Plant Circular RNA Database

Detail information of 1_circ_ag.4

			
						 General Information
					
						CircRNA Name
						1_circ_ag.4
					
						ID in PlantcircBase
						ath_circ_005443
					
						Alias
						Chr1:11778553|11779629
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 11778553-11779629  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							1_circ_igg.3 1_circ_ag.5 1_circ_igg.6 1_circ_ag.7 1_circ_ag.8 1_circ_igg.9 						
					
						Support reads
						15
					
						Tissues
						seedling
					
						Exon boundary  
						
							NA-NA							"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-CA							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
						NA

General Information
CircRNA Name	1_circ_ag.4
ID in PlantcircBase	ath_circ_005443
Alias	Chr1:11778553\|11779629
Organism	Arabidpsis thaliana
Position	chr1: 11778553-11779629 JBrowse»
Reference genome	TAIR10.38
Type	ag-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	1_circ_igg.3 1_circ_ag.5 1_circ_igg.6 1_circ_ag.7 1_circ_ag.8 1_circ_igg.9
Support reads	15
Tissues	seedling
Exon boundary	NA-NA "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-CA 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	NA

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							YES							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   
						
							Convergent:(F):CGATATGAGAAGCTAGGTAAGCCAAC
(R):CAGTGTTCTTCCAATTGAGCAAGTTG.Divergent:(F):AAATTCTCGGGCTATAACCTGGATGAG
(R)AGAATCCATGAGGCAGTTCAGAAGATG
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	YES 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	Convergent:(F):CGATATGAGAAGCTAGGTAAGCCAAC (R):CAGTGTTCTTCCAATTGAGCAAGTTG.Divergent:(F):AAATTCTCGGGCTATAACCTGGATGAG (R)AGAATCCATGAGGCAGTTCAGAAGATG 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  
						
							CTCGGGGTGTAGGATGACAAAATTTCAGCATATTGAAGAAAATTCTCGGGCTATAACCTGGATG
AGTAAAAGATTAACTTCTCTTCATTTGACTCTAAAGgggtttgagtgagacctcgcatttactt
gccaccatcttctgaactgcctcatggattctctggcacaaggtttgaattccgtgttttttcc
ccaaagtt

						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
						
							GGGTTTGAGTGAGACCTCGCATTTACTTGCCACCATCTTCTGAACTGCCTCATGGATTCTCTGG
CACAAGGTTTGAATTCCGTGTTTTTTCCCCAAAGTTCAACAGTTTGATGCGATGCCGCAGATAT
GGATTAATATAAAGTCAGACCAACCGACAAAGGTATTCTAGATATGAAACTCGTTTGATATAGA
TATTCTTTCTTTTGTTCCTCTGAATCATTCAGTTGATTTCTATCATTAATTTTGGTATCTAGAC
AGATGATTTTGTCATTTATTGTCCCAGATGAACAGAAAATCATCCAACGATTGTGACCATATTC
TTGCTTTTGTTCCAGAAGAAGATGAAACAAACTTCATGGTTCTCGGTAAGTTGAGTTAGTTTTA
TAGCTGAATCTTACAATCTTGTATATCTTTCTGGCACTGTGTATTGTAGACCAAAATTTTGTCA
TGGGCTAATTTTTGATAGCTTCATCCTTACAAGGTATTCTGACACTGCAAATATGGATCACGTC
AGCTCCTTGTACCTTTCTGAAGACTAAAAAGTGACATATCAAAAATTAAAGTTATCTACAAGTA
CCTTTCTCATATCGCTTAGTGTTCTCATACTCTTAAGATCAGTAGTGTGTTTGGTGTCTAATTA
AAGTTTTCTTTCATTTTCTTAATGAAACTAATGAACATGTGTTTCTGCTTGGTCGACACTAATT
TAGAGTTTGAGGAGGACATGGAGAGGTCTATATGCGATATGAGAAGCTAGGTAAGCCAACAATC
CCCTAATGAGACTACTGTTAATGAGACGTTCCTTCTTGTAAATTAACATGTAGGGAAAAGGAGA
AGACAATGATAGCCAAACAGGAGAGATAATATACACAACAACTTGCTCAATTGGAAGAACACTG
AAGAAAAAAGAAGCGGGTAAATAATAGCCTTACATTTTTACACCTTCTCTATTTCTCTTGTTGT
ATGACAGAATGTGAAATCTCGGGGTGTAGGATGACAAAATTTCAGCATATTGAAGAAAATTCTC
GGGCTATAACCTGGATGAGTAAAAGATTAACTTCTCTTCATTTGACTCTAAAG

Sequences
Splice junction sequence	CTCGGGGTGTAGGATGACAAAATTTCAGCATATTGAAGAAAATTCTCGGGCTATAACCTGGATG AGTAAAAGATTAACTTCTCTTCATTTGACTCTAAAGgggtttgagtgagacctcgcatttactt gccaccatcttctgaactgcctcatggattctctggcacaaggtttgaattccgtgttttttcc ccaaagtt
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	GGGTTTGAGTGAGACCTCGCATTTACTTGCCACCATCTTCTGAACTGCCTCATGGATTCTCTGG CACAAGGTTTGAATTCCGTGTTTTTTCCCCAAAGTTCAACAGTTTGATGCGATGCCGCAGATAT GGATTAATATAAAGTCAGACCAACCGACAAAGGTATTCTAGATATGAAACTCGTTTGATATAGA TATTCTTTCTTTTGTTCCTCTGAATCATTCAGTTGATTTCTATCATTAATTTTGGTATCTAGAC AGATGATTTTGTCATTTATTGTCCCAGATGAACAGAAAATCATCCAACGATTGTGACCATATTC TTGCTTTTGTTCCAGAAGAAGATGAAACAAACTTCATGGTTCTCGGTAAGTTGAGTTAGTTTTA TAGCTGAATCTTACAATCTTGTATATCTTTCTGGCACTGTGTATTGTAGACCAAAATTTTGTCA TGGGCTAATTTTTGATAGCTTCATCCTTACAAGGTATTCTGACACTGCAAATATGGATCACGTC AGCTCCTTGTACCTTTCTGAAGACTAAAAAGTGACATATCAAAAATTAAAGTTATCTACAAGTA CCTTTCTCATATCGCTTAGTGTTCTCATACTCTTAAGATCAGTAGTGTGTTTGGTGTCTAATTA AAGTTTTCTTTCATTTTCTTAATGAAACTAATGAACATGTGTTTCTGCTTGGTCGACACTAATT TAGAGTTTGAGGAGGACATGGAGAGGTCTATATGCGATATGAGAAGCTAGGTAAGCCAACAATC CCCTAATGAGACTACTGTTAATGAGACGTTCCTTCTTGTAAATTAACATGTAGGGAAAAGGAGA AGACAATGATAGCCAAACAGGAGAGATAATATACACAACAACTTGCTCAATTGGAAGAACACTG AAGAAAAAAGAAGCGGGTAAATAATAGCCTTACATTTTTACACCTTCTCTATTTCTCTTGTTGT ATGACAGAATGTGAAATCTCGGGGTGTAGGATGACAAAATTTCAGCATATTGAAGAAAATTCTC GGGCTATAACCTGGATGAGTAAAAGATTAACTTCTCTTCATTTGACTCTAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.098808232

Conservation Information
Conserved circRNAs	NA
PMCS	0.098808232

			
						 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
						responsive to methyl jasmonate (validated)

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	responsive to methyl jasmonate (validated)

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of 1_circ_ag.4

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