Plant Circular RNA Database

Detail information of AT3G63340_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G63340_circ_g.2
					
						ID in PlantcircBase
						ath_circ_028933
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 23392494-23392866  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT3G63340						
					
						Parent gene annotation
						
							Protein phosphatase 2C family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.4 AT3G63340_circ_g.1 AT3G63340_circ_g.3 AT3G63340_circ_g.4 AT3G63340_circ_g.5 AT3G63340_circ_g.6 AT3G63340_circ_g.7 AT3G63340_circ_g.8 AT3G63340_circ_g.9 AT3G63340_circ_g.10 						
					
						Support reads
						1
					
						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  
						
							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
						AT3G63340.5:2
AT3G63340.2:2
AT3G63340.8:2
AT3G63340.7:2
AT3G63340.10:2
AT3G63340.6:2
AT3G63340.9:2
AT3G63340.1:2
AT3G63340.3:2
AT3G63340.4:2

General Information
CircRNA Name	AT3G63340_circ_g.2
ID in PlantcircBase	ath_circ_028933
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 23392494-23392866 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder
Parent gene	AT3G63340
Parent gene annotation	Protein phosphatase 2C family protein
Parent gene strand	-
Alternative splicing	3_circ_ag.4 AT3G63340_circ_g.1 AT3G63340_circ_g.3 AT3G63340_circ_g.4 AT3G63340_circ_g.5 AT3G63340_circ_g.6 AT3G63340_circ_g.7 AT3G63340_circ_g.8 AT3G63340_circ_g.9 AT3G63340_circ_g.10
Support reads	1
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	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	AT3G63340.5:2 AT3G63340.2:2 AT3G63340.8:2 AT3G63340.7:2 AT3G63340.10:2 AT3G63340.6:2 AT3G63340.9:2 AT3G63340.1:2 AT3G63340.3:2 AT3G63340.4:2

			
						 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  
						
							TTAAAAGAACGAACTGTCCTCTACCTGCTTTGAGCTGGCGCCACCATGTTTTAAAGAGCTACCT
GGGATTAGGATGCACATCTCCATTAAGGATCGAAGCccaatcttcagtgggtctctgctcttta
tctgttctgcaaaaaattcttcagagcatttccatgacgcaagtgaaattccaccctacataca
tcacagga

						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
						
							CCAATCTTCAGTGGGTCTCTGCTCTTTATCTGTTCTGCAAAAAATTCTTCAGAGCATTTCCATG
ACGCAAGTGAAATTCCACCCTACATACATCACAGGATATATTCGATTAAATATGCATGGATCGC
TATGAGACCCCAAAAAAAAAAAAAAAACTGAATGTGCTTAACAAGAATATCTCATAAACATAAT
CTCATTTCAAATTGACTTTTTGATACTGGTCAAATAAAACATACGTTTTTAATAACCTACGTTT
TTAATAACCATTGTAAGTTAAAAGAACGAACTGTCCTCTACCTGCTTTGAGCTGGCGCCACCAT
GTTTTAAAGAGCTACCTGGGATTAGGATGCACATCTCCATTAAGGATCGAAGC

Sequences
Splice junction sequence	TTAAAAGAACGAACTGTCCTCTACCTGCTTTGAGCTGGCGCCACCATGTTTTAAAGAGCTACCT GGGATTAGGATGCACATCTCCATTAAGGATCGAAGCccaatcttcagtgggtctctgctcttta tctgttctgcaaaaaattcttcagagcatttccatgacgcaagtgaaattccaccctacataca tcacagga
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	CCAATCTTCAGTGGGTCTCTGCTCTTTATCTGTTCTGCAAAAAATTCTTCAGAGCATTTCCATG ACGCAAGTGAAATTCCACCCTACATACATCACAGGATATATTCGATTAAATATGCATGGATCGC TATGAGACCCCAAAAAAAAAAAAAAAACTGAATGTGCTTAACAAGAATATCTCATAAACATAAT CTCATTTCAAATTGACTTTTTGATACTGGTCAAATAAAACATACGTTTTTAATAACCTACGTTT TTAATAACCATTGTAAGTTAAAAGAACGAACTGTCCTCTACCTGCTTTGAGCTGGCGCCACCAT GTTTTAAAGAGCTACCTGGGATTAGGATGCACATCTCCATTAAGGATCGAAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.173698079

Conservation Information
Conserved circRNAs	NA
PMCS	0.173698079

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23392854-23392496(-)
23392840-23392863(+)
23392555-23392863(+)
						
						Potential amino acid sequence
						
							MEMCILIPGSSLKHGGASSKQGGISLASWKCSEEFFAEQIKSRDPLKIGLRSLMEMCILIPGSS
LKHGGASSKQGGISLASWKCSEEFFAEQIKSRDPLKIGLRSLMEMCILIPGSSLKHGGASSKQG
GISLASWKCSEEFFAEQIKSRDPLKIGLRSLMEMCILIPGSSLKHGGASSKQGGISLASWKCSE
EFFAEQIKSRDPLKI(-)
MHISIKDRSPIFSGSLLFICSAKNSSEHFHDASEIPPCFELAPPCFKELPGIRMHISIKDRSPI
FSGSLLFICSAKNSSEHFHDASEIPPCFELAPPCFKELPGIRMHISIKDRSPIFSGSLLFICSA
KNSSEHFHDASEIPPCFELAPPCFKELPGIRMHISIKDRS(+)
MTQVKFHPALSWRHHVLKSYLGLGCTSPLRIEAQSSVGLCSLSVLQKILQSISMTQVKFHPALS
WRHHVLKSYLGLGCTSPLRIEAQSSVGLCSLSVLQKILQSISMTQVKFHPALSWRHHVLKSYLG
LGCTSPLRIEAQSSVGLCSLSVLQKILQSISMTQVKFHPALSWRHHVLKSYLGLGCTSPLRIE(
+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	23392854-23392496(-) 23392840-23392863(+) 23392555-23392863(+)
Potential amino acid sequence	MEMCILIPGSSLKHGGASSKQGGISLASWKCSEEFFAEQIKSRDPLKIGLRSLMEMCILIPGSS LKHGGASSKQGGISLASWKCSEEFFAEQIKSRDPLKIGLRSLMEMCILIPGSSLKHGGASSKQG GISLASWKCSEEFFAEQIKSRDPLKIGLRSLMEMCILIPGSSLKHGGASSKQGGISLASWKCSE EFFAEQIKSRDPLKI(-) MHISIKDRSPIFSGSLLFICSAKNSSEHFHDASEIPPCFELAPPCFKELPGIRMHISIKDRSPI FSGSLLFICSAKNSSEHFHDASEIPPCFELAPPCFKELPGIRMHISIKDRSPIFSGSLLFICSA KNSSEHFHDASEIPPCFELAPPCFKELPGIRMHISIKDRS(+) MTQVKFHPALSWRHHVLKSYLGLGCTSPLRIEAQSSVGLCSLSVLQKILQSISMTQVKFHPALS WRHHVLKSYLGLGCTSPLRIEAQSSVGLCSLSVLQKILQSISMTQVKFHPALSWRHHVLKSYLG LGCTSPLRIEAQSSVGLCSLSVLQKILQSISMTQVKFHPALSWRHHVLKSYLGLGCTSPLRIE( +)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G63340_circ_g.2

Address

Any questions?

Supported by