Plant Circular RNA Database

Detail information of AT3G22960_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G22960_circ_g.5
					
						ID in PlantcircBase
						ath_circ_023279
					
						Alias
						3:8140071-8141753
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 8140071-8141753  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G22960						
					
						Parent gene annotation
						
							Plastidial pyruvate kinase 1, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G22960_circ_g.4 AT3G22960_circ_g.6 AT3G22960_circ_g.7 AT3G22960_circ_g.8 						
					
						Support reads
						2/1
					
						Tissues
						seedling
					
						Exon boundary  
						
							Yes-No							"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
						AT3G22960.1:5

General Information
CircRNA Name	AT3G22960_circ_g.5
ID in PlantcircBase	ath_circ_023279
Alias	3:8140071-8141753
Organism	Arabidpsis thaliana
Position	chr3: 8140071-8141753 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G22960
Parent gene annotation	Plastidial pyruvate kinase 1, chloroplastic
Parent gene strand	+
Alternative splicing	AT3G22960_circ_g.4 AT3G22960_circ_g.6 AT3G22960_circ_g.7 AT3G22960_circ_g.8
Support reads	2/1
Tissues	seedling
Exon boundary	Yes-No "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	AT3G22960.1:5

			
						 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  
						
							AAGCAACTTGAACAAAACATTCTCGTTACTGAAATCAAGAGGTATGATCAAATCTGGTGACCTC
GTGATCGCAGTCTCGGACATGCTGCAATCAATCCAGgatggtgaggtttggactttcactgtta
gagcttttgattcttctcgtcctgaacgtaccattagtgttagctacgatggtttcgctgaagg
tatatgca

									
								

					

						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
						
							GATGGTGAGGTTTGGACTTTCACTGTTAGAGCTTTTGATTCTTCTCGTCCTGAACGTACCATTA
GTGTTAGCTACGATGGTTTCGCTGAAGGTATATGCAATTATGTTTATGTAAAAGTGGAAGTGAA
AACATTAGATGAATATTATGGTGACTGCGTATGAAATAGGAATCATTTGGTCTTTGTGTGTGGT
GTAGATGTAAGAGTTGGGGATGAACTTTTGGTTGATGGTGGGATGGTGAGATTTGAAGTGATTG
AGAAGATTGGTCCTGATGTTAAGTGTCTATGTACCGATCCTGGATTGTTGCTTCCTCGAGCTAA
CTTGACGTTTTGGAGAGATGGAAGTCTTGTACGAGAGCGTAATGCCATGCTTCCAACAATTTCT
TCCAAGGTTTGTAATTTTGTATCTTCCCTTTAAGCTTTGAATTATGATTCACTTTACTTGGTAA
ATTTGGGAGGGATCAAAGCAATGGTGAAGATGTACACTTTTGGAAACTAGATGAGTCCATGTTA
GCAAAACAGATGATACCTGAGGGAAAACATACTCATTTTCACTGATGATACCTCAATTCTTTAT
ATTCAGGACTGGTTGGATATTGATTTTGGAATTGCTGAAGGTGTGGATTTCATTGCTGTATCGT
TTGTCAAGTCGGCTGAAGTCATTAATCACCTTAAAAGTTATCTTGCTGCTCGTTCCCGTGGAGG
GTAAGTAAACATGCTCAATATCAACACATCATACTACTGTACAGGAAACATATGATCTACTTTG
GGATTGGGTTTTGCGTCATGTATTCACCATCTTTAGTTATAGTTTTATTTTGATGTTGTATTCA
ACTATGATGCAGGGAAATTGGAGTGATTGCAAAGATCGAGAGTATCGATTCACTGACCAATTTG
GAAGAAATTATTCTAGCATCAGATGGGGCCATGGTTGCAAGAGGAGATCTGGGAGCTCAGATAC
CTCTTGAGCAAGTTCCAGCAGCTCAACAGAGAATCGTCCAAGTATGCAGAGCTCTTAACAAACC
CGTCATTGTCGCTTCACAGCTATTGGAGTCCATGATTGAGTACCCAACTCCAACCAGAGCAGAA
GTTGCCGACGTGTCTGAAGCAGTAAGACAAAGATCAGATGCATTGATGCTCTCTGGAGAATCAG
CTATGGGACAATTCCCAGACAAGGCGCTCACGGTTCTAAGGACTGTCAGTTTAAGAATCGAGAG
ATGGTGGAGGGAAGAGAAACGCCATGAGTCTGTACCGCTTCAAGCCATAGGCTCTTCATTTTCA
GACAAAATCTCAGAAGAGATCTGTAACTCAGCTGCTAAAATGGGTAAATTTAGGTTCTTTGTTT
TCCATAGAAGGCAATATGTCTTTAGTGTCTCATTTTACTATCCAAAAACTTGCAGCTAACAATC
TTGGAGTGGACGCGGTTTTCGTTTACACAACGAGCGGACACATGGCATCACTGGTCTCCCGATG
TCGCCCGGACTGCCCGATCTTTGCTTTCACAACCACAACCTCAGTGAGAAGACGCTTAAACCTA
CAATGGGGACTTATCCCATTCCGTCTCAGCTTCTCAGACGACATGGAAAGCAACTTGAACAAAA
CATTCTCGTTACTGAAATCAAGAGGTATGATCAAATCTGGTGACCTCGTGATCGCAGTCTCGGA
CATGCTGCAATCAATCCAG
						
					

			
		

Sequences
Splice junction sequence	AAGCAACTTGAACAAAACATTCTCGTTACTGAAATCAAGAGGTATGATCAAATCTGGTGACCTC GTGATCGCAGTCTCGGACATGCTGCAATCAATCCAGgatggtgaggtttggactttcactgtta gagcttttgattcttctcgtcctgaacgtaccattagtgttagctacgatggtttcgctgaagg tatatgca
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	GATGGTGAGGTTTGGACTTTCACTGTTAGAGCTTTTGATTCTTCTCGTCCTGAACGTACCATTA GTGTTAGCTACGATGGTTTCGCTGAAGGTATATGCAATTATGTTTATGTAAAAGTGGAAGTGAA AACATTAGATGAATATTATGGTGACTGCGTATGAAATAGGAATCATTTGGTCTTTGTGTGTGGT GTAGATGTAAGAGTTGGGGATGAACTTTTGGTTGATGGTGGGATGGTGAGATTTGAAGTGATTG AGAAGATTGGTCCTGATGTTAAGTGTCTATGTACCGATCCTGGATTGTTGCTTCCTCGAGCTAA CTTGACGTTTTGGAGAGATGGAAGTCTTGTACGAGAGCGTAATGCCATGCTTCCAACAATTTCT TCCAAGGTTTGTAATTTTGTATCTTCCCTTTAAGCTTTGAATTATGATTCACTTTACTTGGTAA ATTTGGGAGGGATCAAAGCAATGGTGAAGATGTACACTTTTGGAAACTAGATGAGTCCATGTTA GCAAAACAGATGATACCTGAGGGAAAACATACTCATTTTCACTGATGATACCTCAATTCTTTAT ATTCAGGACTGGTTGGATATTGATTTTGGAATTGCTGAAGGTGTGGATTTCATTGCTGTATCGT TTGTCAAGTCGGCTGAAGTCATTAATCACCTTAAAAGTTATCTTGCTGCTCGTTCCCGTGGAGG GTAAGTAAACATGCTCAATATCAACACATCATACTACTGTACAGGAAACATATGATCTACTTTG GGATTGGGTTTTGCGTCATGTATTCACCATCTTTAGTTATAGTTTTATTTTGATGTTGTATTCA ACTATGATGCAGGGAAATTGGAGTGATTGCAAAGATCGAGAGTATCGATTCACTGACCAATTTG GAAGAAATTATTCTAGCATCAGATGGGGCCATGGTTGCAAGAGGAGATCTGGGAGCTCAGATAC CTCTTGAGCAAGTTCCAGCAGCTCAACAGAGAATCGTCCAAGTATGCAGAGCTCTTAACAAACC CGTCATTGTCGCTTCACAGCTATTGGAGTCCATGATTGAGTACCCAACTCCAACCAGAGCAGAA GTTGCCGACGTGTCTGAAGCAGTAAGACAAAGATCAGATGCATTGATGCTCTCTGGAGAATCAG CTATGGGACAATTCCCAGACAAGGCGCTCACGGTTCTAAGGACTGTCAGTTTAAGAATCGAGAG ATGGTGGAGGGAAGAGAAACGCCATGAGTCTGTACCGCTTCAAGCCATAGGCTCTTCATTTTCA GACAAAATCTCAGAAGAGATCTGTAACTCAGCTGCTAAAATGGGTAAATTTAGGTTCTTTGTTT TCCATAGAAGGCAATATGTCTTTAGTGTCTCATTTTACTATCCAAAAACTTGCAGCTAACAATC TTGGAGTGGACGCGGTTTTCGTTTACACAACGAGCGGACACATGGCATCACTGGTCTCCCGATG TCGCCCGGACTGCCCGATCTTTGCTTTCACAACCACAACCTCAGTGAGAAGACGCTTAAACCTA CAATGGGGACTTATCCCATTCCGTCTCAGCTTCTCAGACGACATGGAAAGCAACTTGAACAAAA CATTCTCGTTACTGAAATCAAGAGGTATGATCAAATCTGGTGACCTCGTGATCGCAGTCTCGGA CATGCTGCAATCAATCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.256583201

Conservation Information
Conserved circRNAs	NA
PMCS	0.256583201

			
						 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 AT3G22960_circ_g.5

Address

Any questions?

Supported by