFTLDWTAVSAFLYSPL
ParentalVAPWSSIANTAAGFVMFIYLIVPLCYWKFDTFDARKFPIFSNQLFTASGQKYDTTKVLTREFDLNVAAYE
..P....AN..AG.V...Y..VP..YW..D...AR.FPIFS..LFTA.G..YD.T......F......Y.
RetrocopyISPFFATANILAGYVLLMYVVVPVSYWGLDLYNARRFPIFSSHLFTATGSTYDITAIVNDRFEIDMDGYH
ParentalSYGKLYLSPLFAISIGSGFLRFTATIVHVALFHGGDIWRQSRSAMSSAAAKMDVHAKLMRRYKQVPQWWF
..G....S..FA.S.G.GF....AT..HVALFHG..I.R..R........K.DVH..LM..Y..VP.WWF
RetrocopyRMGRINMSTFFALSYGLGFATIAATVTHVALFHGKEIYRRFRASQRD---KPDVHTRLMKSYRDVPSWWF
ParentalLVLLVGSVAVSLVMSFVYREEVQLPWWGMLFAFALAFVVTLPIGVIQATTNQQPGYDIIAQFMIGYALPG
...L..S.AVSL....V.R..VQLPWWG.LFA.A.AFV.TLPI..I.ATTNQ.PG..II....IG..LPG
RetrocopyYAMLALSMAVSLFLCTVLRSAVQLPWWGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLPG
ParentalKPIANLLFKIYGRISTVHALSFLADLKLGHYMKIPPRCMYTAQLVGTVVAGVVNLAVAWWMLGSIDNICD
KPIAN..FK.YG..S...A.SFL.D.KLGHYMKIPP..M...QLVGTVVA..VNL.VA.W.LGSI.NIC.
RetrocopyKPIANVCFKAYGYMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQLVGTVVASTVNLVVAYWLLGSIPNICQ
ParentalVEALHPDSPWTCPKYRVTFDASVIWGLIGPARLFGRHGLYRNLVWLFLAGAVLPVPVWLLSRAFPEKKWI
...L..DSPWTCP..RV.FDASVIWGL.GP.R.FG..G.Y..L.W.FLAGAV.PV.V.LL.RAFP.K.WI
RetrocopyDALLPADSPWTCPNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFPSKTWI
ParentalALINVPVISYGFAGMPPATPTNIASWLVTGTIFNYFVFKYRKGWWQKYNYVLSAALDAGTAFMGVLIFFA
..IN.PV.......MPPAT..N..SWL..G.IFN.FVF.YRK.WW..YNY.LSAALDAG.AFM.VL..F.
RetrocopyPMINLPVLIGATSYMPPATAVNYNSWLIIGIIFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLYFS
ParentalLQNAHHELKWWGTAVDHCPLASCPTAPGI---AVKGCPV
L........WWGTA..HCPLASCPTA.GI...A...CPV
RetrocopyLSMENRSISWWGTAGEHCPLASCPTAKGINLGADSVCPV

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Oryza glaberrima was not studied using ChIP-Seq data.

EST - click to see more details

Oryza glaberrima was not studied using EST data.

TSS - click to see more details

Oryza glaberrima was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogla_2 was not experimentally validated.

Retrocopy orthology:
Oryza glaberrima 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 glaberrima ORGLA03G0313900 1 retrocopy
retro_ogla_2 ,


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