RetrogeneDB ID:

retro_oglu_18

Retrocopy
location
Organism:Oryza glumaepatula
Coordinates:1:27445672..27447937(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:OGLUM01G27350
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OGLUM06G01450
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_oglu_18
ATGGGCGAGGGCGAGTTCGTCGACGTCGAGCGCGGCGTGGTCGCTGAGGGGGCGTTGGACGACGACGCGTCGCCGATCGA
GGAGGTCCGGCTGACGGTTCCGGTCACTGACGACCCGTCCCTTCCGGTGTGGACGTTCCGGATGTGGACACTCGGCCTGC
TCTCGTGCGTGCTCATGAGCTTCCTGAACCAGTTCTTCTCCTACCGCACCGAGCCGCTCATCGTCACCCAGATCACCGTG
CAGGTGGCCTCGCTGCCTCTGGGCCACATCCTCGCCCGCGTGCTGCCGCGCCGCAAGTTCAAGGCCCCCGCGCTGCTCGG
CGGCGGGGAGTGCAGCCTCAACCCGGGGCCCTTCAACATGAAGGAGCACGTGCTCGTCTCCATCTTCGCCAACGCCGGCT
GCGCCTTCGGCAGCGGGTCCGCCTACGCCGTCATGATCGTCGACATCATCCGCGCCTTCTACGGGCGGTCCATCTCCTTC
TTCCCCGCATGGCTCCTCATCACCACCACGCAGGTGCTCGGCTACGGGTGGGCGGGGCTGATGCGCAAGTACGTGGTGGA
GCCGGCGCAAATGTGGTGGCCCGGCACGCTCGTGCAGGTGTCGCTGTTCAGGGCGCTGCACGGGAAGGGGGAAGAGGAGG
AGAATACGGAGGGCAGCGGCGGCGGGATGTCTCAGGCCAAGTTCTTCCTGATCGCGCTCGCCTGCAGCTTCCTGTGGTAC
GCCGTGCCGGGTTACCTGTTCCCGACGCTGACCTCCGTCTCGTGGGTCTGCTGGATCTTCTCCAAGTCCGTCACCGCGCA
GCAGCTGGGCTCCGGCATGAAGGGCCTGGGCCTCGGCGCCTTCACCCTCGACTGGACGGCCGTGTCAGCCTTCCTGTACA
GCCCGCTGATCTCGCCGTTCTTTGCCACCGCCAACATCTTGGCCGGCTACGTGCTCCTGATGTACGTGGTCGTGCCGGTG
TCGTACTGGGGCCTCGACCTGTACAACGCCCGGAGGTTCCCCATCTTCTCGTCGCACCTGTTCACGGCCACCGGCAGCAC
ATACGACATCACGGCCATCGTGAACGACCGCTTCGAGATCGACATGGACGGGTACCATCGGATGGGGCGGATCAACATGA
GCACGTTCTTCGCGCTGTCCTACGGGCTCGGCTTCGCGACGATCGCGGCCACCGTCACGCACGTGGCGCTGTTCCACGGG
AAGGAGATCTACCGCCGGTTCCGCGCGTCGCAGAGGGACAAGCCCGACGTGCACACGAGGCTGATGAAGAGCTACCGCGA
CGTGCCGAGCTGGTGGTTCTACGCGATGCTCGCGCTGTCCATGGCCGTCTCGCTCTTGCTCTGCACCGTCCTCAGGTCGG
CGGTGCAGCTCCCGTGGTGGGGTCTCCTCTTCGCCTGCGCCATGGCCTTCGTGTTCACGCTGCCGATCAGCATCATCACG
GCCACGACCAACCAGACGCCGGGGCTCAACATCATCACCGAGTACGTCATCGGGCTCATGCTTCCGGGCAAGCCCATCGC
CAACGTCTGCTTCAAGGCGTACGGCTACATGAGCATGTCGCAGGCCGTGTCCTTCCTGTCCGACTTCAAGCTCGGCCACT
ACATGAAGATACCCCCCAAGTCCATGTTCCTCGTGCAGTTGGTCGGCACGGTGGTCGCCTCCACGGTCAACCTCGTGGTG
GCGTACTGGCTGCTGGGTTCCATCCCCAACATCTGCCAGGACGCGCTCCTCCCGGCGGATAGCCCGTGGACGTGCCCGAA
CGACCGCGTCTTCTTCGACGCGTCCGTCATCTGGGGCCTCGTCGGGCCGCGCCGCATCTTCGGGCCACTCGGGAACTACG
GCGCGCTCAATTGGTTCTTCCTCGCTGGCGCCGTGGGACCCGTCATTGTGTACTTGCTCCACAGGGCGTTCCCCAGCAAG
ACCTGGATACCGATGATCAACCTGCCGGTGCTCATCGGAGCGACCTCCTACATGCCGCCGGCGACGGCCGTGAACTACAA
CTCGTGGCTGATCATCGGGATCATCTTCAACTTCTTCGTTTTCCGGTACAGGAAGCTGTGGTGGAAGAGGTACAACTACA
TCCTCTCGGCTGCGCTCGACGCCGGCGTCGCGTTCATGGCGGTGCTGCTCTACTTCTCGCTGTCGATGGAGAACAGGAGC
ATCAGCTGGTGGGGTACGGCCGGCGAGCACTGCCCGCTGGCCTCATGCCCTACCGCCAAAGGGATAAACTTGGGCGCTGA
TAGCGTCTGCCCTGTTGTGTTATAA

ORF - retro_oglu_18 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.41 %
Parental protein coverage: 73.64 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalVVDDQVLGFGWAGIFRRYLVEPAAMWWPSNLVQVSLFRALH---EKEARSKG---GLTRNQFFLVAFICS
....QVLG.GWAG..R.Y.VEPA.MWWP..LVQVSLFRALH...E.E....G...G.....FFL.A..CS
RetrocopyITTTQVLGYGWAGLMRKYVVEPAQMWWPGTLVQVSLFRALHGKGEEEENTEGSGGGMSQAKFFLIALACS
ParentalFAYYIFPGYLFQMLTSLSWICWVFPHSVLAQQLGSGLSGLGIGAIGLDWSTVSSYLGSPLASPWFATANV
F..Y..PGYLF..LTS.SW.CW.F..SV.AQQLGSG..GLG.GA..LDW..VS..L.SPL.SP.FATAN.
RetrocopyFLWYAVPGYLFPTLTSVSWVCWIFSKSVTAQQLGSGMKGLGLGAFTLDWTAVSAFLYSPLISPFFATANI
ParentalAAGFFFIMYIITPIAYW-FNFYKAQNFPIFSDGLFTSTGQKYNISSIVDSHFHFDTKAYEKNGPLYLSTF
.AG....MY...P..YW....Y.A..FPIFS..LFT.TG..Y.I..IV...F..D...Y...G....STF
RetrocopyLAGYVLLMYVVVPVSYWGLDLYNARRFPIFSSHLFTATGSTYDITAIVNDRFEIDMDGYHRMGRINMSTF
ParentalFAVTYGVGFASLTATIVHVLLFHGSEIWQLSKSAFQEKRMDIHTKLMRRYKQVPEWWFVCILIANIAVTI
FA..YG.GFA...AT..HV.LFHG.EI......A.Q....D.HT.LM..Y..VP.WWF...L....AV..
RetrocopyFALSYGLGFATIAATVTHVALFHGKEIYRRFR-ASQRDKPDVHTRLMKSYRDVPSWWFYAMLALSMAVSL
ParentalFACEYYIEQLQLPWWGVLLACAIAFFFTLPIGIITATTNQTPGLNIITEYIMGYLYPGRPVANMCFKVYG
..C.......QLPWWG.L.ACA.AF.FTLPI.IITATTNQTPGLNIITEY..G...PG.P.AN.CFK.YG
RetrocopyLLCTVLRSAVQLPWWGLLFACAMAFVFTLPISIITATTNQTPGLNIITEYVIGLMLPGKPIANVCFKAYG
ParentalYISMSQALTFLQDFKLGHYMKIPPRTMFMAQVVGTLIAAFVYIGTAWWLMETIPNICNTELLPSDSPWTC
Y.SMSQA..FL.DFKLGHYMKIPP..MF..Q.VGT..A..V....A.WL...IPNIC...LLP.DSPWTC
RetrocopyYMSMSQAVSFLSDFKLGHYMKIPPKSMFLVQLVGTVVASTVNLVVAYWLLGSIPNICQDALLPADSPWTC
ParentalPGDHVFYDASVIWGLISPRRIFGDLGTYSAVNWFFLGGAIAPILVWFAHKAFPNQNWIMLINMPVLIGAT
P.D.VF.DASVIWGL..PRRIFG.LG.Y.A.NWFFL.GA..P..V...H.AFP...WI..IN.PVLIGAT
RetrocopyPNDRVFFDASVIWGLVGPRRIFGPLGNYGALNWFFLAGAVGPVIVYLLHRAFPSKTWIPMINLPVLIGAT
ParentalGQMPPATAVNYTTWILVGFLSGYVVYRYRRDWWERHNYLLSGALDAGLAFMAVLIYLCLGLENISLNWWG
..MPPATAVNY..W...G......V.RYR..WW.R.NY.LS.ALDAG.AFMAVL.Y..L..EN.S..WWG
RetrocopySYMPPATAVNYNSWLIIGIIFNFFVFRYRKLWWKRYNYILSAALDAGVAFMAVLLYFSLSMENRSISWWG
ParentalNDLDGCPLASCPTAKGV
.....CPLASCPTAKG.
RetrocopyTAGEHCPLASCPTAKGI

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Oryza glumaepatula was not studied using ChIP-Seq data.

EST - click to see more details

Oryza glumaepatula was not studied using EST data.

TSS - click to see more details

Oryza glumaepatula was not studied using FANTOM5 data.

Lab - click to see more details

retro_oglu_18 was not experimentally validated.

Retrocopy orthology:
Oryza glumaepatula 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 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Oryza glumaepatula OGLUM06G01450 1 retrocopy
retro_oglu_18 ,
Oryza rufipogon ORUFI06G014401 retrocopy
retro_oruf_39,


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