Plant Circular RNA Database

Detail information of AT3G23640_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G23640_circ_g.2
					
						ID in PlantcircBase
						ath_circ_023435
					
						Alias
						3:8502327-8503160
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 8502327-8503160  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G23640						
					
						Parent gene annotation
						
							Heteroglycan glucosidase 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G23640_circ_g.1 AT3G23640_circ_g.3 						
					
						Support reads
						1/1/1/1
					
						Tissues
						seedling;root;flower
					
						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
						AT3G23640.2:4
AT3G23640.3:4
AT3G23640.1:4

General Information
CircRNA Name	AT3G23640_circ_g.2
ID in PlantcircBase	ath_circ_023435
Alias	3:8502327-8503160
Organism	Arabidpsis thaliana
Position	chr3: 8502327-8503160 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G23640
Parent gene annotation	Heteroglycan glucosidase 1
Parent gene strand	+
Alternative splicing	AT3G23640_circ_g.1 AT3G23640_circ_g.3
Support reads	1/1/1/1
Tissues	seedling;root;flower
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	AT3G23640.2:4 AT3G23640.3:4 AT3G23640.1:4

			
						 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  
						
							GGAATCATAAGAATTATCTCCCCAGCATCATATCCAATAATCACATTTGGTCCATTCTCCTCGC
CTACTGCTGTCTTGGAGTCCCTCTCGCACGCCATTGaaggaatggagacaaatctttacttagg
atgactttaagtggggatagctcggaaactgtagagatgacttcaactgatatgattttcgagc
cgattttg

									
								

					

						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: 596
Transcript exons: 8502327-8502597,8502669-8502737,8502807-8502944,8503043-
8503160
AAGGAATGGAGACAAATCTTTACTTAGGATGACTTTAAGTGGGGATAGCTCGGAAACTGTAGAG
ATGACTTCAACTGATATGATTTTCGAGCCGATTTTGGAGCATGGAGTTTTCCGGTTTGATTGTT
CTGTTGACCATAGGAAGGCTGCTTTTCCTAGTGTTTCATTTAAGAACAGCAAAGACCGGGAAGT
TCCTATTGTGAGTCACATTGTTCCAGCATATATTCCTACTTGTGGTTGTCTTCAGGACCAACAA
GTTGTCACCTTTGAGTTTTCTCCTGGTACATCGTTTTATGGGACGGGAGAAGTTAGTGGTCAGT
TGGAGAGAACAGGCAAACGGGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAAC
CACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAACACTAGGG
GTTCTTGCTGATACAACACGAAAGTGTGAGATTGATCTACGGAAAGAGGGAATCATAAGAATTA
TCTCCCCAGCATCATATCCAATAATCACATTTGGTCCATTCTCCTCGCCTACTGCTGTCTTGGA
GTCCCTCTCGCACGCCATTG
						
					

						Genomic sequence
						
							AAGGAATGGAGACAAATCTTTACTTAGGATGACTTTAAGTGGGGATAGCTCGGAAACTGTAGAG
ATGACTTCAACTGATATGATTTTCGAGCCGATTTTGGAGCATGGAGTTTTCCGGTTTGATTGTT
CTGTTGACCATAGGAAGGCTGCTTTTCCTAGTGTTTCATTTAAGAACAGCAAAGACCGGGAAGT
TCCTATTGTGAGTCACATTGTTCCAGCATATATTCCTACTTGTGGTTGTCTTCAGGACCAACAA
GTTGTCACCTTTGAGGTTAGTGTTTCAATTTTGACATGATCTAGAAAGATACTAGTAGTTCTCT
TAATGTAAACTTGTGATTGCAGTTTTCTCCTGGTACATCGTTTTATGGGACGGGAGAAGTTAGT
GGTCAGTTGGAGAGAACAGGCAAACGGGTGGGTTCATTCACTTAACAACCATCATCATTTCGTT
ACCCTGATTAATTTGGTGGGTATAATGTTCAGGTTTTTACTTGGAACACTGATGCATGGGGATA
TGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGA
GAAACACTAGGGGTTCTTGCTGATACAACACGAAAGTGTGAGGTATATGAGTATCCTAGCTGGT
GCAATCCCTCTTTTGTGGACCCACGTTGCAGTGCAATCTATCTTGTCCATTGTATTAACATCTT
TTACTTGTCTAGATTGATCTACGGAAAGAGGGAATCATAAGAATTATCTCCCCAGCATCATATC
CAATAATCACATTTGGTCCATTCTCCTCGCCTACTGCTGTCTTGGAGTCCCTCTCGCACGCCAT
TG
						
					

			
		

Sequences
Splice junction sequence	GGAATCATAAGAATTATCTCCCCAGCATCATATCCAATAATCACATTTGGTCCATTCTCCTCGC CTACTGCTGTCTTGGAGTCCCTCTCGCACGCCATTGaaggaatggagacaaatctttacttagg atgactttaagtggggatagctcggaaactgtagagatgacttcaactgatatgattttcgagc cgattttg
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: 596 Transcript exons: 8502327-8502597,8502669-8502737,8502807-8502944,8503043- 8503160 AAGGAATGGAGACAAATCTTTACTTAGGATGACTTTAAGTGGGGATAGCTCGGAAACTGTAGAG ATGACTTCAACTGATATGATTTTCGAGCCGATTTTGGAGCATGGAGTTTTCCGGTTTGATTGTT CTGTTGACCATAGGAAGGCTGCTTTTCCTAGTGTTTCATTTAAGAACAGCAAAGACCGGGAAGT TCCTATTGTGAGTCACATTGTTCCAGCATATATTCCTACTTGTGGTTGTCTTCAGGACCAACAA GTTGTCACCTTTGAGTTTTCTCCTGGTACATCGTTTTATGGGACGGGAGAAGTTAGTGGTCAGT TGGAGAGAACAGGCAAACGGGTTTTTACTTGGAACACTGATGCATGGGGATATGGTTCTGGAAC CACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGAGAAACACTAGGG GTTCTTGCTGATACAACACGAAAGTGTGAGATTGATCTACGGAAAGAGGGAATCATAAGAATTA TCTCCCCAGCATCATATCCAATAATCACATTTGGTCCATTCTCCTCGCCTACTGCTGTCTTGGA GTCCCTCTCGCACGCCATTG
Genomic sequence	AAGGAATGGAGACAAATCTTTACTTAGGATGACTTTAAGTGGGGATAGCTCGGAAACTGTAGAG ATGACTTCAACTGATATGATTTTCGAGCCGATTTTGGAGCATGGAGTTTTCCGGTTTGATTGTT CTGTTGACCATAGGAAGGCTGCTTTTCCTAGTGTTTCATTTAAGAACAGCAAAGACCGGGAAGT TCCTATTGTGAGTCACATTGTTCCAGCATATATTCCTACTTGTGGTTGTCTTCAGGACCAACAA GTTGTCACCTTTGAGGTTAGTGTTTCAATTTTGACATGATCTAGAAAGATACTAGTAGTTCTCT TAATGTAAACTTGTGATTGCAGTTTTCTCCTGGTACATCGTTTTATGGGACGGGAGAAGTTAGT GGTCAGTTGGAGAGAACAGGCAAACGGGTGGGTTCATTCACTTAACAACCATCATCATTTCGTT ACCCTGATTAATTTGGTGGGTATAATGTTCAGGTTTTTACTTGGAACACTGATGCATGGGGATA TGGTTCTGGAACCACTTCGTTATACCAGTCACATCCTTGGGTACTAGTTGTCCTTCCAACTGGA GAAACACTAGGGGTTCTTGCTGATACAACACGAAAGTGTGAGGTATATGAGTATCCTAGCTGGT GCAATCCCTCTTTTGTGGACCCACGTTGCAGTGCAATCTATCTTGTCCATTGTATTAACATCTT TTACTTGTCTAGATTGATCTACGGAAAGAGGGAATCATAAGAATTATCTCCCCAGCATCATATC CAATAATCACATTTGGTCCATTCTCCTCGCCTACTGCTGTCTTGGAGTCCCTCTCGCACGCCAT TG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.339337069

Conservation Information
Conserved circRNAs	NA
PMCS	0.339337069

			
						 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 AT3G23640_circ_g.2

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