Plant Circular RNA Database

Detail information of Os11g0428500_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os11g0428500_circ_g.1
					
						ID in PlantcircBase
						osa_circ_009231
					
						Alias
						Os_ciR233, 
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 13707994-13708205  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI, circRNA_finder, circseq_cup, find_circ, CIRI-long
					
						Parent gene
						
							Os11g0428500						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os11t0428500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0428500_circ_g.2 Os11g0428500_circ_g.3 						
					
						Support reads
						217/41/7
					
						Tissues
						root/root/seed, pistil, root
					
						Exon boundary  
						
							No-No							"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
						Os11t0428500-01:1

General Information
CircRNA Name	Os11g0428500_circ_g.1
ID in PlantcircBase	osa_circ_009231
Alias	Os_ciR233,
Organism	Oryza sativa
Position	chr11: 13707994-13708205 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRI, circRNA_finder, circseq_cup, find_circ, CIRI-long
Parent gene	Os11g0428500
Parent gene annotation	Conserved hypothetical protein. (Os11t0428500-01)
Parent gene strand	-
Alternative splicing	Os11g0428500_circ_g.2 Os11g0428500_circ_g.3
Support reads	217/41/7
Tissues	root/root/seed, pistil, root
Exon boundary	No-No "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	Os11t0428500-01:1

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							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   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							Yes							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   
						
							F: GTCGCTGCTCGGTGGATTCG
 R: GCCAAACCGTGACAGCAATC
PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA 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	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	Yes 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	F: GTCGCTGCTCGGTGGATTCG R: GCCAAACCGTGACAGCAATC PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							ACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGT
TTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGGcacgatggccactcagacggaaccatgc
ctccttctcaacaaaccctagactatcagatcttaaaaaaaaacaagtgaatccggagaaaaaa
gtgaggga

									
								

					

						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: 117
Transcript exons: 13707994-13708062,13708158-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAATGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG
Transcript length: 166
Transcript exons: 13707994-13708032,13708079-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAAGAAAAAAGTGAGGGAAACAGATGCC
AAACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACG
GTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG
Transcript length: 176
Transcript exons: 13707994-13708064,13708101-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAAGCCAAACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCCTACCTGGGAT
TGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG
Transcript length: 181
Transcript exons: 13707994-13708105,13708137-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAATATCGATCTCCTACCT
GGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG
Transcript length: 186
Transcript exons: 13707994-13708073,13708100-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATTGCCAAACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCC
TACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG
Transcript length: 199
Transcript exons: 13707994-13708171,13708185-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGCTCGGTGGATTCG
TAAGCGG
Transcript length: 202
Transcript exons: 13707994-13708068,13708079-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGGGGAAGATGGT
GGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGAT
TCGTAAGCGG
Transcript length: 203
Transcript exons: 13707994-13708091,13708101-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGCCAAACTAAACCAAAAGAGGGGAAGATGG
TGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGA
TTCGTAAGCGG
Transcript length: 210
Transcript exons: 13707994-13708086,13708089-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGAGGGAAACAGATGCCAAACTAAACCAAAAGAGGGG
AAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCT
CGGTGGATTCGTAAGCGG
Transcript length: 211
Transcript exons: 13707994-13708162,13708164-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGCACGGTTTGGCCGCCGTCGCTGC
TCGGTGGATTCGTAAGCGG
Transcript length: 212
Transcript exons: 13707994-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGATGGATTCGTAAGCGG
Transcript length: 212
Transcript exons: 13707994-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGGTGGATTCGTAAGCGG
Transcript length: 212
Transcript exons: 13707994-13708205
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCATATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGGTGGATTCGTAAGCGG
						
					

						Genomic sequence
						
							CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGGTGGATTCGTAAGCGG
						
					

			
		

Sequences
Splice junction sequence	ACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGT TTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGGcacgatggccactcagacggaaccatgc ctccttctcaacaaaccctagactatcagatcttaaaaaaaaacaagtgaatccggagaaaaaa gtgaggga
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: 117 Transcript exons: 13707994-13708062,13708158-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAATGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG Transcript length: 166 Transcript exons: 13707994-13708032,13708079-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAAGAAAAAAGTGAGGGAAACAGATGCC AAACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACG GTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG Transcript length: 176 Transcript exons: 13707994-13708064,13708101-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAAGCCAAACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCCTACCTGGGAT TGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG Transcript length: 181 Transcript exons: 13707994-13708105,13708137-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAATATCGATCTCCTACCT GGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG Transcript length: 186 Transcript exons: 13707994-13708073,13708100-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATTGCCAAACTAAACCAAAAGAGGGGAAGATGGTGGATCTATCGATCTCC TACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGATTCGTAAGCGG Transcript length: 199 Transcript exons: 13707994-13708171,13708185-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGCTCGGTGGATTCG TAAGCGG Transcript length: 202 Transcript exons: 13707994-13708068,13708079-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGGGGAAGATGGT GGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGAT TCGTAAGCGG Transcript length: 203 Transcript exons: 13707994-13708091,13708101-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGCCAAACTAAACCAAAAGAGGGGAAGATGG TGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCTCGGTGGA TTCGTAAGCGG Transcript length: 210 Transcript exons: 13707994-13708086,13708089-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGAGGGAAACAGATGCCAAACTAAACCAAAAGAGGGG AAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTGCT CGGTGGATTCGTAAGCGG Transcript length: 211 Transcript exons: 13707994-13708162,13708164-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGCACGGTTTGGCCGCCGTCGCTGC TCGGTGGATTCGTAAGCGG Transcript length: 212 Transcript exons: 13707994-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGATGGATTCGTAAGCGG Transcript length: 212 Transcript exons: 13707994-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGGTGGATTCGTAAGCGG Transcript length: 212 Transcript exons: 13707994-13708205 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCATATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGGTGGATTCGTAAGCGG
Genomic sequence	CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGGTGGATTCGTAAGCGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.521682075

Conservation Information
Conserved circRNAs	NA
PMCS	0.521682075

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Ye et al., 2016;Chu et al., 2017; this study

circRNA

Detail information of Os11g0428500_circ_g.1

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