Plant Circular RNA Database

Detail information of Os04g0278900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0278900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_023281
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 11803377-11811761  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0278900						
					
						Parent gene annotation
						
							Similar to OSIGBa0113C11.1 protein. (Os04t0278900-01);tRNA-dihyd
rouridine synthase domain containing protein. (Os04t0278900-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0278900_circ_g.1 Os04g0278900_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						root
					
						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
						Os04t0278900-01:1
Os04t0278900-02:3

General Information
CircRNA Name	Os04g0278900_circ_g.3
ID in PlantcircBase	osa_circ_023281
Alias	NA
Organism	Oryza sativa
Position	chr4: 11803377-11811761 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0278900
Parent gene annotation	Similar to OSIGBa0113C11.1 protein. (Os04t0278900-01);tRNA-dihyd rouridine synthase domain containing protein. (Os04t0278900-02)
Parent gene strand	-
Alternative splicing	Os04g0278900_circ_g.1 Os04g0278900_circ_g.2
Support reads	1
Tissues	root
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	Os04t0278900-01:1 Os04t0278900-02:3

			
						 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  
						
							CGATTTTCTGCAGGACTGAGGCCACTTAGCAATGCCTTCCGGGCATGAATAATGAAATGCCTAG
TTGGTGATTTTGAAACAACCTTATCTACAAATTCACttattatatgcagcccggccaaccataa
ctcgatgtgcaccttgtcttatggatgcagtgacctgcaaatgaatataactgatgttcaataa
aaatgact

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CGATTTTCTGCAGGACTGAGGCCACTTAGCAATGCCTTCCGGGCATGAATAATGAAATGCCTAG TTGGTGATTTTGAAACAACCTTATCTACAAATTCACttattatatgcagcccggccaaccataa ctcgatgtgcaccttgtcttatggatgcagtgacctgcaaatgaatataactgatgttcaataa aaatgact
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.182321633

Conservation Information
Conserved circRNAs	NA
PMCS	0.182321633

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11811714-11803761(+)
						
						Potential amino acid sequence
						
							MKCLVGDFETTLSTNSLIICSPANHNSMCTLSYGCSDLINSSYTSI*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11811714-11803761(+)
Potential amino acid sequence	MKCLVGDFETTLSTNSLIICSPANHNSMCTLSYGCSDLINSSYTSI*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0278900_circ_g.3

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