Plant Circular RNA Database

Detail information of AT1G65260_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G65260_circ_g.1
					
						ID in PlantcircBase
						ath_circ_008763
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 24236468-24236806  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							AT1G65260						
					
						Parent gene annotation
						
							Membrane-associated protein VIPP1, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							1_circ_ag.3 AT1G65080_circ_g.1 AT1G65130_circ_g.1 AT1G65220_circ_g.1 AT1G65220_circ_g.2 AT1G65220_circ_g.3 AT1G65220_circ_g.4 AT1G65220_circ_g.5 AT1G65220_circ_g.6 AT1G65230_circ_g.1 AT1G65230_circ_g.2 AT1G65230_circ_g.3 AT1G65230_circ_g.4 AT1G65230_circ_g.5 AT1G65260_circ_g.2 AT1G65260_circ_g.3 AT1G65260_circ_g.4 AT1G65260_circ_g.5 AT1G65260_circ_g.6 AT1G65260_circ_g.7 AT1G65260_circ_g.8 AT1G65260_circ_g.9 AT1G65260_circ_g.10 AT1G65260_circ_g.11 AT1G65260_circ_g.12 AT1G65260_circ_g.13 AT1G65260_circ_g.14 AT1G65260_circ_g.15 AT1G65270_circ_g.1 AT1G65270_circ_g.2 AT1G65270_circ_g.3 AT1G65270_circ_g.4 AT1G65270_circ_g.5 AT1G65270_circ_g.6 AT1G65280_circ_g.1 AT1G65280_circ_g.2 AT1G65280_circ_g.3 AT1G65290_circ_g.1 AT1G65290_circ_g.2 AT1G65295_circ_g.1 AT1G65320_circ_g.1 AT1G65350_circ_g.1 AT1G65370_circ_g.1 AT1G65370_circ_g.2 						
					
						Support reads
						4
					
						Tissues
						seedlings
					
						Exon boundary  
						
							No-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  
						
							GA-AA							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
						AT1G65260.2:1

General Information
CircRNA Name	AT1G65260_circ_g.1
ID in PlantcircBase	ath_circ_008763
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 24236468-24236806 JBrowse»
Reference genome	TAIR10.38
Type	ui-circRNA
Identification method	CIRCexplorer
Parent gene	AT1G65260
Parent gene annotation	Membrane-associated protein VIPP1, chloroplastic
Parent gene strand	+
Alternative splicing	1_circ_ag.3 AT1G65080_circ_g.1 AT1G65130_circ_g.1 AT1G65220_circ_g.1 AT1G65220_circ_g.2 AT1G65220_circ_g.3 AT1G65220_circ_g.4 AT1G65220_circ_g.5 AT1G65220_circ_g.6 AT1G65230_circ_g.1 AT1G65230_circ_g.2 AT1G65230_circ_g.3 AT1G65230_circ_g.4 AT1G65230_circ_g.5 AT1G65260_circ_g.2 AT1G65260_circ_g.3 AT1G65260_circ_g.4 AT1G65260_circ_g.5 AT1G65260_circ_g.6 AT1G65260_circ_g.7 AT1G65260_circ_g.8 AT1G65260_circ_g.9 AT1G65260_circ_g.10 AT1G65260_circ_g.11 AT1G65260_circ_g.12 AT1G65260_circ_g.13 AT1G65260_circ_g.14 AT1G65260_circ_g.15 AT1G65270_circ_g.1 AT1G65270_circ_g.2 AT1G65270_circ_g.3 AT1G65270_circ_g.4 AT1G65270_circ_g.5 AT1G65270_circ_g.6 AT1G65280_circ_g.1 AT1G65280_circ_g.2 AT1G65280_circ_g.3 AT1G65290_circ_g.1 AT1G65290_circ_g.2 AT1G65295_circ_g.1 AT1G65320_circ_g.1 AT1G65350_circ_g.1 AT1G65370_circ_g.1 AT1G65370_circ_g.2
Support reads	4
Tissues	seedlings
Exon boundary	No-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	GA-AA 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	AT1G65260.2:1

			
						 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  
						
							TATAACTTCAGTATGCTTTGACTGTTTCACATGTCTAACATTTAGTTCTCTTGCTTTTTAGTTA
TGTTGTTGGTTTGATGTTTCCATGAACTTATTGTTAgtgcgtctccttcttctctacttcgctt
tagggtttggctttatcttcatttcactagcttgcgccttgtttggattgcttggaggaaaata
gtgcagct

						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
						
							GTGCGTCTCCTTCTTCTCTACTTCGCTTTAGGGTTTGGCTTTATCTTCATTTCACTAGCTTGCG
CCTTGTTTGGATTGCTTGGAGGAAAATAGTGCAGCTATTTGCTCAAATTGGGTAACGTGATTAG
TCAGAGAGAGAATTGAAGTAAAATTGGGTATTGATTGTGCTTTTTAGTGTATGATTTGTCGATT
TTGTGTTTCTTGATTTAGTATAAATGAGGTTACTCTTAGTCAGTGTCTATAACTTCAGTATGCT
TTGACTGTTTCACATGTCTAACATTTAGTTCTCTTGCTTTTTAGTTATGTTGTTGGTTTGATGT
TTCCATGAACTTATTGTTA

Sequences
Splice junction sequence	TATAACTTCAGTATGCTTTGACTGTTTCACATGTCTAACATTTAGTTCTCTTGCTTTTTAGTTA TGTTGTTGGTTTGATGTTTCCATGAACTTATTGTTAgtgcgtctccttcttctctacttcgctt tagggtttggctttatcttcatttcactagcttgcgccttgtttggattgcttggaggaaaata gtgcagct
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	GTGCGTCTCCTTCTTCTCTACTTCGCTTTAGGGTTTGGCTTTATCTTCATTTCACTAGCTTGCG CCTTGTTTGGATTGCTTGGAGGAAAATAGTGCAGCTATTTGCTCAAATTGGGTAACGTGATTAG TCAGAGAGAGAATTGAAGTAAAATTGGGTATTGATTGTGCTTTTTAGTGTATGATTTGTCGATT TTGTGTTTCTTGATTTAGTATAAATGAGGTTACTCTTAGTCAGTGTCTATAACTTCAGTATGCT TTGACTGTTTCACATGTCTAACATTTAGTTCTCTTGCTTTTTAGTTATGTTGTTGGTTTGATGT TTCCATGAACTTATTGTTA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.109408112

Conservation Information
Conserved circRNAs	NA
PMCS	0.109408112

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to heat stress

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to heat stress

			
						 Other Information
					
						References
						Pan et al., 2017

circRNA

Detail information of AT1G65260_circ_g.1

Address

Any questions?

Supported by