Plant Circular RNA Database

Detail information of AT1G09340_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT1G09340_circ_g.5
					
						ID in PlantcircBase
						ath_circ_001654
					
						Alias
						1:3016035-3017524
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3016035-3017524  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G09340						
					
						Parent gene annotation
						
							chloroplast RNA binding
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G09340_circ_g.3 AT1G09340_circ_g.4 AT1G09340_circ_g.6 AT1G09340_circ_g.7 AT1G09340_circ_g.8 AT1G09340_circ_g.9 AT1G09340_circ_g.10 AT1G09340_circ_g.11 AT1G09340_circ_g.12 AT1G09340_circ_g.13 AT1G09340_circ_g.14 AT1G09340_circ_g.15 AT1G09340_circ_g.16 AT1G09340_circ_g.17 AT1G09340_circ_g.18 AT1G09340_circ_g.19 AT1G09340_circ_g.20 AT1G09340_circ_g.21 AT1G09340_circ_g.22 AT1G09340_circ_g.23 AT1G09340_circ_g.24 AT1G09340_circ_g.25 AT1G09340_circ_g.26 AT1G09340_circ_g.27 						
					
						Support reads
						2/1/2
					
						Tissues
						seedling;leaf;flower
					
						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
						AT1G09340.1:7
AT1G09340.2:7

General Information
CircRNA Name	AT1G09340_circ_g.5
ID in PlantcircBase	ath_circ_001654
Alias	1:3016035-3017524
Organism	Arabidpsis thaliana
Position	chr1: 3016035-3017524 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G09340
Parent gene annotation	chloroplast RNA binding
Parent gene strand	+
Alternative splicing	AT1G09340_circ_g.3 AT1G09340_circ_g.4 AT1G09340_circ_g.6 AT1G09340_circ_g.7 AT1G09340_circ_g.8 AT1G09340_circ_g.9 AT1G09340_circ_g.10 AT1G09340_circ_g.11 AT1G09340_circ_g.12 AT1G09340_circ_g.13 AT1G09340_circ_g.14 AT1G09340_circ_g.15 AT1G09340_circ_g.16 AT1G09340_circ_g.17 AT1G09340_circ_g.18 AT1G09340_circ_g.19 AT1G09340_circ_g.20 AT1G09340_circ_g.21 AT1G09340_circ_g.22 AT1G09340_circ_g.23 AT1G09340_circ_g.24 AT1G09340_circ_g.25 AT1G09340_circ_g.26 AT1G09340_circ_g.27
Support reads	2/1/2
Tissues	seedling;leaf;flower
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	AT1G09340.1:7 AT1G09340.2:7

			
						 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  
						
							TCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATAT
GTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGtacaagaggaaggttcatcagccaaaag
gagcactctatgtttcagcgtcgagcgaaaagaagattctgataatgggtggtactcgattcat
tggtctgt

									
								

					

						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: 768
Transcript exons: 3016035-3016169,3016248-3016334,3016458-3016548,3016660-
3016714,3016816-3016876,3017045-3017266,3017408-3017524
TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA
TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG
ACATCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGTGAATCT
GACCAAGACTTTGCTGATTTCTCTTCTAAGATTCTTCACTTGAAAGGAGACAGAAAGGACTATG
ACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGGGAGGGA
GGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTACATCTACTGTTCT
TCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGGAGGATGCAGTTGATCCGA
AGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAACTGGAC
TTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGTTTTTC
CACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCG
GTCACGTTAAGGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGA
GATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG
						
					

						Genomic sequence
						
							TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA
TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG
ACATCAGGTTCCACTACCGATCAAACTCTCTTTTCAGCTAAAAATTTAGTTTCCGTTTCTGAGT
GACCAATGGTTGCTTTTGCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAAT
TGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGGTATTACATGAATCCTTGTA
AAAAACTAGTATGCACACTCAAATATAATATACATTTCAGATGATAGGAACTTGGATGATTAGG
ATTCCAATAAAATAAATGATTTTTCTCGGCCTTTTCTAGATTCTTCACTTGAAAGGAGACAGAA
AGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAA
CGGTAACAGCTAATCACTTTGTTCTTACTGTAAATTCAAGAATATCTAGTCTTTTGCCTTTGAC
AACAAAGATTTTAAGATTTCGTATAATTTATGCTCTCTTTTTTTCTCAGGGAGGGAGGCCGAAG
AAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTAAGTAATACATAACATCTATCA
AGGCCTAGCTTGTTCATTTGGTTTATAGCTTTCAAAACATAGCCCTTCAAAATTTAAATCTTCC
GTTAATGTTATAGGTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCC
ACATTGTGAGGTATGTAAAAGATATCTTATTCTTATTCCTGGAAGATATGAGCTTGTACTTTTC
TTGAATTAGCCATAGAATAGTATGATTATGTAATTTGATCATATGATGTCACCCAGAAGTTTAT
TATCTAAGGCCATTTGTAATAACTTTTTATTTGGGACATAACTGATGCAGGAGGATGCAGTTGA
TCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAAC
TGGACTTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGT
TTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACA
ACTCGGTCACGTTAAGGTCAGTCACACTTTCTCTAATTCTTGAGCTTCCTTTCATGTTCAGAAA
ACTCATTGTTATAGGGACCCACTGACTGAAACTCAGCTCTGATCAATCTTGAAGAGTATTGATC
AATAACATCAAATCATTCTGTAATTTCAGGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAA
CGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTA
GCAAAAGCTTGCGCAAAG
						
					

			
		

Sequences
Splice junction sequence	TCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATAT GTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAGtacaagaggaaggttcatcagccaaaag gagcactctatgtttcagcgtcgagcgaaaagaagattctgataatgggtggtactcgattcat tggtctgt
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: 768 Transcript exons: 3016035-3016169,3016248-3016334,3016458-3016548,3016660- 3016714,3016816-3016876,3017045-3017266,3017408-3017524 TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG ACATCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAATTGCCCGGTGAATCT GACCAAGACTTTGCTGATTTCTCTTCTAAGATTCTTCACTTGAAAGGAGACAGAAAGGACTATG ACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAACGGGAGGGA GGCCGAAGAAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTACATCTACTGTTCT TCAGCTGGTGTTTATCTGAAATCTGATATCTTGCCACATTGTGAGGAGGATGCAGTTGATCCGA AGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAACTGGAC TTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGTTTTTC CACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACAACTCG GTCACGTTAAGGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGA GATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAGCAAAAGCTTGCGCAAAG
Genomic sequence	TACAAGAGGAAGGTTCATCAGCCAAAAGGAGCACTCTATGTTTCAGCGTCGAGCGAAAAGAAGA TTCTGATAATGGGTGGTACTCGATTCATTGGTCTGTTCTTGTCCAGGATCCTTGTCAAAGAGGG ACATCAGGTTCCACTACCGATCAAACTCTCTTTTCAGCTAAAAATTTAGTTTCCGTTTCTGAGT GACCAATGGTTGCTTTTGCAGGTTACATTGTTCACAAGGGGTAAATCTCCTATTGCCAAACAAT TGCCCGGTGAATCTGACCAAGACTTTGCTGATTTCTCTTCTAAGGTATTACATGAATCCTTGTA AAAAACTAGTATGCACACTCAAATATAATATACATTTCAGATGATAGGAACTTGGATGATTAGG ATTCCAATAAAATAAATGATTTTTCTCGGCCTTTTCTAGATTCTTCACTTGAAAGGAGACAGAA AGGACTATGACTTTGTGAAGTCAAGTCTTTCAGCAGAAGGCTTCGATGTTGTTTATGATATCAA CGGTAACAGCTAATCACTTTGTTCTTACTGTAAATTCAAGAATATCTAGTCTTTTGCCTTTGAC AACAAAGATTTTAAGATTTCGTATAATTTATGCTCTCTTTTTTTCTCAGGGAGGGAGGCCGAAG AAGTTGAGCCCATACTAGAAGCACTACCCAAACTAGAGCAGTAAGTAATACATAACATCTATCA AGGCCTAGCTTGTTCATTTGGTTTATAGCTTTCAAAACATAGCCCTTCAAAATTTAAATCTTCC GTTAATGTTATAGGTACATCTACTGTTCTTCAGCTGGTGTTTATCTGAAATCTGATATCTTGCC ACATTGTGAGGTATGTAAAAGATATCTTATTCTTATTCCTGGAAGATATGAGCTTGTACTTTTC TTGAATTAGCCATAGAATAGTATGATTATGTAATTTGATCATATGATGTCACCCAGAAGTTTAT TATCTAAGGCCATTTGTAATAACTTTTTATTTGGGACATAACTGATGCAGGAGGATGCAGTTGA TCCGAAGAGCAGGCACAAGGGGAAGCTGGAGACTGAGAGCTTACTGCAATCAAAAGGTGTAAAC TGGACTTCTATACGTCCTGTCTACATCTACGGTCCATTGAATTACAACCCCGTCGAAGAATGGT TTTTCCACCGTCTAAAGGCAGGTCGCCCAATCCCGGTTCCAAACTCTGGGATACAGATCTCACA ACTCGGTCACGTTAAGGTCAGTCACACTTTCTCTAATTCTTGAGCTTCCTTTCATGTTCAGAAA ACTCATTGTTATAGGGACCCACTGACTGAAACTCAGCTCTGATCAATCTTGAAGAGTATTGATC AATAACATCAAATCATTCTGTAATTTCAGGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAA CGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTA GCAAAAGCTTGCGCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.237130501

Conservation Information
Conserved circRNAs	NA
PMCS	0.237130501

			
						 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 AT1G09340_circ_g.5

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