Plant Circular RNA Database

Detail information of AT1G12240_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G12240_circ_g.2
					
						ID in PlantcircBase
						ath_circ_002211
					
						Alias
						Ath_circ_FC0320
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 4155090-4155334  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, CIRI-full, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							AT1G12240						
					
						Parent gene annotation
						
							Acid beta-fructofuranosidase 4, vacuolar
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.2 AT1G11400_circ_g.1 AT1G11400_circ_g.2 AT1G11400_circ_g.3 AT1G11400_circ_g.4 AT1G11430_circ_g.1 1_circ_ag.2 AT1G11430_circ_g.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 1_circ_ag.7 1_circ_ag.8 AT1G11480_circ_g.1 AT1G11545_circ_g.1 AT1G11580_circ_g.1 AT1G11580_circ_g.2 AT1G11580_circ_g.3 AT1G11580_circ_g.4 AT1G11580_circ_g.5 AT1G11650_circ_g.1 AT1G11660_circ_g.1 AT1G11660_circ_g.2 AT1G11670_circ_g.1 AT1G11680_circ_g.1 AT1G11720_circ_g.1 AT1G11720_circ_g.2 AT1G11750_circ_g.1 AT1G11750_circ_g.2 AT1G11750_circ_g.3 AT1G11750_circ_g.4 AT1G11750_circ_g.5 AT1G11780_circ_g.1 AT1G11790_circ_g.1 AT1G11790_circ_g.2 AT1G11840_circ_g.1 AT1G11840_circ_g.2 AT1G11840_circ_g.3 AT1G11840_circ_g.4 AT1G11840_circ_g.5 AT1G11850_circ_g.1 AT1G11850_circ_g.2 AT1G11850_circ_g.3 AT1G11860_circ_g.1 AT1G11860_circ_g.2 AT1G11860_circ_g.3 AT1G11860_circ_g.4 AT1G11860_circ_g.5 AT1G11870_circ_g.1 AT1G11880_circ_g.1 AT1G11880_circ_g.2 AT1G11880_circ_g.3 AT1G11880_circ_g.4 AT1G11890_circ_g.1 AT1G11890_circ_g.2 AT1G11890_circ_g.3 AT1G11890_circ_g.4 AT1G11910_circ_g.1 AT1G11910_circ_g.2 AT1G11910_circ_g.3 AT1G11910_circ_g.4 AT1G11910_circ_g.5 AT1G11910_circ_g.6 AT1G11910_circ_g.7 AT1G11910_circ_g.8 AT1G11910_circ_g.9 AT1G11910_circ_g.10 AT1G11910_circ_g.11 AT1G11910_circ_g.12 AT1G11930_circ_g.1 AT1G11950_circ_g.1 AT1G11960_circ_g.1 AT1G11960_circ_g.2 AT1G11960_circ_g.3 AT1G11960_circ_g.4 AT1G11960_circ_g.5 AT1G12000_circ_g.1 AT1G12000_circ_g.2 AT1G12000_circ_g.3 AT1G12000_circ_g.4 AT1G12000_circ_g.5 AT1G12000_circ_g.6 AT1G12000_circ_g.7 AT1G12000_circ_g.8 AT1G12050_circ_g.1 AT1G12050_circ_g.2 AT1G12080_circ_g.1 AT1G12080_circ_g.2 AT1G12080_circ_g.3 AT1G12080_circ_g.4 AT1G12080_circ_g.5 AT1G12080_circ_g.6 AT1G12080_circ_g.7 AT1G12080_circ_g.8 AT1G12080_circ_g.9 AT1G12080_circ_g.10 AT1G12090_circ_g.1 AT1G12090_circ_g.2 AT1G12090_circ_g.3 AT1G12090_circ_g.4 AT1G12090_circ_g.5 AT1G12110_circ_g.1 AT1G12110_circ_g.2 1_circ_ag.3 AT1G04927_circ_g.1 1_circ_ag.2 AT1G12200_circ_g.1 AT1G12220_circ_g.1 AT1G12230_circ_g.1 AT1G12230_circ_g.2 AT1G12230_circ_g.3 AT1G12230_circ_g.4 AT1G12240_circ_g.1 AT1G12240_circ_g.3 AT1G12270_circ_g.1 AT1G12270_circ_g.2 AT1G12270_circ_g.3 AT1G12270_circ_g.4 AT1G12270_circ_g.5 AT1G12290_circ_g.1 1_circ_igg.2 AT1G12290_circ_g.3 1_circ_igg.4 AT1G12310_circ_g.1 AT1G12310_circ_g.2 AT1G12330_circ_g.1 AT1G12330_circ_g.2 AT1G12330_circ_g.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 1_circ_ag.7 1_circ_ag.8 AT1G12350_circ_g.1 AT1G12350_circ_g.2 AT1G12350_circ_g.3 AT1G12360_circ_g.1 AT1G12360_circ_g.2 AT1G12360_circ_g.3 AT1G12360_circ_g.4 AT1G12360_circ_g.5 AT1G12360_circ_g.6 AT1G12360_circ_g.7 AT1G12380_circ_g.1 						
					
						Support reads
						40
					
						Tissues
						root, inflorescences, whole_plant
					
						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
						AT1G12240.1:1

General Information
CircRNA Name	AT1G12240_circ_g.2
ID in PlantcircBase	ath_circ_002211
Alias	Ath_circ_FC0320
Organism	Arabidpsis thaliana
Position	chr1: 4155090-4155334 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, CIRI-full, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ
Parent gene	AT1G12240
Parent gene annotation	Acid beta-fructofuranosidase 4, vacuolar
Parent gene strand	+
Alternative splicing	1_circ_ag.2 AT1G11400_circ_g.1 AT1G11400_circ_g.2 AT1G11400_circ_g.3 AT1G11400_circ_g.4 AT1G11430_circ_g.1 1_circ_ag.2 AT1G11430_circ_g.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 1_circ_ag.7 1_circ_ag.8 AT1G11480_circ_g.1 AT1G11545_circ_g.1 AT1G11580_circ_g.1 AT1G11580_circ_g.2 AT1G11580_circ_g.3 AT1G11580_circ_g.4 AT1G11580_circ_g.5 AT1G11650_circ_g.1 AT1G11660_circ_g.1 AT1G11660_circ_g.2 AT1G11670_circ_g.1 AT1G11680_circ_g.1 AT1G11720_circ_g.1 AT1G11720_circ_g.2 AT1G11750_circ_g.1 AT1G11750_circ_g.2 AT1G11750_circ_g.3 AT1G11750_circ_g.4 AT1G11750_circ_g.5 AT1G11780_circ_g.1 AT1G11790_circ_g.1 AT1G11790_circ_g.2 AT1G11840_circ_g.1 AT1G11840_circ_g.2 AT1G11840_circ_g.3 AT1G11840_circ_g.4 AT1G11840_circ_g.5 AT1G11850_circ_g.1 AT1G11850_circ_g.2 AT1G11850_circ_g.3 AT1G11860_circ_g.1 AT1G11860_circ_g.2 AT1G11860_circ_g.3 AT1G11860_circ_g.4 AT1G11860_circ_g.5 AT1G11870_circ_g.1 AT1G11880_circ_g.1 AT1G11880_circ_g.2 AT1G11880_circ_g.3 AT1G11880_circ_g.4 AT1G11890_circ_g.1 AT1G11890_circ_g.2 AT1G11890_circ_g.3 AT1G11890_circ_g.4 AT1G11910_circ_g.1 AT1G11910_circ_g.2 AT1G11910_circ_g.3 AT1G11910_circ_g.4 AT1G11910_circ_g.5 AT1G11910_circ_g.6 AT1G11910_circ_g.7 AT1G11910_circ_g.8 AT1G11910_circ_g.9 AT1G11910_circ_g.10 AT1G11910_circ_g.11 AT1G11910_circ_g.12 AT1G11930_circ_g.1 AT1G11950_circ_g.1 AT1G11960_circ_g.1 AT1G11960_circ_g.2 AT1G11960_circ_g.3 AT1G11960_circ_g.4 AT1G11960_circ_g.5 AT1G12000_circ_g.1 AT1G12000_circ_g.2 AT1G12000_circ_g.3 AT1G12000_circ_g.4 AT1G12000_circ_g.5 AT1G12000_circ_g.6 AT1G12000_circ_g.7 AT1G12000_circ_g.8 AT1G12050_circ_g.1 AT1G12050_circ_g.2 AT1G12080_circ_g.1 AT1G12080_circ_g.2 AT1G12080_circ_g.3 AT1G12080_circ_g.4 AT1G12080_circ_g.5 AT1G12080_circ_g.6 AT1G12080_circ_g.7 AT1G12080_circ_g.8 AT1G12080_circ_g.9 AT1G12080_circ_g.10 AT1G12090_circ_g.1 AT1G12090_circ_g.2 AT1G12090_circ_g.3 AT1G12090_circ_g.4 AT1G12090_circ_g.5 AT1G12110_circ_g.1 AT1G12110_circ_g.2 1_circ_ag.3 AT1G04927_circ_g.1 1_circ_ag.2 AT1G12200_circ_g.1 AT1G12220_circ_g.1 AT1G12230_circ_g.1 AT1G12230_circ_g.2 AT1G12230_circ_g.3 AT1G12230_circ_g.4 AT1G12240_circ_g.1 AT1G12240_circ_g.3 AT1G12270_circ_g.1 AT1G12270_circ_g.2 AT1G12270_circ_g.3 AT1G12270_circ_g.4 AT1G12270_circ_g.5 AT1G12290_circ_g.1 1_circ_igg.2 AT1G12290_circ_g.3 1_circ_igg.4 AT1G12310_circ_g.1 AT1G12310_circ_g.2 AT1G12330_circ_g.1 AT1G12330_circ_g.2 AT1G12330_circ_g.3 1_circ_ag.4 1_circ_ag.5 1_circ_ag.6 1_circ_ag.7 1_circ_ag.8 AT1G12350_circ_g.1 AT1G12350_circ_g.2 AT1G12350_circ_g.3 AT1G12360_circ_g.1 AT1G12360_circ_g.2 AT1G12360_circ_g.3 AT1G12360_circ_g.4 AT1G12360_circ_g.5 AT1G12360_circ_g.6 AT1G12360_circ_g.7 AT1G12380_circ_g.1
Support reads	40
Tissues	root, inflorescences, whole_plant
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	AT1G12240.1:1

			
						 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  
						
							ATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGATGGCTCTATAGTC
ATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAGgtccattgttctacaagggatggtacca
tttcttctaccaatataacccaaacgcagccgtatggggtgacattgtttggggtcacgccgtg
tctaggga

									
								

					

						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: 171
Transcript exons: 4155090-4155149,4155224-4155334
GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGGTCG
CTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGATGGCTC
TATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
Transcript length: 177
Transcript exons: 4155090-4155156,4155225-4155334
GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG
GGGTCGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGA
TGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
Transcript length: 184
Transcript exons: 4155090-4155176,4155238-4155334
GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG
GGGTGACATTGTTTGGGGTCACGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTC
TCCCTGATGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
Transcript length: 237
Transcript exons: 4155090-4155127,4155136-4155334
GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCCCAAACGCAGCCGTATGGGGTGACA
TTGTTTGGGGTCACGCCGTGTCTAGGGACCTAATCCATTGGGTCCATTTGCCCATAGCCATGGT
CGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGATGGC
TCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
Transcript length: 245
Transcript exons: 4155090-4155334
GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG
GGGTGACATTGTTTGGGGTCACGCCGTGTCTAGGGACCTAATCCATTGGGTCCATTTGCCCATA
GCCATGGTCGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCC
CTGATGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
						
					

						Genomic sequence
						
							GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG
GGGTGACATTGTTTGGGGTCACGCCGTGTCTAGGGACCTAATCCATTGGGTCCATTTGCCCATA
GCCATGGTCGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCC
CTGATGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
						
					

			
		

Sequences
Splice junction sequence	ATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGATGGCTCTATAGTC ATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAGgtccattgttctacaagggatggtacca tttcttctaccaatataacccaaacgcagccgtatggggtgacattgtttggggtcacgccgtg tctaggga
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: 171 Transcript exons: 4155090-4155149,4155224-4155334 GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGGTCG CTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGATGGCTC TATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG Transcript length: 177 Transcript exons: 4155090-4155156,4155225-4155334 GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG GGGTCGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGA TGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG Transcript length: 184 Transcript exons: 4155090-4155176,4155238-4155334 GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG GGGTGACATTGTTTGGGGTCACGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTC TCCCTGATGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG Transcript length: 237 Transcript exons: 4155090-4155127,4155136-4155334 GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCCCAAACGCAGCCGTATGGGGTGACA TTGTTTGGGGTCACGCCGTGTCTAGGGACCTAATCCATTGGGTCCATTTGCCCATAGCCATGGT CGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCCCTGATGGC TCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG Transcript length: 245 Transcript exons: 4155090-4155334 GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG GGGTGACATTGTTTGGGGTCACGCCGTGTCTAGGGACCTAATCCATTGGGTCCATTTGCCCATA GCCATGGTCGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCC CTGATGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG
Genomic sequence	GTCCATTGTTCTACAAGGGATGGTACCATTTCTTCTACCAATATAACCCAAACGCAGCCGTATG GGGTGACATTGTTTGGGGTCACGCCGTGTCTAGGGACCTAATCCATTGGGTCCATTTGCCCATA GCCATGGTCGCTGATCAATGGTACGACTCCAACGGTGTGTGGACCGGCTCAGCCACATTTCTCC CTGATGGCTCTATAGTCATGCTCTATACCGGTTCCACCGACAAAGCGGTGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.660380691

Conservation Information
Conserved circRNAs	NA
PMCS	0.660380691

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

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT1G12240_circ_g.2

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