RetrogeneDB ID:

retro_opun_19

Retrocopy
location
Organism:Red rice (Oryza punctata)
Coordinates:2:316258..319057(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:OPUNC02G00410
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:OPUNC07G20150
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_opun_19
ATGGCGCAGCCGAGAGTCATCTGGGTGCGCACCCACGACGGGCGCTCCACCACCGTCACGCTCGCCGCCTCCTCCACCGT
CAAGGACCTCAGGACGGCGCTCCGTTCATCCTTCGCTCCCGCGCTGGTTTCCCCCGACTTCCACCTCTTCCTCAAGGGCA
CCAAGCTCATCGCCGACGCCAAGGTCGGGAACCTCCCCGTCGGCCCCGGCGAGCCCATCTCTTTCATCCCGGTCAACGCC
AAGTCAACGCCGCTGCACCCTCCCGCTTGGAAACCGTCGTCGAGCGCGCCGAATCCATGGAGAAAACGGAAGTTTTCTTG
GCACGACGGCGGCGGCGAAGACATCTATGCCAAGAAGCCAACAAACTCAGCGCCGCCGCCTCCGCCGCTCTCCTGCCATG
GCACGCAACCTCTGGACCCTACCCAAATGGTGGAGCATCTCAGGCAAGGGCTCGGGAAGGCCAACCAGATCACCCATGTC
GAGGAGATCCCGGGCAGGGAGCCGACGTTCGCCGACCTCCCCGGCCATCTCTCCTCCTCCATGAGGGACGCGCTGAGAAG
CATCGGCGTCACCAAGCTCTACGCCCACCAGGCGCAGGCCGTGCAATCCGCCGTCTCCGGCGAGCACGTCGTGGTGTCCA
CCTCGACGTCGAGCGGCAAGTCGCTGTGCTACAACATCCCCGTCCTCGAGTCCATCTCCCAGAGCTCCACGCCATGCGCG
CTCTACATCTTCCCCACCAAGGCTCTGGCCCAAGACCAGCTCAAGACATTGCTCGAGATGAAGCCGGCGTTCAGCTCCGA
CTTCGATGTCAGCATCTACGACGGCGACACCGCCATGAAAGACCGGACAAGGATCAGGAACAACGCAAGGCTGCTGATCA
CCAATCCTGACATGCTCCACATGTCGATCTTGCCATGCCATGCTCAGTTCAAGAGGATCCTCTTCAACCTCAAGTACATT
GTCATCGACGAGGCGCATTCGTACAGGGGCGCATTCGGCTGCCACGTTGCGTTGATTCTGAGAAGATTAAAGCGCATCTG
TTCATATGTTTATGGCAGCAATCCGACATTCATATTCTGCACCGCGACATTGGCCAATCCGAGGGAGCATGTCATGGAGC
TGGCAAATCTTGATCGAGTCGTGCTTGTTGATAATGACACGAGTCCTTGCGGCTCAAAGAACTTCCTCCTGTGGAATCCA
CCATTGCCATTGGCGAATGCGAAAGACAGAAGACCAAACCCAGTACTAGAGGTTTCCTATCTGTTCGCCGAGATGGTTCA
GCATGGGCTTCGTTGCATCGCCTTCTGCAAGACGAGGAAGATGTGTGAGCAGGTGCTGATGCAGACGCGTCAGATTCTTA
AGGAGACTGCTGCAGAATTGGTAGATTCTATCTGTGTCTACCGTGGTGGCTATGTTGCAAGTGACAGGAGGAAGATCGAG
GCTGATCTCTTCGGTGGAATTCTTCGCGGTGTCGCGGCTACCAATGCTCTTGAGCTGGGGATCGACGTCGGGCACATCGA
TGCGACGCTGCACCTGGGATTTCCTGGAAGCATGGCCAGCTTCTGGCAGCAGGCAGGGAGATCAGGGAGAAGAGCAAAGC
AGTCCATTGCTGTTTATGTCGCCTTTGAGGGTGCTCTTGATCAGTACTTCATGAGATCACCACACAAGCTGTTTGGGAAG
CCCATTGAGCACTGCCAGGTTGATTCACAAAACCACAAGGTTCTTGAACAGCATCTTGCTTGCGCCGCTTATGAATATCC
ACTGCGTCAGGAACATGATGAGAGCTACTTTGGTTCTTGCATGAAGAGTGTTATGATGACACTGAAAGATAAGGGCTGTC
TCATGAACAATCCATCTGGAGGAGATTCAAGTGTGTGGAAGTATATTGGACCTGATAAGAAACCTTCCCATAGTGTAAGC
ATACGGGCAATTGAGAATCACAGGTACAAGGTGATCGACAGGAAAAGCAATCGAGTTCTCGAGGAGATTGAGGAAAGCAA
GGCTTTCTTTCAGGTGTATGATGGTGCTGTCTACATGCACCAAGGTGTCAGCTACTTGGTTGATAAGCTTGATCTGACAT
CAAGGATAGCTTACTGCAAGGTGTTTGATCTGAACTACTACACCAAAGTTCAGGACTACACTGAAATCAGTGTCGTTGGA
GGTGATGTTGATGAACATCCCGCGAGTAAGTGTAAACCTGATGTCAGGAGGACAACAGCTCAAGCAAATGACTGCAGGGT
GACAACCAGATGGGTTGGCTTTGATCGAATATTGAAGTCAAGCAACCAGATATCTGACAGCATTAGCCTTGATCATCTAC
CTCCATACTCCTTTGAAACTCAAGCCGTTTGGGTACAAATTCCTGAGTCAGTAAGGACGAATATGGAGCAAAGGGAATAT
CAGCTCCGAGGTGGTGTACACGCTGCTTCGCATGCGCTCCTAAGTATAATACCTCTGCACATGATGTGTAGTGGTTCTGA
TCTAGGAACACAATGTGCAGAGCCTCAAGAAAATTCTGAAACTTCAGACAAAATTCTGTTGTACGACAAACATCCCGGTG
GCATCGGCTTAGCATCACAGGCCAAGCTGCTCTTTGGTGAGCTTCTGGTTGCTGCTTTAGAGCTTGTTTCATCATGCAGC
TGCGCCAACTCTGATGGATGTCCAAATTGCATCCAATCATTTGCATGCAGTGATTACAATAGGGATTTGGACAAGGAAGC
TGCAATTTTGCTTCTCAAGGGCGTAATTCAGTATGAGAATTTGTATTTTGAAGCCAACGATGGTTGTTATCAGAGGTGA

ORF - retro_opun_19 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.51 %
Parental protein coverage: 52.5 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRRSSPIVEVSYLLSEMVQHGLRCIAFCKTRKLCELVLAYTREILQETAKELVDTICVYRAGYIAEDRRKI
RR..P..EVSYL..EMVQHGLRCIAFCKTRK.CE.VL..TR.IL.ETA.ELVD.ICVYR.GY.A.DRRKI
RetrocopyRRPNPVLEVSYLFAEMVQHGLRCIAFCKTRKMCEQVLMQTRQILKETAAELVDSICVYRGGYVASDRRKI
ParentalEAGLFQGKLLGVAATNALELGIDVGHIDATLHLGFPGSIASLWQQAGRSGRRAKQSLAIYVAFEGPLDQY
EA.LF.G.L.GVAATNALELGIDVGHIDATLHLGFPGS.AS.WQQAGRSGRRAKQS.A.YVAFEG.LDQY
RetrocopyEADLFGGILRGVAATNALELGIDVGHIDATLHLGFPGSMASFWQQAGRSGRRAKQSIAVYVAFEGALDQY
ParentalFMKFPHKLFGKPIEHCQVDSHNQKLLEQHLACAAYEHPLCVQYDADYFSSSLNSVMMALKDKGYLINNPS
FM..PHKLFGKPIEHCQVDS.N.K.LEQHLACAAYE.PL....D..YF.S...SVMM.LKDKG.L.NNPS
RetrocopyFMRSPHKLFGKPIEHCQVDSQNHKVLEQHLACAAYEYPLRQEHDESYFGSCMKSVMMTLKDKGCLMNNPS
ParentalGPFSSSMWSYIGPEKIPSQAVSIRAIEHDKYRVIDKLNNRLLEEIEESKAFFQVYDGAVYMHQGVNYLVE
G...SS.W.YIGP.K.PS..VSIRAIE...Y.VID...NR.LEEIEESKAFFQVYDGAVYMHQGV.YLV.
RetrocopyGG-DSSVWKYIGPDKKPSHSVSIRAIENHRYKVIDRKSNRVLEEIEESKAFFQVYDGAVYMHQGVSYLVD
ParentalELDLSSRTAFCRKVDLKYYTKTRDYTDINVLGGEFAHLPPSTCKTNQVKTTAQANDCKVTTKWFGFYRIW
.LDL.SR.A.C...DL.YYTK..DYT.I.V.GG.....P.S.CK.....TTAQANDC.VTT.W.GF.RI.
RetrocopyKLDLTSRIAYCKVFDLNYYTKVQDYTEISVVGGDVDEHPASKCKPDVRRTTAQANDCRVTTRWVGFDRIL
ParentalKSNNKISDSIEL-NLPPYSFDSQAVWVRIPHSVKITVEERELQFRGGSHAASHALLNIVPLHMTCNASDL
KS.N.ISDSI.L..LPPYSF..QAVWV.IP.SV....E.RE.Q.RGG.HAASHALL.I.PLHM.C..SDL
RetrocopyKSSNQISDSISLDHLPPYSFETQAVWVQIPESVRTNMEQREYQLRGGVHAASHALLSIIPLHMMCSGSDL
ParentalGTECANPHETRGIPDRILLYDKHPGGIGIALQIKSLFGQLLLAALELVSECNCTSSAGCPNCIQTLTCGE
GT.CA.P.E.....D.ILLYDKHPGGIG.A.Q.K.LFG.LL.AALELVS.C.C..S.GCPNCIQ...C..
RetrocopyGTQCAEPQENSETSDKILLYDKHPGGIGLASQAKLLFGELLVAALELVSSCSCANSDGCPNCIQSFACSD
ParentalYNEVLDKEAAILILKGVIEYERSYFE
YN..LDKEAAIL.LKGVI.YE..YFE
RetrocopyYNRDLDKEAAILLLKGVIQYENLYFE

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_19 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 OPUNC07G20150 1 retrocopy
retro_opun_19 ,


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