Plant Circular RNA Database

Detail information of AT3G28970_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G28970_circ_g.4
					
						ID in PlantcircBase
						ath_circ_024283
					
						Alias
						3:10988605-10988864
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 10988605-10988864  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G28970						
					
						Parent gene annotation
						
							Defective in cullin neddylation protein
							
						Parent gene strand
						-
					
						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 3_circ_ig.9 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 AT3G28980_circ_g.1 						
					
						Support reads
						1/1/1/2
					
						Tissues
						seedling;root;leaf;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  
						
							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
						AT3G28970.2:2
AT3G28970.1:2

General Information
CircRNA Name	AT3G28970_circ_g.4
ID in PlantcircBase	ath_circ_024283
Alias	3:10988605-10988864
Organism	Arabidpsis thaliana
Position	chr3: 10988605-10988864 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G28970
Parent gene annotation	Defective in cullin neddylation protein
Parent gene strand	-
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 3_circ_ig.9 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 AT3G28980_circ_g.1
Support reads	1/1/1/2
Tissues	seedling;root;leaf;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	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	AT3G28970.2:2 AT3G28970.1:2

			
						 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  
						
							AAACAACCAAAAAGTACCTCGATAAAGTCACACCAGCGGTTAAGTAACCTAAATCTCCCAGCCA
AAACAAGTTTCCATGCAGTAATAGCTCTACTTATAGcttcagagtcatatccttctagattctc
atgtacacaacgactaaacgccaagacttgttgccaagtatcttctgaaatattgtgccgttga
tttttcta

						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: 180
Transcript exons: 10988605-10988701,10988782-10988864
CTTCAGAGTCATATCCTTCTAGATTCTCATGTACACAACGACTAAACGCCAAGACTTGTTGCCA
AGTATCTTCTGAAATATTGTGCCGTTGATTTTTCTCGATAAAGTCACACCAGCGGTTAAGTAAC
CTAAATCTCCCAGCCAAAACAAGTTTCCATGCAGTAATAGCTCTACTTATAG
						
						Genomic sequence
						
							CTTCAGAGTCATATCCTTCTAGATTCTCATGTACACAACGACTAAACGCCAAGACTTGTTGCCA
AGTATCTTCTGAAATATTGTGCCGTTGATTTTTCTACAAGTTAACATCATCTCCTTCTCATTAG
ATATACAAACACAAAGAGCCATTTGGTACAAAAAACAACCAAAAAGTACCTCGATAAAGTCACA
CCAGCGGTTAAGTAACCTAAATCTCCCAGCCAAAACAAGTTTCCATGCAGTAATAGCTCTACTT
ATAG

Sequences
Splice junction sequence	AAACAACCAAAAAGTACCTCGATAAAGTCACACCAGCGGTTAAGTAACCTAAATCTCCCAGCCA AAACAAGTTTCCATGCAGTAATAGCTCTACTTATAGcttcagagtcatatccttctagattctc atgtacacaacgactaaacgccaagacttgttgccaagtatcttctgaaatattgtgccgttga tttttcta
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: 180 Transcript exons: 10988605-10988701,10988782-10988864 CTTCAGAGTCATATCCTTCTAGATTCTCATGTACACAACGACTAAACGCCAAGACTTGTTGCCA AGTATCTTCTGAAATATTGTGCCGTTGATTTTTCTCGATAAAGTCACACCAGCGGTTAAGTAAC CTAAATCTCCCAGCCAAAACAAGTTTCCATGCAGTAATAGCTCTACTTATAG
Genomic sequence	CTTCAGAGTCATATCCTTCTAGATTCTCATGTACACAACGACTAAACGCCAAGACTTGTTGCCA AGTATCTTCTGAAATATTGTGCCGTTGATTTTTCTACAAGTTAACATCATCTCCTTCTCATTAG ATATACAAACACAAAGAGCCATTTGGTACAAAAAACAACCAAAAAGTACCTCGATAAAGTCACA CCAGCGGTTAAGTAACCTAAATCTCCCAGCCAAAACAAGTTTCCATGCAGTAATAGCTCTACTT ATAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.264734486

Conservation Information
Conserved circRNAs	NA
PMCS	0.264734486

			
						 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 AT3G28970_circ_g.4

Address

Any questions?

Supported by