Plant Circular RNA Database

Detail information of 3_circ_ig.9

			
						 General Information
					
						CircRNA Name
						3_circ_ig.9
					
						ID in PlantcircBase
						ath_circ_024274
					
						Alias
						3:10963899-10965716
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10963899-10965716  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							3_circ_ag.3 3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.3 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28900_circ_g.3 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1 						
					
						Support reads
						2/2/1
					
						Tissues
						root;flower
					
						Exon boundary  
						
							NA-NA							"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
						NA

General Information
CircRNA Name	3_circ_ig.9
ID in PlantcircBase	ath_circ_024274
Alias	3:10963899-10965716
Organism	Arabidpsis thaliana
Position	chr3: 10963899-10965716 JBrowse»
Reference genome	TAIR10.38
Type	ig-circRNA
Identification method	find_circ; CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	3_circ_ag.3 3_circ_ag.4 AT3G28830_circ_g.1 AT3G28860_circ_g.1 AT3G28860_circ_g.2 AT3G28860_circ_g.3 AT3G28860_circ_g.4 AT3G28860_circ_g.5 AT3G28860_circ_g.6 3_circ_ag.7 AT3G28900_circ_g.1 AT3G28900_circ_g.2 AT3G28900_circ_g.3 AT3G28910_circ_g.1 3_circ_ig.2 AT3G28930_circ_g.1 AT3G28930_circ_g.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ig.8 AT3G28940_circ_g.1 AT3G28940_circ_g.2 AT3G28940_circ_g.3 AT3G28940_circ_g.4 AT3G28950_circ_g.1 AT3G28970_circ_g.1 AT3G28970_circ_g.2 AT3G28970_circ_g.3 AT3G28970_circ_g.4 AT3G28980_circ_g.1
Support reads	2/2/1
Tissues	root;flower
Exon boundary	NA-NA "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	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  
						
							CTAACCCTGAACAATTAAAACTATAAAAAAAAAGAAAATTAGATACAAAGAGAGAAAGTTAAAG
AGAAAAGTACCCTTTGAGAGTCTCCATCTGTAATATcttttcctgaaatcggtttcttactctg
gttcttgtcttttttctgtaactacatatgttcaacgaatgaagggattcattgatgtatatat
ggatatgc

									
								

					

						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
						
							CTTTTCCTGAAATCGGTTTCTTACTCTGGTTCTTGTCTTTTTTCTGTAACTACATATGTTCAAC
GAATGAAGGGATTCATTGATGTATATATGGATATGCAATAAGCTGATAACAATTATAGCTCGAG
CGTAACAATTTGATTAACCTACCTTGAGCTCATTGTAGGTTGTGTGAAGAGAGTTGACGAGTGG
ATTGTCAAACAATGTCAAGCAGCGATCTGCATATTTCACATCAACGTTTTGGCATGTATCAAAT
AGAGTTTATAGCATTCATTTATTCAATCACGATGCACATGGATTTTAATTTGAAGACTATCATA
GGTAGTTAAGTAGGTTTCTTCTGCTTACCAAGGTTCTATAATTCTAATGTATGTTGTGAACTTG
GCCGGGGGTGTGAGATCTTATGTGGATTTACCTCTCTGGAGACATCTGGGTCCAAGTTTCCTTT
ATACACTTCTTTCCACTATCTACCTACTATACACAGGTAAGCACTGTAATTAAACAAACATTTA
GTGAGATTGTAGTGAGATTGGTGCACCTCACTCACCGGTTCCCTAATGTGAGAGAGAGTAGGAT
ATACCTGAACGAAAAGGCATGGAGAGGACTTTGAGATAATGCCACCGCATCCAGTTAGATCAGT
CGTATTCAAGATTTTTGATCATATCCCATCTCCAAAACATTTCAAAGAAGAACAACTAACAGAA
CATAATAAAAGACATAATTGAATGGTCCAAAAATTAGTATAGTGATCATGAAGTCATTGTAAGA
TTGATGTATTCTCACCTTTCCAGTAGCTACGACGAAGTTAAGTCCCCTCACCATGACTTCTTTT
CAACCTTTGCATTTGCATCCAAAATTTGACCAGTGTGCCTAGTAAGCGTTCACACCAAAGAAGA
AAACGCTGAGCAAAAACAACATTGCTGAGTAAACCTTACCATCCACATCACATTATATATAGGA
GTACTTTGTTTTGTCGAATCTTAGGCCGTCCCACTTTTTCCTGTCTTTCATGGACATTTTGGAG
TTTGGGCATATAGATACCTAAAATTGAAAATAACATTCTATAGGAAATCATTAAGAAAGCTTGG
ATAAGAAATCTCAATTGTTACTAACAAAGTATTAGGTTGGTTATTTACGATATAGATGCAAGAT
TACTTACTGAATACTGATTAATAGATGTGTATGTGGCAGAATCTTTGAAGATGGCCTAAATAGC
TTGTCAAAAGTATTTGTTCCTTCCTTTACATATCTCCCATCCTGAAAAAGTCTGAGAAACTGGT
TATAACAAATACCCTAAGAGAAAGATGGGTATAGCTATTTCCAATCTGCTACTAGTAGTTTTAC
TCTGAGCATGTTTACCTATTCAGCTGCCAAACACTAGCTCTTTCCACTCTGCTTAGTTTCTTTG
GAGGAATTCACTTGATTCTCTGCCAGGTATGTTCTCTATGTCTCTTACGCGACAAAACTTACAA
CCTATGGCAGAAACTCTAATTTCGGACAATTTGGTTCTCGCAAAGAGTTCTGAAACATATTCAT
GATATGCTACCTTTGAGAGACGTATTCGTTCATGGGGTTTGTTGGTTCCTACCGCTTGTGCGTA
CCAAGAAAAACCGAAGATAAGTTAAAATAGTTATACCTTATCTGATTCACACGGTATTTAGCCT
TAAAACCTTGTGTCAGAGAATCCAAGAAGCTGGTTGCAAGTAACACCAAGCTCTCTAACCCTGA
ACAATTAAAACTATAAAAAAAAAGAAAATTAGATACAAAGAGAGAAAGTTAAAGAGAAAAGTAC
CCTTTGAGAGTCTCCATCTGTAATAT
						
					

			
		

Sequences
Splice junction sequence	CTAACCCTGAACAATTAAAACTATAAAAAAAAAGAAAATTAGATACAAAGAGAGAAAGTTAAAG AGAAAAGTACCCTTTGAGAGTCTCCATCTGTAATATcttttcctgaaatcggtttcttactctg gttcttgtcttttttctgtaactacatatgttcaacgaatgaagggattcattgatgtatatat ggatatgc
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	CTTTTCCTGAAATCGGTTTCTTACTCTGGTTCTTGTCTTTTTTCTGTAACTACATATGTTCAAC GAATGAAGGGATTCATTGATGTATATATGGATATGCAATAAGCTGATAACAATTATAGCTCGAG CGTAACAATTTGATTAACCTACCTTGAGCTCATTGTAGGTTGTGTGAAGAGAGTTGACGAGTGG ATTGTCAAACAATGTCAAGCAGCGATCTGCATATTTCACATCAACGTTTTGGCATGTATCAAAT AGAGTTTATAGCATTCATTTATTCAATCACGATGCACATGGATTTTAATTTGAAGACTATCATA GGTAGTTAAGTAGGTTTCTTCTGCTTACCAAGGTTCTATAATTCTAATGTATGTTGTGAACTTG GCCGGGGGTGTGAGATCTTATGTGGATTTACCTCTCTGGAGACATCTGGGTCCAAGTTTCCTTT ATACACTTCTTTCCACTATCTACCTACTATACACAGGTAAGCACTGTAATTAAACAAACATTTA GTGAGATTGTAGTGAGATTGGTGCACCTCACTCACCGGTTCCCTAATGTGAGAGAGAGTAGGAT ATACCTGAACGAAAAGGCATGGAGAGGACTTTGAGATAATGCCACCGCATCCAGTTAGATCAGT CGTATTCAAGATTTTTGATCATATCCCATCTCCAAAACATTTCAAAGAAGAACAACTAACAGAA CATAATAAAAGACATAATTGAATGGTCCAAAAATTAGTATAGTGATCATGAAGTCATTGTAAGA TTGATGTATTCTCACCTTTCCAGTAGCTACGACGAAGTTAAGTCCCCTCACCATGACTTCTTTT CAACCTTTGCATTTGCATCCAAAATTTGACCAGTGTGCCTAGTAAGCGTTCACACCAAAGAAGA AAACGCTGAGCAAAAACAACATTGCTGAGTAAACCTTACCATCCACATCACATTATATATAGGA GTACTTTGTTTTGTCGAATCTTAGGCCGTCCCACTTTTTCCTGTCTTTCATGGACATTTTGGAG TTTGGGCATATAGATACCTAAAATTGAAAATAACATTCTATAGGAAATCATTAAGAAAGCTTGG ATAAGAAATCTCAATTGTTACTAACAAAGTATTAGGTTGGTTATTTACGATATAGATGCAAGAT TACTTACTGAATACTGATTAATAGATGTGTATGTGGCAGAATCTTTGAAGATGGCCTAAATAGC TTGTCAAAAGTATTTGTTCCTTCCTTTACATATCTCCCATCCTGAAAAAGTCTGAGAAACTGGT TATAACAAATACCCTAAGAGAAAGATGGGTATAGCTATTTCCAATCTGCTACTAGTAGTTTTAC TCTGAGCATGTTTACCTATTCAGCTGCCAAACACTAGCTCTTTCCACTCTGCTTAGTTTCTTTG GAGGAATTCACTTGATTCTCTGCCAGGTATGTTCTCTATGTCTCTTACGCGACAAAACTTACAA CCTATGGCAGAAACTCTAATTTCGGACAATTTGGTTCTCGCAAAGAGTTCTGAAACATATTCAT GATATGCTACCTTTGAGAGACGTATTCGTTCATGGGGTTTGTTGGTTCCTACCGCTTGTGCGTA CCAAGAAAAACCGAAGATAAGTTAAAATAGTTATACCTTATCTGATTCACACGGTATTTAGCCT TAAAACCTTGTGTCAGAGAATCCAAGAAGCTGGTTGCAAGTAACACCAAGCTCTCTAACCCTGA ACAATTAAAACTATAAAAAAAAAGAAAATTAGATACAAAGAGAGAAAGTTAAAGAGAAAAGTAC CCTTTGAGAGTCTCCATCTGTAATAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.096675478

Conservation Information
Conserved circRNAs	NA
PMCS	0.096675478

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

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of 3_circ_ig.9

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