RetrogeneDB ID:

retro_opun_29

Retrocopy
location
Organism:Red rice (Oryza punctata)
Coordinates:2:508719..510792(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:OPUNC02G00640
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OPUNC04G26930
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opun_29
ATGGCGGCGGAGGGGGAGGCGGAGGTGACGCGGGAGGTGATATCGATATCGACGGAGAAGGCGTTCGAGGGGAAGGCGTT
GCCGGCGTGGTCGGAGCAGATCACGGTGAGGTCGCTGGTGGTGAGCGCGCTCCTCGGCATGTTCCTGAGCTTCATCGTGA
TGAAGCTGAACCTCACCTCCGGCATCGTCCCTTCCCTCAACGTCTCCGCTGGTCTCCTCGCCTTCTTCCTCATGAAGACC
TGGACCAGCGCCCTCGAGCGCTGCGGCGTGTTCCCCAAGCCGTTCACCCGCCAGGAGAACACCGTCGTCCAGACCTGCGT
CATCTCCTGCTCCAGCATCGCCTTCTCCGGCGGATTCGGCACCTACATCCTCGGCATGAGCAAGAAGATCGCCGAGGGCT
TCGACGAGGCCGAGGCCAAGACCAGCATCAACGTCGAGGAGCCATCGCTGGGGCGCCTCATCGCCTTCCTCTTCCTCGTC
AGCTTCGTCGGCCTCTTCTCCATCGTGCCGCTTCGCAAGATCATGATCATCAGCTACAAGCTCACCTACCCGAGTGGATC
CGCCACCGCGCACCTCATCAACAGCTTCCACACGCCGCAGGGCGCCATCCAGGCCAAGCATCAGGTCTCCATCCTCTTCA
AATCCTTCGTCGGAAGCTTCCTCTGGTCGCTGTTCCAGTGGTTCTACGCCGCCGGACCGAGTTGTGGGTTCAGCTCGTTC
CCGACGTTCGGGATGGTGGCGTACAGCCGGCGATTCTACTTCGATTTCTCGGCAACCTACATCGGCGTCGGGATGATCTG
CCCCTACATTATCAACTTCTCGTTGCTCGTCGGCTCCATCGTGTCGTGGGGGATCATGTGGCCGTACATCGAGAGCAAGA
AGGGGAGCTGGTACGACGCGGGGCTCCCCAAGAGCAGCCTCCATGGGCTGAACGGATACCAGGTGTTCATCTCCATCGCC
ATGATCGTCGGCGACGGCCTCTTCAACTTCTTCTCCATCGTGCTACGCACCGCCTACGACCTCTACCTGAAGCGGCGCGG
CGGCGTCAACAAGCAGCAGCAGGAGATGCCGTTCGCCGGAGCCACGGGAACGGAGCGGCAGGTGCTCAGCTTCGACGACC
GGAGGCGGACGCAGGTGTTCCTCAAGGACCAGATCCCGACGACGATCGCGGCGGCGGCGTACGTGCTCCTCGCCGCCATA
TCGGTGGTCGCCATCCCGCACATCTTCCGGCAGCTGCGGCCCAAGCACGTGGTGTGGGCGTACGTGGTGGCGCCGCTCTT
CGCCTTCTGCAACGCCTACGGCACGGGGCTCACCGACTGGTCGCTCTCCAGCAGCTACGGCAAGCTCGCCATCTTCATCT
TCGGCGCAAACATCGGCGCCAAGGACGGCGGCGTCGTCGCCGGGCTCGCCGCCTGCGGGCTCATGATGGGCATCGTCTCC
ACCGCCTCCGACCTCGTCCAGGACTTCAAGACGGGATACCTCACCCTCACCTCGCCGCGCTCCATGTTCGTCAGCCAGGT
GTTGGGGACGGGGATGGGGTGCATAATAAGCCCGATGGTGTTCTGGATGTTCTACAAGGCGAACAACATCGGCATGGAGG
ACGGCTTCCCGGCGCCGTACGCCAAGATCTACAGGGGGATAGCTCTCCTGGGCGTCAATGGCTGGGACCAGCTGCCGCGC
TACTGCCTCCGCTTCTGCCTCGCCTTCTTCCTCCTCGCCATCGCCATCTGCGCGCTCAAGGAGGTCGCCAAGCAGCGCGG
GTGGTGGATCCAGGACTTCATCCCCAGCGCCCTCGGCATGGCCGTGCCCTTCTTCCTCGGCTCCTTCTTCACCATCGACA
TGTGCGTCGGTAGCCTCGTGCTCTTCCTCTGGTCCCGGAGTGATCCCGTCAGGGCGCACACCTTCGCCCCCGCCGTCGCC
TCCGGCCTCATCTGCGGCGACGGCATCTGGTCCTTGCCGGCGTCGATCCTCTCGCTGGCCAACGTCAGCCCGCCGATGTG
CATGCGCGTCTTCTCCACCGCCACCAACGAGAAGGTCCAGCTCTTCCTCAGGACGCTGCCCGCGCCGCCATGA

ORF - retro_opun_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.13 %
Parental protein coverage: 82.33 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIGGTGGFGSYIFAMSDRISD--QSGEARDEHNIKNPSLGWMIGFLFIVSFLGLFSVVPLRKIMIIDYKLI
I...GGFG.YI..MS..I.......EA....N...PSLG..I.FLF.VSF.GLFS.VPLRKIMII.YKL.
RetrocopyIAFSGGFGTYILGMSKKIAEGFDEAEAKTSINVEEPSLGRLIAFLFLVSFVGLFSIVPLRKIMIISYKLT
ParentalYPSGTATAHLINSFHTPQGAKLAKMQVKTLGKFFVMSFSWGFFQWFYTGGDGCGFMSFPTLGLEAYRNKF
YPSG.ATAHLINSFHTPQGA..AK.QV..L.K.FV.SF.W..FQWFY..G..CGF.SFPT.G..AY...F
RetrocopyYPSGSATAHLINSFHTPQGAIQAKHQVSILFKSFVGSFLWSLFQWFYAAGPSCGFSSFPTFGMVAYSRRF
ParentalFFDFSATYVGVGMICPYLVNISVLLGGVMSWGIMWPFIEQKKGDWYPADLKPSSLRGIVGYRVFISISLI
.FDFSATY.GVGMICPY..N.S.L.G...SWGIMWP.IE.KKG.WY.A.L..SSL.G..GY.VFISI..I
RetrocopyYFDFSATYIGVGMICPYIINFSLLVGSIVSWGIMWPYIESKKGSWYDAGLPKSSLHGLNGYQVFISIAMI
ParentalLGDGLYNFLKVMTRTTTALVMQVRAMMSEPTLPISGGSGGGGQTPEETFDDKRRTELFLKDQIPNWLALS
.GDGL.NF.....RT...L....R................G.......FDD.RRT..FLKDQIP...A..
RetrocopyVGDGLFNFFSIVLRTAYDLYLKRRGGVNKQQQEMPFAGATGTERQVLSFDDRRRTQVFLKDQIPTTIAAA
ParentalAYVVIAAVSIATVPRIFQQLRWYHVAVSYVVAPVLAFCNAYGCGLTDWSLATTYGKLAIFTVGAWADASD
AYV..AA.S....P.IF.QLR..HV...YVVAP..AFCNAYG.GLTDWSL...YGKLAIF..GA...A.D
RetrocopyAYVLLAAISVVAIPHIFRQLRPKHVVWAYVVAPLFAFCNAYGTGLTDWSLSSSYGKLAIFIFGANIGAKD
ParentalGGIIAGLAACGVMIGIVSTASDLTQDFKTGYMTLASPRSMFVSQVIGTAMGCVIAPSVFWLFYKAFHDIG
GG..AGLAACG.M.GIVSTASDL.QDFKTGY.TL.SPRSMFVSQV.GT.MGC.I.P.VFW.FYKA...IG
RetrocopyGGVVAGLAACGLMMGIVSTASDLVQDFKTGYLTLTSPRSMFVSQVLGTGMGCIISPMVFWMFYKA-NNIG
ParentalMPGSEYPSPNALVYRNMAILGVQGLGSLPKHCLDLCIGFFVAAIAVNLARDLAAPK---VARFLPLPMAM
M.....P.P.A..YR..A.LGV.G...LP..CL..C..FF..AIA.......A.........F.P....M
RetrocopyMEDG-FPAPYAKIYRGIALLGVNGWDQLPRYCLRFCLAFFLLAIAICALKEVAKQRGWWIQDFIPSALGM
ParentalAIPFYLGPYFGIDMCIGSLIRFVWDRLDGARAKAFAPPVASGLICGDGIWTLPQSVLALAGVKPPICMKF
A.PF.LG..F.IDMC.GSL..F.W.R.D..RA..FAP.VASGLICGDGIW.LP.S.L.LA.V.PP.CM..
RetrocopyAVPFFLGSFFTIDMCVGSLVLFLWSRSDPVRAHTFAPAVASGLICGDGIWSLPASILSLANVSPPMCMRV
ParentalLSRSTNVKVDAFIATLPS
.S..TN.KV..F..TLP.
RetrocopyFSTATNEKVQLFLRTLPA

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






RNA-Seq - click to see more details

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

ChIP-Seq - click to see more details

Oryza punctata was not studied using ChIP-Seq data.

EST - click to see more details

Oryza punctata was not studied using EST data.

TSS - click to see more details

Oryza punctata was not studied using FANTOM5 data.

Lab - click to see more details

retro_opun_29 was not experimentally validated.

Retrocopy orthology:
Oryza punctata 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 punctata OPUNC04G26930 1 retrocopy
retro_opun_29 ,


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