Plant Circular RNA Database

Detail information of Os11g0428500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os11g0428500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_009232
					
						Alias
						Os_ciR5178
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 13707994-13708315  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI, circseq_cup, find_circ
					
						Parent gene
						
							Os11g0428500						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os11t0428500-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0428500_circ_g.1 Os11g0428500_circ_g.3 						
					
						Support reads
						3/4/3
					
						Tissues
						root/root/anther
					
						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.2
ID in PlantcircBase	osa_circ_009232
Alias	Os_ciR5178
Organism	Oryza sativa
Position	chr11: 13707994-13708315 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRI, circseq_cup, find_circ
Parent gene	Os11g0428500
Parent gene annotation	Conserved hypothetical protein. (Os11t0428500-01)
Parent gene strand	-
Alternative splicing	Os11g0428500_circ_g.1 Os11g0428500_circ_g.3
Support reads	3/4/3
Tissues	root/root/anther
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   
						
							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	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	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  
						
							TTTTTAGGGGAGGCGGAGTGAAACGACGAAGAAACAACGCCTTTTTCTGTCCACGCGCGCCAAG
GGGCAAGATGGACATTTCACCATCCGAATTCCACGTcacgatggccactcagacggaaccatgc
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: 322
Transcript exons: 13707994-13708315
CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGGTGGATTCGTAAGCGGCTGCTCATGTTTTTTAGGGGAGGCGGAGTGAAACGACGAAGAAA
CAACGCCTTTTTCTGTCCACGCGCGCCAAGGGGCAAGATGGACATTTCACCATCCGAATTCCAC
GT
Transcript length: 224
Transcript exons: 13707994-13708315
TTTAGGGGAGGCGGAGTGAAACGACGAAGAAACAACGCCTTTTTCTGTCCACGCGCGCCAAGGG
GCAAGATGGACATTTCACCATCCGAATTCCACGTCACGATGGCCACTCAGACGGAACCATGCCT
CCTTCTCAACAAACCCTAGACTATCAGATCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGGTGGATTCGTAAGCGGCTGCTCATGTTT
						
						Genomic sequence
						
							CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA
AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG
GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG
CTCGGTGGATTCGTAAGCGGCTGCTCATGTTTTTTAGGGGAGGCGGAGTGAAACGACGAAGAAA
CAACGCCTTTTTCTGTCCACGCGCGCCAAGGGGCAAGATGGACATTTCACCATCCGAATTCCAC
GT

Sequences
Splice junction sequence	TTTTTAGGGGAGGCGGAGTGAAACGACGAAGAAACAACGCCTTTTTCTGTCCACGCGCGCCAAG GGGCAAGATGGACATTTCACCATCCGAATTCCACGTcacgatggccactcagacggaaccatgc 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: 322 Transcript exons: 13707994-13708315 CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGGTGGATTCGTAAGCGGCTGCTCATGTTTTTTAGGGGAGGCGGAGTGAAACGACGAAGAAA CAACGCCTTTTTCTGTCCACGCGCGCCAAGGGGCAAGATGGACATTTCACCATCCGAATTCCAC GT Transcript length: 224 Transcript exons: 13707994-13708315 TTTAGGGGAGGCGGAGTGAAACGACGAAGAAACAACGCCTTTTTCTGTCCACGCGCGCCAAGGG GCAAGATGGACATTTCACCATCCGAATTCCACGTCACGATGGCCACTCAGACGGAACCATGCCT CCTTCTCAACAAACCCTAGACTATCAGATCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGGTGGATTCGTAAGCGGCTGCTCATGTTT
Genomic sequence	CACGATGGCCACTCAGACGGAACCATGCCTCCTTCTCAACAAACCCTAGACTATCAGATCTTAA AAAAAAACAAGTGAATCCGGAGAAAAAAGTGAGGGAAACAGATGCCAAACTAAACCAAAAGAGG GGAAGATGGTGGATCTATCGATCTCCTACCTGGGATTGCTGTCACGGTTTGGCCGCCGTCGCTG CTCGGTGGATTCGTAAGCGGCTGCTCATGTTTTTTAGGGGAGGCGGAGTGAAACGACGAAGAAA CAACGCCTTTTTCTGTCCACGCGCGCCAAGGGGCAAGATGGACATTTCACCATCCGAATTCCAC GT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.633060161

Conservation Information
Conserved circRNAs	NA
PMCS	0.633060161

			
						 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

circRNA

Detail information of Os11g0428500_circ_g.2

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