Plant Circular RNA Database

Detail information of AT3G49180_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G49180_circ_g.1
					
						ID in PlantcircBase
						ath_circ_026673
					
						Alias
						AT3G49180_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 18230091-18230338  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT3G49180						
					
						Parent gene annotation
						
							Protein ROOT INITIATION DEFECTIVE 3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G49180_circ_g.2 AT3G49180_circ_g.3 AT3G49180_circ_g.4 AT3G49180_circ_g.5 						
					
						Support reads
						7
					
						Tissues
						root, whole_plant, leaf
					
						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
						AT3G49180.1:1

General Information
CircRNA Name	AT3G49180_circ_g.1
ID in PlantcircBase	ath_circ_026673
Alias	AT3G49180_C1
Organism	Arabidpsis thaliana
Position	chr3: 18230091-18230338 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT3G49180
Parent gene annotation	Protein ROOT INITIATION DEFECTIVE 3
Parent gene strand	+
Alternative splicing	AT3G49180_circ_g.2 AT3G49180_circ_g.3 AT3G49180_circ_g.4 AT3G49180_circ_g.5
Support reads	7
Tissues	root, whole_plant, leaf
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	AT3G49180.1:1

			
						 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  
						
							GTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGATTCTTTGTTGGTTTCTGGATC
TCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAGcctcaagctgaagtgaagagctacccag
tggaaccaataaaggctcttgcagcaaacaatgaaggaacttacttagttggtggtggaatctc
tggagata

									
								

					

						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: 197
Transcript exons: 18230091-18230236,18230288-18230338
CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG
GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA
GTTGCTTAAGAAGTGGCAGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTT
ATAAG
Transcript length: 236
Transcript exons: 18230091-18230235,18230248-18230338
CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG
GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA
GTTGCTTAAGAAGTGGCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGATTCTTTGTTGGTT
TCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG
Transcript length: 245
Transcript exons: 18230091-18230277,18230281-18230338
CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG
GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA
GTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATTCT
TTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG
Transcript length: 248
Transcript exons: 18230091-18230338
CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG
GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA
GTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGAT
TCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG
Transcript length: 248
Transcript exons: 18230091-18230338
CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG
GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA
GTTGCTTAAGAAGTGGCATGTTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGAT
TCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG
						
					

						Genomic sequence
						
							CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG
GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA
GTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGAT
TCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG
						
					

			
		

Sequences
Splice junction sequence	GTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGATTCTTTGTTGGTTTCTGGATC TCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAGcctcaagctgaagtgaagagctacccag tggaaccaataaaggctcttgcagcaaacaatgaaggaacttacttagttggtggtggaatctc tggagata
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: 197 Transcript exons: 18230091-18230236,18230288-18230338 CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA GTTGCTTAAGAAGTGGCAGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTT ATAAG Transcript length: 236 Transcript exons: 18230091-18230235,18230248-18230338 CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA GTTGCTTAAGAAGTGGCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGATTCTTTGTTGGTT TCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG Transcript length: 245 Transcript exons: 18230091-18230277,18230281-18230338 CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA GTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATTCT TTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG Transcript length: 248 Transcript exons: 18230091-18230338 CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA GTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGAT TCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG Transcript length: 248 Transcript exons: 18230091-18230338 CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA GTTGCTTAAGAAGTGGCATGTTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGAT TCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG
Genomic sequence	CCTCAAGCTGAAGTGAAGAGCTACCCAGTGGAACCAATAAAGGCTCTTGCAGCAAACAATGAAG GAACTTACTTAGTTGGTGGTGGAATCTCTGGAGATATTTACCTTTGGGAGGTTGCGACTGGGAA GTTGCTTAAGAAGTGGCATGGTCATTATCGTTCAGTAACATGTTTGGTGTTCTCTGGAGATGAT TCTTTGTTGGTTTCTGGATCTCAAGATGGGTCTATTAGAGTTTGGTCTCTTATAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.794034507

Conservation Information
Conserved circRNAs	NA
PMCS	0.794034507

			
						 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
						response to drought 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	response to drought stress

			
						 Other Information
					
						References
						Chu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT3G49180_circ_g.1

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