Plant Circular RNA Database

Detail information of Os01g0680700_circ_g.7

			
						 General Information
					
						CircRNA Name
						Os01g0680700_circ_g.7
					
						ID in PlantcircBase
						osa_circ_003246
					
						Alias
						Os01circ20329/Os_ciR1440, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 28019655-28020275  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ, CIRI-long
					
						Parent gene
						
							Os01g0680700						
					
						Parent gene annotation
						
							Protein of unknown function DUF1639 family protein. (Os01t068070
0-01);Hypothetical conserved gene. (Os01t0680700-02);Hypothetica
l conserved gene. (Os01t0680700-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						18/12/17
					
						Tissues
						leaf and panicle/root/shoot, root, leaf
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Os01t0680700-01:1
Os01t0680700-02:1
Os01t0680700-03:1

General Information
CircRNA Name	Os01g0680700_circ_g.7
ID in PlantcircBase	osa_circ_003246
Alias	Os01circ20329/Os_ciR1440,
Organism	Oryza sativa
Position	chr1: 28019655-28020275 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ, CIRI-long
Parent gene	Os01g0680700
Parent gene annotation	Protein of unknown function DUF1639 family protein. (Os01t068070 0-01);Hypothetical conserved gene. (Os01t0680700-02);Hypothetica l conserved gene. (Os01t0680700-03)
Parent gene strand	-
Alternative splicing	NA
Support reads	18/12/17
Tissues	leaf and panicle/root/shoot, root, leaf
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Os01t0680700-01:1 Os01t0680700-02:1 Os01t0680700-03:1

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							F: GCTTGGAATCGAGCTGTGAC
 R: AACCTGAGGTCCGCTTCGT
PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	Yes Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	F: GCTTGGAATCGAGCTGTGAC R: AACCTGAGGTCCGCTTCGT PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							GTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCCGCCGCCGTTG
GCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTACctgtggtggtgtgcgtctccgacggcgg
cggcggcggcggaccgcgtcgggaaggacgaagcggacctcaggttggacccgcgcgtgtacga
cccggtgg

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 238
Transcript exons: 28019655-28019737,28020121-28020275
CTGTGGTGGTGTGCGTCTCCGACGGCGGCGGCGGCGGCGGACCGCGTCGGGAAGGACGAAGCGG
ACCTCAGGTTGGACCCGCGGGAGGTACGACGAGAGGCGGGAGCTGTCCGCGGCGACGGCCATGC
CGCCATCGTCGTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCC
GCCGCCGTTGGCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTAC
Transcript length: 621
Transcript exons: 28019655-28020275
CTGTGGTGGTGTGCGTCTCCGACGGCGGCGGCGGCGGCGGACCGCGTCGGGAAGGACGAAGCGG
ACCTCAGGTTGGACCCGCGCGTGTACGACCCGGTGGTGGTGGATGGGGGCGGCGGCGGCATGAG
CTTCTCCGCCGGCGCCGACGAGCGGCGCAGGATCTTGCCGGCGGCGGAGGCGGTCTGGCGGCGC
TGCGAGGAGGAGGGAGCCGCGTTGGCCGAGGAGGACGCGTCGCGCCGGCAGCGGGACCGCTTGT
TGTGCCCCCACTGCAGCAGCACGTCGCCACCGGTGCCCGCGCCGTTGGAGCTCGGCGAGGCCGT
GTCGGAGGAGTCGGACGGGTGGTGGTGGTGGTGGTGGTTGTGGTGGGCGTGCGCGTGGTCGCGC
GCCGGGCTCCAGGCGGCGGCCGACGAGGACGACGGCTGCGGCGCCCGAGCGCGCAGCGGCTTGG
AATCGAGCTGTGACGACGGGAGGTACGACGAGAGGCGGGAGCTGTCCGCGGCGACGGCCATGCC
GCCATCGTCGTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCCG
CCGCCGTTGGCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTAC
						
					

						Genomic sequence
						
							CTGTGGTGGTGTGCGTCTCCGACGGCGGCGGCGGCGGCGGACCGCGTCGGGAAGGACGAAGCGG
ACCTCAGGTTGGACCCGCGCGTGTACGACCCGGTGGTGGTGGATGGGGGCGGCGGCGGCATGAG
CTTCTCCGCCGGCGCCGACGAGCGGCGCAGGATCTTGCCGGCGGCGGAGGCGGTCTGGCGGCGC
TGCGAGGAGGAGGGAGCCGCGTTGGCCGAGGAGGACGCGTCGCGCCGGCAGCGGGACCGCTTGT
TGTGCCCCCACTGCAGCAGCACGTCGCCACCGGTGCCCGCGCCGTTGGAGCTCGGCGAGGCCGT
GTCGGAGGAGTCGGACGGGTGGTGGTGGTGGTGGTGGTTGTGGTGGGCGTGCGCGTGGTCGCGC
GCCGGGCTCCAGGCGGCGGCCGACGAGGACGACGGCTGCGGCGCCCGAGCGCGCAGCGGCTTGG
AATCGAGCTGTGACGACGGGAGGTACGACGAGAGGCGGGAGCTGTCCGCGGCGACGGCCATGCC
GCCATCGTCGTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCCG
CCGCCGTTGGCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTAC
						
					

			
		

Sequences
Splice junction sequence	GTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCCGCCGCCGTTG GCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTACctgtggtggtgtgcgtctccgacggcgg cggcggcggcggaccgcgtcgggaaggacgaagcggacctcaggttggacccgcgcgtgtacga cccggtgg
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 238 Transcript exons: 28019655-28019737,28020121-28020275 CTGTGGTGGTGTGCGTCTCCGACGGCGGCGGCGGCGGCGGACCGCGTCGGGAAGGACGAAGCGG ACCTCAGGTTGGACCCGCGGGAGGTACGACGAGAGGCGGGAGCTGTCCGCGGCGACGGCCATGC CGCCATCGTCGTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCC GCCGCCGTTGGCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTAC Transcript length: 621 Transcript exons: 28019655-28020275 CTGTGGTGGTGTGCGTCTCCGACGGCGGCGGCGGCGGCGGACCGCGTCGGGAAGGACGAAGCGG ACCTCAGGTTGGACCCGCGCGTGTACGACCCGGTGGTGGTGGATGGGGGCGGCGGCGGCATGAG CTTCTCCGCCGGCGCCGACGAGCGGCGCAGGATCTTGCCGGCGGCGGAGGCGGTCTGGCGGCGC TGCGAGGAGGAGGGAGCCGCGTTGGCCGAGGAGGACGCGTCGCGCCGGCAGCGGGACCGCTTGT TGTGCCCCCACTGCAGCAGCACGTCGCCACCGGTGCCCGCGCCGTTGGAGCTCGGCGAGGCCGT GTCGGAGGAGTCGGACGGGTGGTGGTGGTGGTGGTGGTTGTGGTGGGCGTGCGCGTGGTCGCGC GCCGGGCTCCAGGCGGCGGCCGACGAGGACGACGGCTGCGGCGCCCGAGCGCGCAGCGGCTTGG AATCGAGCTGTGACGACGGGAGGTACGACGAGAGGCGGGAGCTGTCCGCGGCGACGGCCATGCC GCCATCGTCGTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCCG CCGCCGTTGGCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTAC
Genomic sequence	CTGTGGTGGTGTGCGTCTCCGACGGCGGCGGCGGCGGCGGACCGCGTCGGGAAGGACGAAGCGG ACCTCAGGTTGGACCCGCGCGTGTACGACCCGGTGGTGGTGGATGGGGGCGGCGGCGGCATGAG CTTCTCCGCCGGCGCCGACGAGCGGCGCAGGATCTTGCCGGCGGCGGAGGCGGTCTGGCGGCGC TGCGAGGAGGAGGGAGCCGCGTTGGCCGAGGAGGACGCGTCGCGCCGGCAGCGGGACCGCTTGT TGTGCCCCCACTGCAGCAGCACGTCGCCACCGGTGCCCGCGCCGTTGGAGCTCGGCGAGGCCGT GTCGGAGGAGTCGGACGGGTGGTGGTGGTGGTGGTGGTTGTGGTGGGCGTGCGCGTGGTCGCGC GCCGGGCTCCAGGCGGCGGCCGACGAGGACGACGGCTGCGGCGCCCGAGCGCGCAGCGGCTTGG AATCGAGCTGTGACGACGGGAGGTACGACGAGAGGCGGGAGCTGTCCGCGGCGACGGCCATGCC GCCATCGTCGTCCTTGCAGGATCTCGACGCCGGCTTCCGTGTCACGCTACCGCTTCCTCCGCCG CCGCCGTTGGCTAGCGGGAGGCAGTCCGGGCTAAGCCTTTGGTAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002302* osi_circ_010566 						
					
						PMCS
						0.454710655

Conservation Information
Conserved circRNAs	osi_circ_002302* osi_circ_010566
PMCS	0.454710655

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							28019779-28020272(+)
28020165-28019657(-)
						
					

						Potential amino acid sequence
						
							MSFSAGADERRRILPAAEAVWRRCEEEGAALAEEDASRRQRDRLLCPHCSSTSPPVPAPLELGE
AVSEESDGWWWWWWLWWACAWSRAGLQAAADEDDGCGARARSGLESSCDDGRYDERRELSAATA
MPPSSSLQDLDAGFRVTLPLPPPPPLASGRQSGLSLWYLWWCASPTAAAAADRVGKDEADLRLD
PRVYDPVVVDGGGGGMSFSAGADERRRILPAAEAVWRRCEEEGAALAEEDASRRQRDRLLCPHC
SSTSPPVPAPLELGEAVSEESDGWWWWWWLWWACAWSRAGLQAAADEDDGCGARARSGLESSCD
DGRYDERRELSAATAMPPSSSLQDLDAGFRVTLPLPPPPPLASGRQSGLSLWYLWWCASPTAAA
AADRVGKDEADLRLDPRVYDPVVVDGGGGGMSFSAGADERRRILPAAEAVWRRCEEEGAALAEE
DASRRQRDRLLCPHCSSTSPPVPAPLELGEAVSEESDGWWWWWWLWWACAWSRAGLQAAADEDD
GCGARARSGLESSCDDGRYDERRELSAATAMPPSSSLQDLDAGFRVTLPLPPPPPLASGRQSGL
SLWYLWWCASPTAAAAADRVGKDEADLRLDPRVYDPVVVDGGGGGMSFSAGADERRRILPAAEA
VWRRCEEEGAALAEEDASRRQRDRLLCPHCSSTSPPVPAPLELGEAVSEESDGWWWWWWLWWAC
AWSRAGLQAAADEDDGCGARARSGLESSCDDGRYDERRELSAATAMPPSSSLQDLDAGFRVTLP
LPPPPPLASGRQSGLSLWY(+)
MAVAADSSRLSSYLPSSQLDSKPLRARAPQPSSSSAAAWSPARDHAHAHHNHHHHHHPSDSSDT
ASPSSNGAGTGGDVLLQWGHNKRSRCRRDASSSANAAPSSSQRRQTASAAGKILRRSSAPAEKL
MPPPPPSTTTGSYTRGSNLRSASSFPTRSAAAAAVGDAHHHRYQRLSPDCLPLANGGGGGSGSV
TRKPASRSCKDDDGGMAVAADSSRLSSYLPSSQLDSKPLRARAPQPSSSSAAAWSPARDHAHAH
HNHHHHHHPSDSSDTASPSSNGAGTGGDVLLQWGHNKRSRCRRDASSSANAAPSSSQRRQTASA
AGKILRRSSAPAEKLMPPPPPSTTTGSYTRGSNLRSASSFPTRSAAAAAVGDAHHHRYQRLSPD
CLPLANGGGGGSGSVTRKPASRSCKDDDGGMAVAADSSRLSSYLPSSQLDSKPLRARAPQPSSS
SAAAWSPARDHAHAHHNHHHHHHPSDSSDTASPSSNGAGTGGDVLLQWGHNKRSRCRRDASSSA
NAAPSSSQRRQTASAAGKILRRSSAPAEKLMPPPPPSTTTGSYTRGSNLRSASSFPTRSAAAAA
VGDAHHHRYQRLSPDCLPLANGGGGGSGSVTRKPASRSCKDDDGGMAVAADSSRLSSYLPSSQL
DSKPLRARAPQPSSSSAAAWSPARDHAHAHHNHHHHHHPSDSSDTASPSSNGAGTGGDVLLQWG
HNKRSRCRRDASSSANAAPSSSQRRQTASAAGKILRRSSAPAEKLMPPPPPSTTTGSYTRGSNL
RSASSFPTRSAAAAAVGDAHHH(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	28019779-28020272(+) 28020165-28019657(-)
Potential amino acid sequence	MSFSAGADERRRILPAAEAVWRRCEEEGAALAEEDASRRQRDRLLCPHCSSTSPPVPAPLELGE AVSEESDGWWWWWWLWWACAWSRAGLQAAADEDDGCGARARSGLESSCDDGRYDERRELSAATA MPPSSSLQDLDAGFRVTLPLPPPPPLASGRQSGLSLWYLWWCASPTAAAAADRVGKDEADLRLD PRVYDPVVVDGGGGGMSFSAGADERRRILPAAEAVWRRCEEEGAALAEEDASRRQRDRLLCPHC SSTSPPVPAPLELGEAVSEESDGWWWWWWLWWACAWSRAGLQAAADEDDGCGARARSGLESSCD DGRYDERRELSAATAMPPSSSLQDLDAGFRVTLPLPPPPPLASGRQSGLSLWYLWWCASPTAAA AADRVGKDEADLRLDPRVYDPVVVDGGGGGMSFSAGADERRRILPAAEAVWRRCEEEGAALAEE DASRRQRDRLLCPHCSSTSPPVPAPLELGEAVSEESDGWWWWWWLWWACAWSRAGLQAAADEDD GCGARARSGLESSCDDGRYDERRELSAATAMPPSSSLQDLDAGFRVTLPLPPPPPLASGRQSGL SLWYLWWCASPTAAAAADRVGKDEADLRLDPRVYDPVVVDGGGGGMSFSAGADERRRILPAAEA VWRRCEEEGAALAEEDASRRQRDRLLCPHCSSTSPPVPAPLELGEAVSEESDGWWWWWWLWWAC AWSRAGLQAAADEDDGCGARARSGLESSCDDGRYDERRELSAATAMPPSSSLQDLDAGFRVTLP LPPPPPLASGRQSGLSLWY(+) MAVAADSSRLSSYLPSSQLDSKPLRARAPQPSSSSAAAWSPARDHAHAHHNHHHHHHPSDSSDT ASPSSNGAGTGGDVLLQWGHNKRSRCRRDASSSANAAPSSSQRRQTASAAGKILRRSSAPAEKL MPPPPPSTTTGSYTRGSNLRSASSFPTRSAAAAAVGDAHHHRYQRLSPDCLPLANGGGGGSGSV TRKPASRSCKDDDGGMAVAADSSRLSSYLPSSQLDSKPLRARAPQPSSSSAAAWSPARDHAHAH HNHHHHHHPSDSSDTASPSSNGAGTGGDVLLQWGHNKRSRCRRDASSSANAAPSSSQRRQTASA AGKILRRSSAPAEKLMPPPPPSTTTGSYTRGSNLRSASSFPTRSAAAAAVGDAHHHRYQRLSPD CLPLANGGGGGSGSVTRKPASRSCKDDDGGMAVAADSSRLSSYLPSSQLDSKPLRARAPQPSSS SAAAWSPARDHAHAHHNHHHHHHPSDSSDTASPSSNGAGTGGDVLLQWGHNKRSRCRRDASSSA NAAPSSSQRRQTASAAGKILRRSSAPAEKLMPPPPPSTTTGSYTRGSNLRSASSFPTRSAAAAA VGDAHHHRYQRLSPDCLPLANGGGGGSGSVTRKPASRSCKDDDGGMAVAADSSRLSSYLPSSQL DSKPLRARAPQPSSSSAAAWSPARDHAHAHHNHHHHHHPSDSSDTASPSSNGAGTGGDVLLQWG HNKRSRCRRDASSSANAAPSSSQRRQTASAAGKILRRSSAPAEKLMPPPPPSTTTGSYTRGSNL RSASSFPTRSAAAAAVGDAHHH(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015;Chu et al., 2017; this study

circRNA

Detail information of Os01g0680700_circ_g.7

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