Plant Circular RNA Database

Detail information of AT2G39840_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT2G39840_circ_g.2
					
						ID in PlantcircBase
						ath_circ_017545
					
						Alias
						At_ciR4638, Ath_circ_FC3858
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 16627963-16628802  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							AT2G39840						
					
						Parent gene annotation
						
							Serine/threonine-protein phosphatase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/4
					
						Tissues
						leaf/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
						AT2G39840.1:2

General Information
CircRNA Name	AT2G39840_circ_g.2
ID in PlantcircBase	ath_circ_017545
Alias	At_ciR4638, Ath_circ_FC3858
Organism	Arabidpsis thaliana
Position	chr2: 16627963-16628802 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
Parent gene	AT2G39840
Parent gene annotation	Serine/threonine-protein phosphatase
Parent gene strand	+
Alternative splicing	NA
Support reads	3/4
Tissues	leaf/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	AT2G39840.1:2

			
						 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  
						
							AGCGTGGACGAGAACCTTATGTGCTCGTTTCAGATTTTGAAGCCCGCTGAGAAGAAGACCAAGT
TCATGATGTCCACAAAGATTTGATACTTTCATTGAGgtgacatacatgggcaatatagtgattt
gttgaggctatttgagtatggtggcttccctcctagtgccaattatctatttcttggggactat
gtggacag

									
								

					

						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: 762
Transcript exons: 16627963-16628522,16628601-16628802
GTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAG
TGCCAATTATCTATTTCTTGGGGACTATGTGGACAGAGGCAAACAGAGTCTTGAAACAATATGT
CTCTTACTAGCTTACAAGATCAAATACCCTGGCAACTTTTTTCTACTAAGGGGAAACCACGAAT
GTGCTTCTATCAATAGGATATATGGATTTTATGATGAGTGTAAAAGGAGGTTCAATGTGAGAGT
ATGGAAGGTTTTTACTGATTGTTTTAACTGCCTTCCTGTTGCGGCGCTTATAGATGACAAAATA
TTGTGTATGCACGGTGGACTTTCGCCGGATCTTGACCATTTGGATGAGATTAGAAACTTGCCGA
GACCAACTATGATTCCGGATACCGGGCTTCTCTGTGATTTGCTCTGGTCTGATCCTGGGAAAGA
TGTTAAAGGATGGGGAATGAATGATAGAGGTGTTTCATACACCTTTGGTCCAGATAAAGTTTCC
GAGTTTCTTACGAAACATGATTTAGATCTTGTGTGTCGTGCCCATCAGGTCGTGGAGGATGGGT
ATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATT
TGATAATGCTGGTGCGATGATGAGCGTGGACGAGAACCTTATGTGCTCGTTTCAGATTTTGAAG
CCCGCTGAGAAGAAGACCAAGTTCATGATGTCCACAAAGATTTGATACTTTCATTGAG
						
					

						Genomic sequence
						
							GTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAG
TGCCAATTATCTATTTCTTGGGGACTATGTGGACAGAGGCAAACAGAGTCTTGAAACAATATGT
CTCTTACTAGCTTACAAGATCAAATACCCTGGCAACTTTTTTCTACTAAGGGGAAACCACGAAT
GTGCTTCTATCAATAGGATATATGGATTTTATGATGAGTGTAAAAGGAGGTTCAATGTGAGAGT
ATGGAAGGTTTTTACTGATTGTTTTAACTGCCTTCCTGTTGCGGCGCTTATAGATGACAAAATA
TTGTGTATGCACGGTGGACTTTCGCCGGATCTTGACCATTTGGATGAGATTAGAAACTTGCCGA
GACCAACTATGATTCCGGATACCGGGCTTCTCTGTGATTTGCTCTGGTCTGATCCTGGGAAAGA
TGTTAAAGGATGGGGAATGAATGATAGAGGTGTTTCATACACCTTTGGTCCAGATAAAGTTTCC
GAGTTTCTTACGAAACATGATTTAGATCTTGTGTGTCGTGCCCATCAGGTAGATATTTTTCAAT
CATGTCTCTTTGATACTACTGCTTTTGTGATGTTAACAAGGGAGTTGGATTTTTTATGGCAGGT
CGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAAC
TACTGTGGTGAATTTGATAATGCTGGTGCGATGATGAGCGTGGACGAGAACCTTATGTGCTCGT
TTCAGATTTTGAAGCCCGCTGAGAAGAAGACCAAGTTCATGATGTCCACAAAGATTTGATACTT
TCATTGAG
						
					

			
		

Sequences
Splice junction sequence	AGCGTGGACGAGAACCTTATGTGCTCGTTTCAGATTTTGAAGCCCGCTGAGAAGAAGACCAAGT TCATGATGTCCACAAAGATTTGATACTTTCATTGAGgtgacatacatgggcaatatagtgattt gttgaggctatttgagtatggtggcttccctcctagtgccaattatctatttcttggggactat gtggacag
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: 762 Transcript exons: 16627963-16628522,16628601-16628802 GTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAG TGCCAATTATCTATTTCTTGGGGACTATGTGGACAGAGGCAAACAGAGTCTTGAAACAATATGT CTCTTACTAGCTTACAAGATCAAATACCCTGGCAACTTTTTTCTACTAAGGGGAAACCACGAAT GTGCTTCTATCAATAGGATATATGGATTTTATGATGAGTGTAAAAGGAGGTTCAATGTGAGAGT ATGGAAGGTTTTTACTGATTGTTTTAACTGCCTTCCTGTTGCGGCGCTTATAGATGACAAAATA TTGTGTATGCACGGTGGACTTTCGCCGGATCTTGACCATTTGGATGAGATTAGAAACTTGCCGA GACCAACTATGATTCCGGATACCGGGCTTCTCTGTGATTTGCTCTGGTCTGATCCTGGGAAAGA TGTTAAAGGATGGGGAATGAATGATAGAGGTGTTTCATACACCTTTGGTCCAGATAAAGTTTCC GAGTTTCTTACGAAACATGATTTAGATCTTGTGTGTCGTGCCCATCAGGTCGTGGAGGATGGGT ATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAACTACTGTGGTGAATT TGATAATGCTGGTGCGATGATGAGCGTGGACGAGAACCTTATGTGCTCGTTTCAGATTTTGAAG CCCGCTGAGAAGAAGACCAAGTTCATGATGTCCACAAAGATTTGATACTTTCATTGAG
Genomic sequence	GTGACATACATGGGCAATATAGTGATTTGTTGAGGCTATTTGAGTATGGTGGCTTCCCTCCTAG TGCCAATTATCTATTTCTTGGGGACTATGTGGACAGAGGCAAACAGAGTCTTGAAACAATATGT CTCTTACTAGCTTACAAGATCAAATACCCTGGCAACTTTTTTCTACTAAGGGGAAACCACGAAT GTGCTTCTATCAATAGGATATATGGATTTTATGATGAGTGTAAAAGGAGGTTCAATGTGAGAGT ATGGAAGGTTTTTACTGATTGTTTTAACTGCCTTCCTGTTGCGGCGCTTATAGATGACAAAATA TTGTGTATGCACGGTGGACTTTCGCCGGATCTTGACCATTTGGATGAGATTAGAAACTTGCCGA GACCAACTATGATTCCGGATACCGGGCTTCTCTGTGATTTGCTCTGGTCTGATCCTGGGAAAGA TGTTAAAGGATGGGGAATGAATGATAGAGGTGTTTCATACACCTTTGGTCCAGATAAAGTTTCC GAGTTTCTTACGAAACATGATTTAGATCTTGTGTGTCGTGCCCATCAGGTAGATATTTTTCAAT CATGTCTCTTTGATACTACTGCTTTTGTGATGTTAACAAGGGAGTTGGATTTTTTATGGCAGGT CGTGGAGGATGGGTATGAGTTCTTTGCTGATAGACAACTTGTGACGGTGTTTTCAGCTCCTAAC TACTGTGGTGAATTTGATAATGCTGGTGCGATGATGAGCGTGGACGAGAACCTTATGTGCTCGT TTCAGATTTTGAAGCCCGCTGAGAAGAAGACCAAGTTCATGATGTCCACAAAGATTTGATACTT TCATTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.86195844

Conservation Information
Conserved circRNAs	NA
PMCS	0.86195844

			
						 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
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT2G39840_circ_g.2

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