Plant Circular RNA Database

Detail information of AT3G23540_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT3G23540_circ_g.7
					
						ID in PlantcircBase
						ath_circ_023412
					
						Alias
						At_ciR4453
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 8445303-8446013  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							AT3G23540						
					
						Parent gene annotation
						
							Alpha/beta-Hydrolases superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 AT3G23470_circ_g.1 3_circ_ag.2 3_circ_ag.3 AT3G23470_circ_g.4 AT3G23470_circ_g.5 AT3G23470_circ_g.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 AT3G23480_circ_g.1 AT3G23480_circ_g.2 AT3G23480_circ_g.3 AT3G23490_circ_g.1 3_circ_ag.2 3_circ_ag.3 AT3G23510_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 3_circ_ag.10 3_circ_ag.11 3_circ_ag.12 3_circ_ag.13 AT3G23510_circ_g.14 3_circ_ag.15 3_circ_ag.16 3_circ_ag.17 3_circ_ag.18 3_circ_ag.19 3_circ_ag.20 3_circ_igg.21 AT3G23530_circ_g.1 AT3G23530_circ_g.2 AT3G23530_circ_g.3 AT3G23530_circ_g.4 AT3G23530_circ_g.5 AT3G23530_circ_g.6 AT3G23530_circ_g.7 AT3G23530_circ_g.8 AT3G23530_circ_g.9 AT3G23540_circ_g.1 AT3G23540_circ_g.2 AT3G23540_circ_g.3 AT3G23540_circ_g.4 AT3G23540_circ_g.5 AT3G23540_circ_g.6 AT3G23540_circ_g.8 AT3G23540_circ_g.9 AT3G23540_circ_g.10 AT3G23540_circ_g.11 						
					
						Support reads
						3
					
						Tissues
						leaf
					
						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
						AT3G23540.3:3
AT3G23540.2:3
AT3G23540.1:3

General Information
CircRNA Name	AT3G23540_circ_g.7
ID in PlantcircBase	ath_circ_023412
Alias	At_ciR4453
Organism	Arabidpsis thaliana
Position	chr3: 8445303-8446013 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	AT3G23540
Parent gene annotation	Alpha/beta-Hydrolases superfamily protein
Parent gene strand	+
Alternative splicing	3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 AT3G23470_circ_g.1 3_circ_ag.2 3_circ_ag.3 AT3G23470_circ_g.4 AT3G23470_circ_g.5 AT3G23470_circ_g.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 AT3G23480_circ_g.1 AT3G23480_circ_g.2 AT3G23480_circ_g.3 AT3G23490_circ_g.1 3_circ_ag.2 3_circ_ag.3 AT3G23510_circ_g.1 3_circ_ag.2 3_circ_ag.3 3_circ_ag.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 3_circ_ag.10 3_circ_ag.11 3_circ_ag.12 3_circ_ag.13 AT3G23510_circ_g.14 3_circ_ag.15 3_circ_ag.16 3_circ_ag.17 3_circ_ag.18 3_circ_ag.19 3_circ_ag.20 3_circ_igg.21 AT3G23530_circ_g.1 AT3G23530_circ_g.2 AT3G23530_circ_g.3 AT3G23530_circ_g.4 AT3G23530_circ_g.5 AT3G23530_circ_g.6 AT3G23530_circ_g.7 AT3G23530_circ_g.8 AT3G23530_circ_g.9 AT3G23540_circ_g.1 AT3G23540_circ_g.2 AT3G23540_circ_g.3 AT3G23540_circ_g.4 AT3G23540_circ_g.5 AT3G23540_circ_g.6 AT3G23540_circ_g.8 AT3G23540_circ_g.9 AT3G23540_circ_g.10 AT3G23540_circ_g.11
Support reads	3
Tissues	leaf
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	AT3G23540.3:3 AT3G23540.2:3 AT3G23540.1:3

			
						 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  
						
							CTCTCTACTGTATATTCAGGTAAAATTTGCTATACAGTTTATGCGGAGAGCTATTCAGAAAAAA
GCAAAGTTTGATATAATGGAATTGAACACCATTAAGaaggatgatctgaaggctgtggttgagt
ttttgcggcaggatggaaacatatccttgattgggctatgggggcggtcaatgggtgctgttac
taggtttg

						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
						
							AAGGATGATCTGAAGGCTGTGGTTGAGTTTTTGCGGCAGGATGGAAACATATCCTTGATTGGGC
TATGGGGGCGGTCAATGGGTGCTGTTACTAGGTTTGGCCCAGTCTATAATTTGTTAATTTACTA
AGAGCTTATCGTTTTTCTGCTTTGCATGAAGTTTCAGTTGATGGTATGAGACTGTCACTGTGTC
AATGGAACTTAATTATACCGGAAGTTTACATTTGTTGTGAAGCTTCATTAGTTTTAGAGGGTAG
AATAGGTGCTGTGATAGTTTCTGGTGATTAGTCATAGCTATCACATGTCACAAGGGAAGAATTA
TAAGAGACTAATGTTTGAGATAAGCAATTTATCATGGCAATCACTTGTACTGCCTTAAACTATG
ATAGCTTTGTGTTGAATCGTCCTTTTTTTTGTTACAGCTTGATGTATGGAGTCGAGGATCCTTC
GATTGCAGGAATGATTCTAGACAGCCCCTTCTCCGATTTAGTTGATCTGATGATGGAACTTGTT
GATACATATAAGTTTCGTCTGCCAAAGTTTACTGTAAGTAAATGTATATTTTGGTGGGAGTTGT
TCTTTATACTGCAAGGCTTCCACATGTATTCAGCTCTCTCTACTGTATATTCAGGTAAAATTTG
CTATACAGTTTATGCGGAGAGCTATTCAGAAAAAAGCAAAGTTTGATATAATGGAATTGAACAC
CATTAAG

Sequences
Splice junction sequence	CTCTCTACTGTATATTCAGGTAAAATTTGCTATACAGTTTATGCGGAGAGCTATTCAGAAAAAA GCAAAGTTTGATATAATGGAATTGAACACCATTAAGaaggatgatctgaaggctgtggttgagt ttttgcggcaggatggaaacatatccttgattgggctatgggggcggtcaatgggtgctgttac taggtttg
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	AAGGATGATCTGAAGGCTGTGGTTGAGTTTTTGCGGCAGGATGGAAACATATCCTTGATTGGGC TATGGGGGCGGTCAATGGGTGCTGTTACTAGGTTTGGCCCAGTCTATAATTTGTTAATTTACTA AGAGCTTATCGTTTTTCTGCTTTGCATGAAGTTTCAGTTGATGGTATGAGACTGTCACTGTGTC AATGGAACTTAATTATACCGGAAGTTTACATTTGTTGTGAAGCTTCATTAGTTTTAGAGGGTAG AATAGGTGCTGTGATAGTTTCTGGTGATTAGTCATAGCTATCACATGTCACAAGGGAAGAATTA TAAGAGACTAATGTTTGAGATAAGCAATTTATCATGGCAATCACTTGTACTGCCTTAAACTATG ATAGCTTTGTGTTGAATCGTCCTTTTTTTTGTTACAGCTTGATGTATGGAGTCGAGGATCCTTC GATTGCAGGAATGATTCTAGACAGCCCCTTCTCCGATTTAGTTGATCTGATGATGGAACTTGTT GATACATATAAGTTTCGTCTGCCAAAGTTTACTGTAAGTAAATGTATATTTTGGTGGGAGTTGT TCTTTATACTGCAAGGCTTCCACATGTATTCAGCTCTCTCTACTGTATATTCAGGTAAAATTTG CTATACAGTTTATGCGGAGAGCTATTCAGAAAAAAGCAAAGTTTGATATAATGGAATTGAACAC CATTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.196622752

Conservation Information
Conserved circRNAs	NA
PMCS	0.196622752

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							8445381-8446010(+)
						
						Potential amino acid sequence
						
							MGAVTSLMYGVEDPSIAGMILDSPFSDLVDLMMELVDTYKFRLPKFTVKFAIQFMRRAIQKKAK
FDIMELNTIKKDDLKAVVEFLRQDGNISLIGLWGRSMGAVTSLMYGVEDPSIAGMILDSPFSDL
VDLMMELVDTYKFRLPKFTVKFAIQFMRRAIQKKAKFDIMELNTIKKDDLKAVVEFLRQDGNIS
LIGLWGRSMGAVTSLMYGVEDPSIAGMILDSPFSDLVDLMMELVDTYKFRLPKFTVKFAIQFMR
RAIQKKAKFDIMELNTIKKDDLKAVVEFLRQDGNISLIGLWGRSMGAVTSLMYGVEDPSIAGMI
LDSPFSDLVDLMMELVDTYKFRLPKFTVKFAIQFMRRAIQKKAKFDIMELNTIK(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	8445381-8446010(+)
Potential amino acid sequence	MGAVTSLMYGVEDPSIAGMILDSPFSDLVDLMMELVDTYKFRLPKFTVKFAIQFMRRAIQKKAK FDIMELNTIKKDDLKAVVEFLRQDGNISLIGLWGRSMGAVTSLMYGVEDPSIAGMILDSPFSDL VDLMMELVDTYKFRLPKFTVKFAIQFMRRAIQKKAKFDIMELNTIKKDDLKAVVEFLRQDGNIS LIGLWGRSMGAVTSLMYGVEDPSIAGMILDSPFSDLVDLMMELVDTYKFRLPKFTVKFAIQFMR RAIQKKAKFDIMELNTIKKDDLKAVVEFLRQDGNISLIGLWGRSMGAVTSLMYGVEDPSIAGMI LDSPFSDLVDLMMELVDTYKFRLPKFTVKFAIQFMRRAIQKKAKFDIMELNTIK(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015

circRNA

Detail information of AT3G23540_circ_g.7

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