Plant Circular RNA Database

Detail information of AT4G33240_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT4G33240_circ_g.4
					
						ID in PlantcircBase
						ath_circ_034362
					
						Alias
						4:16032899-16033227
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 16032899-16033227  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G33240						
					
						Parent gene annotation
						
							1-phosphatidylinositol-3-phosphate 5-kinase FAB1A
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G33240_circ_g.1 AT4G33240_circ_g.2 AT4G33240_circ_g.3 						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT4G33240.3:1
AT4G33240.7:1
AT4G33240.5:1
AT4G33240.6:1
AT4G33240.1:1
AT4G33240.2:1
AT4G33240.4:1

General Information
CircRNA Name	AT4G33240_circ_g.4
ID in PlantcircBase	ath_circ_034362
Alias	4:16032899-16033227
Organism	Arabidpsis thaliana
Position	chr4: 16032899-16033227 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G33240
Parent gene annotation	1-phosphatidylinositol-3-phosphate 5-kinase FAB1A
Parent gene strand	-
Alternative splicing	AT4G33240_circ_g.1 AT4G33240_circ_g.2 AT4G33240_circ_g.3
Support reads	1/1
Tissues	seedling;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	AT4G33240.3:1 AT4G33240.7:1 AT4G33240.5:1 AT4G33240.6:1 AT4G33240.1:1 AT4G33240.2:1 AT4G33240.4:1

			
						 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  
						
							CAGGCAGTTTCTTAACAGATATTGTCAGACTACCTTGCCTATGAGTATAACAATGAATGTGTGC
TTCCGCTGGCATCGTACATGACGGGCAGCACTGATCccgtagaaccggagacagtctctgtgaa
gggaatgaccacagttggccacacgactagccgctgcatggttagaaaagctcagctccaaaaa
tttgccaa

						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: 329
Transcript exons: 16032899-16033227
CCGTAGAACCGGAGACAGTCTCTGTGAAGGGAATGACCACAGTTGGCCACACGACTAGCCGCTG
CATGGTTAGAAAAGCTCAGCTCCAAAAATTTGCCAAAAGACAGGCCCCACGCAGCATCTGACAT
TACAATTCTGCGTGTGGCTGGAGGAAAGCCATTGATCCGAGGACATTTCAGGCACCGATGCCAC
ATCCAAATCTTCCCTTCACGTTGCCCAGGTAGCAATTCAGGCAGTTTCTTAACAGATATTGTCA
GACTACCTTGCCTATGAGTATAACAATGAATGTGTGCTTCCGCTGGCATCGTACATGACGGGCA
GCACTGATC
						
						Genomic sequence
						
							CCGTAGAACCGGAGACAGTCTCTGTGAAGGGAATGACCACAGTTGGCCACACGACTAGCCGCTG
CATGGTTAGAAAAGCTCAGCTCCAAAAATTTGCCAAAAGACAGGCCCCACGCAGCATCTGACAT
TACAATTCTGCGTGTGGCTGGAGGAAAGCCATTGATCCGAGGACATTTCAGGCACCGATGCCAC
ATCCAAATCTTCCCTTCACGTTGCCCAGGTAGCAATTCAGGCAGTTTCTTAACAGATATTGTCA
GACTACCTTGCCTATGAGTATAACAATGAATGTGTGCTTCCGCTGGCATCGTACATGACGGGCA
GCACTGATC

Sequences
Splice junction sequence	CAGGCAGTTTCTTAACAGATATTGTCAGACTACCTTGCCTATGAGTATAACAATGAATGTGTGC TTCCGCTGGCATCGTACATGACGGGCAGCACTGATCccgtagaaccggagacagtctctgtgaa gggaatgaccacagttggccacacgactagccgctgcatggttagaaaagctcagctccaaaaa tttgccaa
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: 329 Transcript exons: 16032899-16033227 CCGTAGAACCGGAGACAGTCTCTGTGAAGGGAATGACCACAGTTGGCCACACGACTAGCCGCTG CATGGTTAGAAAAGCTCAGCTCCAAAAATTTGCCAAAAGACAGGCCCCACGCAGCATCTGACAT TACAATTCTGCGTGTGGCTGGAGGAAAGCCATTGATCCGAGGACATTTCAGGCACCGATGCCAC ATCCAAATCTTCCCTTCACGTTGCCCAGGTAGCAATTCAGGCAGTTTCTTAACAGATATTGTCA GACTACCTTGCCTATGAGTATAACAATGAATGTGTGCTTCCGCTGGCATCGTACATGACGGGCA GCACTGATC
Genomic sequence	CCGTAGAACCGGAGACAGTCTCTGTGAAGGGAATGACCACAGTTGGCCACACGACTAGCCGCTG CATGGTTAGAAAAGCTCAGCTCCAAAAATTTGCCAAAAGACAGGCCCCACGCAGCATCTGACAT TACAATTCTGCGTGTGGCTGGAGGAAAGCCATTGATCCGAGGACATTTCAGGCACCGATGCCAC ATCCAAATCTTCCCTTCACGTTGCCCAGGTAGCAATTCAGGCAGTTTCTTAACAGATATTGTCA GACTACCTTGCCTATGAGTATAACAATGAATGTGTGCTTCCGCTGGCATCGTACATGACGGGCA GCACTGATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.529192865

Conservation Information
Conserved circRNAs	NA
PMCS	0.529192865

			
						 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 AT4G33240_circ_g.4

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