RetrogeneDB ID:

retro_ogla_13

Retrocopy
location
Organism:African rice (Oryza glaberrima)
Coordinates:12:18764551..18765940(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ORGLA12G0173200
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ORGLA12G0173300
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_ogla_13
ATGGCAATGGAGGCGGCGTGCGTGCTCGCCGTGGTGGTGGTGGTGCTGGCGTTCTTGTCCTCGGCGGCGCGCGGCGGCGT
CACGAGCACGTACCGGAGGAGCCTGCAGGCGCTCCCAGACATGCCGATCGACGCCGACGTGTTCCGGCCGCCGCCCGGTT
TCAACGCGCCGGAGCAGGTCCACATCACGCTGGGCGACCAGACCGGCCGCGCCATGACCGTCTCCTGGGTGACGCCGAAG
CTCCCCGACAGCAACGTCGTCCGCTACGGCCTCCGCGCCGACAACCTCACCCACACCGCCAATGGCACCTTCCGGCGCTA
CTCCTTCGGGCGCAAGTACCGGTCGGGATTCATCCACCACGCCACCCTTACCGGCCTCGACTACGGCACCAAGTACCACT
ACGCCGTCGGCTCCGGCGACACCGCCAGCGCCAGGTCCTTCTCCTTCACGACGCCGCCCAAGCCCGGGCCCGACGTGCCG
TACAAGTTCGGGCTCATCGGCGACCTCGGGCAGACGTTCCACTCCAACGACACGCTGAGCCACTACGAGGCGTGCGGCGG
CGACGCGGTGCTGTTCATCGGCGACCTGTCGTACGCGGACAACCACCCGGGGCACGACAACAACCGGTGGGACACGTGGG
CGCGGTTCGTGGAGCGGAGCGTGGCGTACCAGCCGTGGATCTGGACGACGGGGAACCACGAGCTGGACTTCGCGCCGGAG
CTGGGGGAGACGACGCCGTTCAAGCCGTTCACGAACAGGTACCCGACGCCGTTCGGGGCGTCGGGGAGCACGCGGCCGCT
GTGGTACTCGGTGAGGATGGCGTCGGCGCACGTGATCGTGCTGGCGTCGTACGCGGCGTACGGCAAGTACACGCCGCAGT
GGAGGTGGCTGGAGGGGGAGCTGAGGCGCGTGGACAGGGCGGTGACGCCATGGCTGATCGTGTGCGTGCACTCGCCGTGG
TACAGCAGCAACGGATACCACTACATGGAGGGGGAGTCGATGCGCGTGGAGTTCGAGCGGTGGCTCGTCGACGCCAAGGC
CGACGTGGTGCTCGCCGGGCACGTCCACTCGTACGAGCGGACGCGGCGGGTGTCGAACGTGGCGTACGACATCGCCAACG
GGATGGCGACGCCGGTGTTCAACCGGTCGGCGCCGGTGTACATCAACATCGGCGACGGGGGGAACATCGAGGGGCTCGCC
GACGACTTCCGGTGGCCGCAGCCGGACTACTCGGTGTTCCGGGAGGCCAGCTTCGGCCACGCCACGCTGCAGATCGTCAA
CCGGACGCACGCCTTCTACGAGTGGCACCGCAACAGCGACGGCGTCAAGGTCGTCGCCGACCATGCCTGGTTCACCAACC
GATACTGGTTTCCCACCGACACCAACTAG

ORF - retro_ogla_13 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.15 %
Parental protein coverage: 96.99 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLLLLLLAAATWTCAGAGAGVTSEYRRKLEATVDMPLDADVFRVPPGYNAPQQVHITLGDQTGTAMTVSWV
.L.............A..GVTS.YRR.L.A..DMP.DADVFR.PPG.NAP.QVHITLGDQTG.AMTVSWV
RetrocopyVLAVVVVVLAFLSSAARGGVTSTYRRSLQALPDMPIDADVFRPPPGFNAPEQVHITLGDQTGRAMTVSWV
ParentalTANELGSNTVRYGSSPEKLDRAAEGSHTRYDYFN-YTSGFIHHCTLTGLTHATKYYYAMGFDHTV--RTF
T.....SN.VRYG.....L...A.G...RY.....Y.SGFIHH.TLTGL...TKY.YA.G...T...R.F
RetrocopyTPKLPDSNVVRYGLRADNLTHTANGTFRRYSFGRKYRSGFIHHATLTGLDYGTKYHYAVGSGDTASARSF
ParentalSFTTPPKPAPDAPFKFGLIGDLGQTFDSNSTLAHYEANGGDAVLFVGDLSYADNYPLHDNNRWDTWARFV
SFTTPPKP.PD.P.KFGLIGDLGQTF.SN.TL.HYEA.GGDAVLF.GDLSYADN.P.HDNNRWDTWARFV
RetrocopySFTTPPKPGPDVPYKFGLIGDLGQTFHSNDTLSHYEACGGDAVLFIGDLSYADNHPGHDNNRWDTWARFV
ParentalERSVAYQPWIWTAGNHELDYAPELGETVPFKPFTHRYPTPYRAAGSTEPFWYSVKIASAHVIVLASYSAY
ERSVAYQPWIWT.GNHELD.APELGET.PFKPFT.RYPTP..A.GST.P.WYSV..ASAHVIVLASY.AY
RetrocopyERSVAYQPWIWTTGNHELDFAPELGETTPFKPFTNRYPTPFGASGSTRPLWYSVRMASAHVIVLASYAAY
ParentalGKYTPQWTWLQEELATRVDRKLTPWLIVLMHSPWYNSNNYHYMEGETMRVQFERWLVDAKVDVVLAGHVH
GKYTPQW.WL..EL..RVDR..TPWLIV..HSPWY.SN.YHYMEGE.MRV.FERWLVDAK.DVVLAGHVH
RetrocopyGKYTPQWRWLEGEL-RRVDRAVTPWLIVCVHSPWYSSNGYHYMEGESMRVEFERWLVDAKADVVLAGHVH
ParentalSYERSRRFANIEYNIVNGKATPAANVDAPVYITIGDGGNIEGIANNFTVPQPAYSAFREASFGHATLEIK
SYER.RR..N..Y.I.NG.ATP..N..APVYI.IGDGGNIEG.A..F..PQP.YS.FREASFGHATL.I.
RetrocopySYERTRRVSNVAYDIANGMATPVFNRSAPVYINIGDGGNIEGLADDFRWPQPDYSVFREASFGHATLQIV
ParentalNRTHAHYAWHRNHDGAKAVADAVWLTNRYWMPTN
NRTHA.Y.WHRN.DG.K.VAD..W.TNRYW.PT.
RetrocopyNRTHAFYEWHRNSDGVKVVADHAWFTNRYWFPTD

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_13 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 ORGLA12G0173300 1 retrocopy
retro_ogla_13 ,


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