Plant Circular RNA Database

Detail information of AT4G16260_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G16260_circ_g.1
					
						ID in PlantcircBase
						ath_circ_031179
					
						Alias
						Chr4:9200790|9201274
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 9200790-9201274  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplorer; CIRI
					
						Parent gene
						
							AT4G16260						
					
						Parent gene annotation
						
							Probable glucan endo-1,3-beta-glucosidase At4g16260
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G16260_circ_g.2 						
					
						Support reads
						4
					
						Tissues
						seedling
					
						Exon boundary  
						
							No-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  
						
							CT-TA							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
						AT4G16260.1:1
AT4G16260.2:1

General Information
CircRNA Name	AT4G16260_circ_g.1
ID in PlantcircBase	ath_circ_031179
Alias	Chr4:9200790\|9201274
Organism	Arabidpsis thaliana
Position	chr4: 9200790-9201274 JBrowse»
Reference genome	TAIR10.38
Type	ui-circRNA
Identification method	CIRCexplorer; CIRI
Parent gene	AT4G16260
Parent gene annotation	Probable glucan endo-1,3-beta-glucosidase At4g16260
Parent gene strand	-
Alternative splicing	AT4G16260_circ_g.2
Support reads	4
Tissues	seedling
Exon boundary	No-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	CT-TA 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	AT4G16260.1:1 AT4G16260.2:1

			
						 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  
						
							ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC
CCATCATTCCATAGCATACACCTACTGATTCTCCACcccgatgacgggatcgatataccatcta
acgtcaccacgaaactctccggaggaaggagggaaagagtttccaatcaaagtcatatcaatgg
cggtagaa

						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
						
							CCCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAA
GAGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCAC
CTCTTAGAGCATCGTAAACGTTACGCATGGCAGGGAGCACAACATCACCGCCGTTCGACGGAGA
TACTTCGTTACCTACGGCGATGTACTTGAAGCTAACGGCGGGGTAATAGTTGAGGACGTTGTTT
TGGAGCCATGATCTAGCGGAAGAAGGGTTAGTGAGTGAACGAAGATCGGTGTTTGGAACGCCGA
TGATGACTTCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCT
AACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTC
CCCATCATTCCATAGCATACACCTACTGATTCTCCAC

Sequences
Splice junction sequence	ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC CCATCATTCCATAGCATACACCTACTGATTCTCCACcccgatgacgggatcgatataccatcta acgtcaccacgaaactctccggaggaaggagggaaagagtttccaatcaaagtcatatcaatgg cggtagaa
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	CCCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAA GAGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCAC CTCTTAGAGCATCGTAAACGTTACGCATGGCAGGGAGCACAACATCACCGCCGTTCGACGGAGA TACTTCGTTACCTACGGCGATGTACTTGAAGCTAACGGCGGGGTAATAGTTGAGGACGTTGTTT TGGAGCCATGATCTAGCGGAAGAAGGGTTAGTGAGTGAACGAAGATCGGTGTTTGGAACGCCGA TGATGACTTCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCT AACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTC CCCATCATTCCATAGCATACACCTACTGATTCTCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.248257742

Conservation Information
Conserved circRNAs	NA
PMCS	0.248257742

			
						 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

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

			
						 Other Information
					
						References
						Zhang et al., 2020

circRNA

Detail information of AT4G16260_circ_g.1

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