Plant Circular RNA Database

Detail information of AT4G39350_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G39350_circ_g.2
					
						ID in PlantcircBase
						ath_circ_035663
					
						Alias
						4:18297667-18298524
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 18297667-18298524  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G39350						
					
						Parent gene annotation
						
							Cellulose synthase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT4G39350_circ_g.3 AT4G39350_circ_g.4 						
					
						Support reads
						2/1
					
						Tissues
						seedling;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
						AT4G39350.1:3

General Information
CircRNA Name	AT4G39350_circ_g.2
ID in PlantcircBase	ath_circ_035663
Alias	4:18297667-18298524
Organism	Arabidpsis thaliana
Position	chr4: 18297667-18298524 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G39350
Parent gene annotation	Cellulose synthase
Parent gene strand	+
Alternative splicing	AT4G39350_circ_g.3 AT4G39350_circ_g.4
Support reads	2/1
Tissues	seedling;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	AT4G39350.1:3

			
						 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  
						
							GACGACAAGGCGAAAAGCTTCAAGTCATTAAGCATGAAGGAGGAAACAATGGTCGAGGTTCCAA
TGATGACGACGAACTAGATGATCCTGACATGCCTATatacgatcagtacaagaactgagtgggc
aaacatgtcaaatctgtggagatgaaatcgaattaacggttagcagtgagctctttgttgcttg
caacgaat

									
								

					

						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: 680
Transcript exons: 18297667-18298053,18298136-18298238,18298335-18298524
ATACGATCAGTACAAGAACTGAGTGGGCAAACATGTCAAATCTGTGGAGATGAAATCGAATTAA
CGGTTAGCAGTGAGCTCTTTGTTGCTTGCAACGAATGCGCATTCCCGGTTTGTAGACCATGCTA
TGAGTATGAACGTAGAGAAGGAAATCAAGCTTGTCCTCAGTGCAAAACTCGATACAAAAGGATT
AAAGGTAGTCCACGGGTTGATGGAGATGATGAAGAAGAAGAAGACATTGATGATCTTGAGTATG
AGTTTGATCATGGGATGGACCCTGAACATGCCGCTGAAGCCGCACTCTCTTCACGCCTTAACAC
CGGTCGTGGTGGATTGGATTCAGCTCCACCTGGCTCTCAGATTCCTCTTTTGACTTATTGTGAT
GAAGATGCTGATATGTATTCTGATCGTCATGCTCTTATCGTGCCTCCTTCAACGGGATATGGGA
ATCGCGTCTATCCTGCACCGTTTACAGATTCTTCTGCACCTCCACAGGCGAGATCAATGGTTCC
TCAGAAAGATATTGCGGAATATGGTTATGGAAGTGTTGCTTGGAAGGACCGTATGGAAGTTTGG
AAGAGACGACAAGGCGAAAAGCTTCAAGTCATTAAGCATGAAGGAGGAAACAATGGTCGAGGTT
CCAATGATGACGACGAACTAGATGATCCTGACATGCCTAT
						
					

						Genomic sequence
						
							ATACGATCAGTACAAGAACTGAGTGGGCAAACATGTCAAATCTGTGGAGATGAAATCGAATTAA
CGGTTAGCAGTGAGCTCTTTGTTGCTTGCAACGAATGCGCATTCCCGGTTTGTAGACCATGCTA
TGAGTATGAACGTAGAGAAGGAAATCAAGCTTGTCCTCAGTGCAAAACTCGATACAAAAGGATT
AAAGGTAGTCCACGGGTTGATGGAGATGATGAAGAAGAAGAAGACATTGATGATCTTGAGTATG
AGTTTGATCATGGGATGGACCCTGAACATGCCGCTGAAGCCGCACTCTCTTCACGCCTTAACAC
CGGTCGTGGTGGATTGGATTCAGCTCCACCTGGCTCTCAGATTCCTCTTTTGACTTATTGTGAT
GAAGTGAGGAATCCAAATTGTTTGTTTTCTCTGACAATGTTGTTGCTTAGATGATTCTTTTTCT
TATTAGTCTATGTGTTTTCAGGATGCTGATATGTATTCTGATCGTCATGCTCTTATCGTGCCTC
CTTCAACGGGATATGGGAATCGCGTCTATCCTGCACCGTTTACAGATTCTTCTGCACCTCGTAT
GTGTTTACTTTTATGATTCCTACAATTTTTCTTCTTATATGATTTGGTCACCTTCTAATGAGTT
ATGAAATGGTTTTGTTTGTTGTTTTCAGCACAGGCGAGATCAATGGTTCCTCAGAAAGATATTG
CGGAATATGGTTATGGAAGTGTTGCTTGGAAGGACCGTATGGAAGTTTGGAAGAGACGACAAGG
CGAAAAGCTTCAAGTCATTAAGCATGAAGGAGGAAACAATGGTCGAGGTTCCAATGATGACGAC
GAACTAGATGATCCTGACATGCCTAT
						
					

			
		

Sequences
Splice junction sequence	GACGACAAGGCGAAAAGCTTCAAGTCATTAAGCATGAAGGAGGAAACAATGGTCGAGGTTCCAA TGATGACGACGAACTAGATGATCCTGACATGCCTATatacgatcagtacaagaactgagtgggc aaacatgtcaaatctgtggagatgaaatcgaattaacggttagcagtgagctctttgttgcttg caacgaat
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: 680 Transcript exons: 18297667-18298053,18298136-18298238,18298335-18298524 ATACGATCAGTACAAGAACTGAGTGGGCAAACATGTCAAATCTGTGGAGATGAAATCGAATTAA CGGTTAGCAGTGAGCTCTTTGTTGCTTGCAACGAATGCGCATTCCCGGTTTGTAGACCATGCTA TGAGTATGAACGTAGAGAAGGAAATCAAGCTTGTCCTCAGTGCAAAACTCGATACAAAAGGATT AAAGGTAGTCCACGGGTTGATGGAGATGATGAAGAAGAAGAAGACATTGATGATCTTGAGTATG AGTTTGATCATGGGATGGACCCTGAACATGCCGCTGAAGCCGCACTCTCTTCACGCCTTAACAC CGGTCGTGGTGGATTGGATTCAGCTCCACCTGGCTCTCAGATTCCTCTTTTGACTTATTGTGAT GAAGATGCTGATATGTATTCTGATCGTCATGCTCTTATCGTGCCTCCTTCAACGGGATATGGGA ATCGCGTCTATCCTGCACCGTTTACAGATTCTTCTGCACCTCCACAGGCGAGATCAATGGTTCC TCAGAAAGATATTGCGGAATATGGTTATGGAAGTGTTGCTTGGAAGGACCGTATGGAAGTTTGG AAGAGACGACAAGGCGAAAAGCTTCAAGTCATTAAGCATGAAGGAGGAAACAATGGTCGAGGTT CCAATGATGACGACGAACTAGATGATCCTGACATGCCTAT
Genomic sequence	ATACGATCAGTACAAGAACTGAGTGGGCAAACATGTCAAATCTGTGGAGATGAAATCGAATTAA CGGTTAGCAGTGAGCTCTTTGTTGCTTGCAACGAATGCGCATTCCCGGTTTGTAGACCATGCTA TGAGTATGAACGTAGAGAAGGAAATCAAGCTTGTCCTCAGTGCAAAACTCGATACAAAAGGATT AAAGGTAGTCCACGGGTTGATGGAGATGATGAAGAAGAAGAAGACATTGATGATCTTGAGTATG AGTTTGATCATGGGATGGACCCTGAACATGCCGCTGAAGCCGCACTCTCTTCACGCCTTAACAC CGGTCGTGGTGGATTGGATTCAGCTCCACCTGGCTCTCAGATTCCTCTTTTGACTTATTGTGAT GAAGTGAGGAATCCAAATTGTTTGTTTTCTCTGACAATGTTGTTGCTTAGATGATTCTTTTTCT TATTAGTCTATGTGTTTTCAGGATGCTGATATGTATTCTGATCGTCATGCTCTTATCGTGCCTC CTTCAACGGGATATGGGAATCGCGTCTATCCTGCACCGTTTACAGATTCTTCTGCACCTCGTAT GTGTTTACTTTTATGATTCCTACAATTTTTCTTCTTATATGATTTGGTCACCTTCTAATGAGTT ATGAAATGGTTTTGTTTGTTGTTTTCAGCACAGGCGAGATCAATGGTTCCTCAGAAAGATATTG CGGAATATGGTTATGGAAGTGTTGCTTGGAAGGACCGTATGGAAGTTTGGAAGAGACGACAAGG CGAAAAGCTTCAAGTCATTAAGCATGAAGGAGGAAACAATGGTCGAGGTTCCAATGATGACGAC GAACTAGATGATCCTGACATGCCTAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.369962865

Conservation Information
Conserved circRNAs	NA
PMCS	0.369962865

			
						 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 AT4G39350_circ_g.2

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