Plant Circular RNA Database

Detail information of 1_circ_ag.3

			
						 General Information
					
						CircRNA Name
						1_circ_ag.3
					
						ID in PlantcircBase
						ath_circ_004095
					
						Alias
						At_ciR754
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 8442246-8468211  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							AT1G23900_circ_g.1 1_circ_ag.2 AT1G23900_circ_g.4 1_circ_ag.5 1_circ_ag.6 AT1G23900_circ_g.7 AT1G23900_circ_g.8 AT1G23900_circ_g.9 AT1G23900_circ_g.10 AT1G23900_circ_g.11 AT1G23900_circ_g.12 AT1G23900_circ_g.13 1_circ_ag.14 1_circ_ag.15 AT1G23935_circ_g.1 AT1G23935_circ_g.2 						
					
						Support reads
						11
					
						Tissues
						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  
						
							GT-AG							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
						NA

General Information
CircRNA Name	1_circ_ag.3
ID in PlantcircBase	ath_circ_004095
Alias	At_ciR754
Organism	Arabidpsis thaliana
Position	chr1: 8442246-8468211 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	AT1G23900_circ_g.1 1_circ_ag.2 AT1G23900_circ_g.4 1_circ_ag.5 1_circ_ag.6 AT1G23900_circ_g.7 AT1G23900_circ_g.8 AT1G23900_circ_g.9 AT1G23900_circ_g.10 AT1G23900_circ_g.11 AT1G23900_circ_g.12 AT1G23900_circ_g.13 1_circ_ag.14 1_circ_ag.15 AT1G23935_circ_g.1 AT1G23935_circ_g.2
Support reads	11
Tissues	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	GT-AG 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	NA

			
						 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  
						
							CTTGCTTAAAGAAAAGCATCATGGGGTTCTAATAAGAGGAGTTCAACTTTGTTATGAATTATGC
ACGATTAATGATGAAGCCCTAGAGTACTTCAGAACGagatcttaatcactcgaaccagtatgtt
gtaggacttgctctctgtgctttagggaatatttgttcagcagaaatggcccgtgatcttgcgc
cagaagta

						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	CTTGCTTAAAGAAAAGCATCATGGGGTTCTAATAAGAGGAGTTCAACTTTGTTATGAATTATGC ACGATTAATGATGAAGCCCTAGAGTACTTCAGAACGagatcttaatcactcgaaccagtatgtt gtaggacttgctctctgtgctttagggaatatttgttcagcagaaatggcccgtgatcttgcgc cagaagta
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
						0.09445454

Conservation Information
Conserved circRNAs	NA
PMCS	0.09445454

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5021 ath-miR5658 						
					
						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	ath-miR5021 ath-miR5658
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of 1_circ_ag.3

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