Plant Circular RNA Database

Detail information of AT3G22380_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT3G22380_circ_g.7
					
						ID in PlantcircBase
						ath_circ_023228
					
						Alias
						3:7914278-7915656
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 7914278-7915656  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G22380						
					
						Parent gene annotation
						
							Time for coffee
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G22380_circ_g.5 AT3G22380_circ_g.6 AT3G22380_circ_g.8 AT3G22380_circ_g.9 AT3G22380_circ_g.10 AT3G22380_circ_g.11 AT3G22380_circ_g.12 AT3G22380_circ_g.13 AT3G22380_circ_g.14 						
					
						Support reads
						2
					
						Tissues
						root
					
						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
						AT3G22380.2:5
AT3G22380.1:5
AT3G22380.3:5

General Information
CircRNA Name	AT3G22380_circ_g.7
ID in PlantcircBase	ath_circ_023228
Alias	3:7914278-7915656
Organism	Arabidpsis thaliana
Position	chr3: 7914278-7915656 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G22380
Parent gene annotation	Time for coffee
Parent gene strand	+
Alternative splicing	AT3G22380_circ_g.5 AT3G22380_circ_g.6 AT3G22380_circ_g.8 AT3G22380_circ_g.9 AT3G22380_circ_g.10 AT3G22380_circ_g.11 AT3G22380_circ_g.12 AT3G22380_circ_g.13 AT3G22380_circ_g.14
Support reads	2
Tissues	root
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	AT3G22380.2:5 AT3G22380.1:5 AT3G22380.3:5

			
						 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  
						
							AAACTCGACTTGGATAAATCTGATCATGTGGGTTTAGTAAACAAGCATCATGTTCAGAAACCGC
CACCGCAACAGCAACTATCTGTTCCTGATAAAACTGccgtcggggacgaaacagaagccgttac
cgccgaagtcatcatcgagtaagttatcatcgccagtggctgtacaagacgagatcgagatcga
gattgcag

									
								

					

						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: 958
Transcript exons: 7914278-7914572,7914664-7914967,7915053-7915092,7915176-
7915271,7915434-7915656
CCGTCGGGGACGAAACAGAAGCCGTTACCGCCGAAGTCATCATCGAGTAAGTTATCATCGCCAG
TGGCTGTACAAGACGAGATCGAGATCGAGATTGCAGAAGTGTTGTATGGTATGATGAGGATGCC
TTCCACATCAAAACAAGAAGCAGCCGGTAACGATTTGACGGAGGCAGCGAAATCAACTGTAGAA
GTCAAATCTCGAGTCTCTTCACCGATCTCAAATCCTCAGACTCTTCCTCAATCATCTATCACAC
TAGCTGCAAATTCTAGCTCCTCTAATGTTTCAGCCATCGCTCCTAAGAGAAAGAAGCCGAGACA
TGTCAAGTACGAAGACGATAACAGTTCACGCGTCACTACAATCAAATCCGAAGCCGAAGCTCCT
TCAAAAAGTCAAGTTCCGTTCAGTAATCAACTAAAGAGCTCAGGATCCGGCGAAGGAAACAGCT
CCGTATTGGATTCTATCATACCACTGACGAGAGAAAGCAACGCTTCGTTAGATTCGGAGAAAAA
AGAGAACAATCTGTCAAAAGACGAAACAATATTGCCGAAAGTGGAATCTTCTTCAGGATTTAGA
TCCGATGGTGAAGGAGCTAAATCGAGTTCGCCGGAAAAAGAGAAGTTTGAGATAGATCTGATGG
CGCCACCGCCGGTGAGATCGTCGTCGGAGAGAGGCGGAGAGATGATGGAATGTGTGGCGGCAGA
AGCTAAACCTAAAGTCACGGAAGTGGAAACGGAAGCAAAGCCTCTGCTTAAGGAAGATAGAAGT
GATCCGGCGATTCATGATTCTCAGGAGAAGAAGAGACCTAGAATGGTTGCTGAAGCTGAACACC
ATAAGTTTGAGAGGAATTGTGAACTCAAACTCGACTTGGATAAATCTGATCATGTGGGTTTAGT
AAACAAGCATCATGTTCAGAAACCGCCACCGCAACAGCAACTATCTGTTCCTGATAAAACTG
						
					

						Genomic sequence
						
							CCGTCGGGGACGAAACAGAAGCCGTTACCGCCGAAGTCATCATCGAGTAAGTTATCATCGCCAG
TGGCTGTACAAGACGAGATCGAGATCGAGATTGCAGAAGTGTTGTATGGTATGATGAGGATGCC
TTCCACATCAAAACAAGAAGCAGCCGGTAACGATTTGACGGAGGCAGCGAAATCAACTGTAGAA
GTCAAATCTCGAGTCTCTTCACCGATCTCAAATCCTCAGACTCTTCCTCAATCATCTATCACAC
TAGCTGCAAATTCTAGCTCCTCTAATGTTTCAGCCATCGGTAACATCCTCTCTCCATTCACAAA
TCGGAACGACTATTTTTGTTTTTTTTTTTCTTTTTTGCTCACTTTGTTTTACCATTTTCGCTTC
AGCTCCTAAGAGAAAGAAGCCGAGACATGTCAAGTACGAAGACGATAACAGTTCACGCGTCACT
ACAATCAAATCCGAAGCCGAAGCTCCTTCAAAAAGTCAAGTTCCGTTCAGTAATCAACTAAAGA
GCTCAGGATCCGGCGAAGGAAACAGCTCCGTATTGGATTCTATCATACCACTGACGAGAGAAAG
CAACGCTTCGTTAGATTCGGAGAAAAAAGAGAACAATCTGTCAAAAGACGAAACAATATTGCCG
AAAGTGGAATCTTCTTCAGGATTTAGATCCGATGGTGAAGGAGCTAAATCGTAAGCATTCAATC
TATACATTCATTTTTTCTGGATTTTTTACCCAAGTTTTGGTACTGAATGTTTTTTGTTTTTAAT
CATGCAGGAGTTCGCCGGAAAAAGAGAAGTTTGAGATAGATCTGATGGTAAGTGTCAATAACAT
ATATATTTTATTTTATTTTCCTTTTTTTTTGAAGTTCCGTACTAAATTAATTGTCCGTCGGTTC
AGGCGCCACCGCCGGTGAGATCGTCGTCGGAGAGAGGCGGAGAGATGATGGAATGTGTGGCGGC
AGAAGCTAAACCTAAAGTCACGGAAGTGGAAACGGTGAGTGGGGCCTACTTTTGTTTGGTAATA
TTGTGATAATTGGGGATATCCATCATTACTTTTTCATTTTTGCTTTTTTTGGCTCTCTTTTTCT
TATCTTCATCTTTTTGGCTCCCTCTTTTTTTTAATTCTCTCCTGTGTCCACACTAATGCATGTA
GCAGGAAGCAAAGCCTCTGCTTAAGGAAGATAGAAGTGATCCGGCGATTCATGATTCTCAGGAG
AAGAAGAGACCTAGAATGGTTGCTGAAGCTGAACACCATAAGTTTGAGAGGAATTGTGAACTCA
AACTCGACTTGGATAAATCTGATCATGTGGGTTTAGTAAACAAGCATCATGTTCAGAAACCGCC
ACCGCAACAGCAACTATCTGTTCCTGATAAAACTG
						
					

			
		

Sequences
Splice junction sequence	AAACTCGACTTGGATAAATCTGATCATGTGGGTTTAGTAAACAAGCATCATGTTCAGAAACCGC CACCGCAACAGCAACTATCTGTTCCTGATAAAACTGccgtcggggacgaaacagaagccgttac cgccgaagtcatcatcgagtaagttatcatcgccagtggctgtacaagacgagatcgagatcga gattgcag
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: 958 Transcript exons: 7914278-7914572,7914664-7914967,7915053-7915092,7915176- 7915271,7915434-7915656 CCGTCGGGGACGAAACAGAAGCCGTTACCGCCGAAGTCATCATCGAGTAAGTTATCATCGCCAG TGGCTGTACAAGACGAGATCGAGATCGAGATTGCAGAAGTGTTGTATGGTATGATGAGGATGCC TTCCACATCAAAACAAGAAGCAGCCGGTAACGATTTGACGGAGGCAGCGAAATCAACTGTAGAA GTCAAATCTCGAGTCTCTTCACCGATCTCAAATCCTCAGACTCTTCCTCAATCATCTATCACAC TAGCTGCAAATTCTAGCTCCTCTAATGTTTCAGCCATCGCTCCTAAGAGAAAGAAGCCGAGACA TGTCAAGTACGAAGACGATAACAGTTCACGCGTCACTACAATCAAATCCGAAGCCGAAGCTCCT TCAAAAAGTCAAGTTCCGTTCAGTAATCAACTAAAGAGCTCAGGATCCGGCGAAGGAAACAGCT CCGTATTGGATTCTATCATACCACTGACGAGAGAAAGCAACGCTTCGTTAGATTCGGAGAAAAA AGAGAACAATCTGTCAAAAGACGAAACAATATTGCCGAAAGTGGAATCTTCTTCAGGATTTAGA TCCGATGGTGAAGGAGCTAAATCGAGTTCGCCGGAAAAAGAGAAGTTTGAGATAGATCTGATGG CGCCACCGCCGGTGAGATCGTCGTCGGAGAGAGGCGGAGAGATGATGGAATGTGTGGCGGCAGA AGCTAAACCTAAAGTCACGGAAGTGGAAACGGAAGCAAAGCCTCTGCTTAAGGAAGATAGAAGT GATCCGGCGATTCATGATTCTCAGGAGAAGAAGAGACCTAGAATGGTTGCTGAAGCTGAACACC ATAAGTTTGAGAGGAATTGTGAACTCAAACTCGACTTGGATAAATCTGATCATGTGGGTTTAGT AAACAAGCATCATGTTCAGAAACCGCCACCGCAACAGCAACTATCTGTTCCTGATAAAACTG
Genomic sequence	CCGTCGGGGACGAAACAGAAGCCGTTACCGCCGAAGTCATCATCGAGTAAGTTATCATCGCCAG TGGCTGTACAAGACGAGATCGAGATCGAGATTGCAGAAGTGTTGTATGGTATGATGAGGATGCC TTCCACATCAAAACAAGAAGCAGCCGGTAACGATTTGACGGAGGCAGCGAAATCAACTGTAGAA GTCAAATCTCGAGTCTCTTCACCGATCTCAAATCCTCAGACTCTTCCTCAATCATCTATCACAC TAGCTGCAAATTCTAGCTCCTCTAATGTTTCAGCCATCGGTAACATCCTCTCTCCATTCACAAA TCGGAACGACTATTTTTGTTTTTTTTTTTCTTTTTTGCTCACTTTGTTTTACCATTTTCGCTTC AGCTCCTAAGAGAAAGAAGCCGAGACATGTCAAGTACGAAGACGATAACAGTTCACGCGTCACT ACAATCAAATCCGAAGCCGAAGCTCCTTCAAAAAGTCAAGTTCCGTTCAGTAATCAACTAAAGA GCTCAGGATCCGGCGAAGGAAACAGCTCCGTATTGGATTCTATCATACCACTGACGAGAGAAAG CAACGCTTCGTTAGATTCGGAGAAAAAAGAGAACAATCTGTCAAAAGACGAAACAATATTGCCG AAAGTGGAATCTTCTTCAGGATTTAGATCCGATGGTGAAGGAGCTAAATCGTAAGCATTCAATC TATACATTCATTTTTTCTGGATTTTTTACCCAAGTTTTGGTACTGAATGTTTTTTGTTTTTAAT CATGCAGGAGTTCGCCGGAAAAAGAGAAGTTTGAGATAGATCTGATGGTAAGTGTCAATAACAT ATATATTTTATTTTATTTTCCTTTTTTTTTGAAGTTCCGTACTAAATTAATTGTCCGTCGGTTC AGGCGCCACCGCCGGTGAGATCGTCGTCGGAGAGAGGCGGAGAGATGATGGAATGTGTGGCGGC AGAAGCTAAACCTAAAGTCACGGAAGTGGAAACGGTGAGTGGGGCCTACTTTTGTTTGGTAATA TTGTGATAATTGGGGATATCCATCATTACTTTTTCATTTTTGCTTTTTTTGGCTCTCTTTTTCT TATCTTCATCTTTTTGGCTCCCTCTTTTTTTTAATTCTCTCCTGTGTCCACACTAATGCATGTA GCAGGAAGCAAAGCCTCTGCTTAAGGAAGATAGAAGTGATCCGGCGATTCATGATTCTCAGGAG AAGAAGAGACCTAGAATGGTTGCTGAAGCTGAACACCATAAGTTTGAGAGGAATTGTGAACTCA AACTCGACTTGGATAAATCTGATCATGTGGGTTTAGTAAACAAGCATCATGTTCAGAAACCGCC ACCGCAACAGCAACTATCTGTTCCTGATAAAACTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.187683291

Conservation Information
Conserved circRNAs	NA
PMCS	0.187683291

			
						 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 AT3G22380_circ_g.7

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