Plant Circular RNA Database

Detail information of AT5G05610_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G05610_circ_g.4
					
						ID in PlantcircBase
						ath_circ_036593
					
						Alias
						AT5G05610_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 1678373-1678595  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, CIRI2
					
						Parent gene
						
							AT5G05610						
					
						Parent gene annotation
						
							AL1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G05610_circ_g.1 AT5G05610_circ_g.2 AT5G05610_circ_g.3 						
					
						Support reads
						34
					
						Tissues
						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  
						
							CT-AC							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
						AT5G05610.2:1
AT5G05610.1:1

General Information
CircRNA Name	AT5G05610_circ_g.4
ID in PlantcircBase	ath_circ_036593
Alias	AT5G05610_C1
Organism	Arabidpsis thaliana
Position	chr5: 1678373-1678595 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, CIRI2
Parent gene	AT5G05610
Parent gene annotation	AL1
Parent gene strand	-
Alternative splicing	AT5G05610_circ_g.1 AT5G05610_circ_g.2 AT5G05610_circ_g.3
Support reads	34
Tissues	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	CT-AC 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	AT5G05610.2:1 AT5G05610.1:1

			
						 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  
						
							CCAAGAGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCC
CATTCGGGTGTCCGTACAAACACAGATTCTCCATTTctctcattgcgattaagacgagcgccga
agtaagaagaaacagagagtaaccaacaatcactgtggacagcaactaaagagagccaatcttt
acgctgca

									
								

					

						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: 181
Transcript exons: 1678373-1678513,1678556-1678595
CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT
GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG
AGCTGGCTCAGGTGTCCCATTCGGGTGTCCGTACAAACACAGATTCTCCATTT
Transcript length: 194
Transcript exons: 1678373-1678528,1678558-1678595
CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT
GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG
AGCTGGCTCAGGTAGCTCCGGAGGCACTCCCATTCGGGTGTCCGTACAAACACAGATTCTCCAT
TT
Transcript length: 204
Transcript exons: 1678373-1678549,1678569-1678595
CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT
GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG
AGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTGTCCGTACAAACACA
GATTCTCCATTT
Transcript length: 214
Transcript exons: 1678373-1678513,1678523-1678595
CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT
GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG
AGCTGGCTCAGGTGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCCCATTCGGGTGTCCG
TACAAACACAGATTCTCCATTT
Transcript length: 223
Transcript exons: 1678373-1678595
CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT
GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG
AGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCCCATTC
GGGTGTCCGTACAAACACAGATTCTCCATTT
						
					

						Genomic sequence
						
							CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT
GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG
AGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCCCATTC
GGGTGTCCGTACAAACACAGATTCTCCATTT
						
					

			
		

Sequences
Splice junction sequence	CCAAGAGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCC CATTCGGGTGTCCGTACAAACACAGATTCTCCATTTctctcattgcgattaagacgagcgccga agtaagaagaaacagagagtaaccaacaatcactgtggacagcaactaaagagagccaatcttt acgctgca
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: 181 Transcript exons: 1678373-1678513,1678556-1678595 CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG AGCTGGCTCAGGTGTCCCATTCGGGTGTCCGTACAAACACAGATTCTCCATTT Transcript length: 194 Transcript exons: 1678373-1678528,1678558-1678595 CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG AGCTGGCTCAGGTAGCTCCGGAGGCACTCCCATTCGGGTGTCCGTACAAACACAGATTCTCCAT TT Transcript length: 204 Transcript exons: 1678373-1678549,1678569-1678595 CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG AGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTGTCCGTACAAACACA GATTCTCCATTT Transcript length: 214 Transcript exons: 1678373-1678513,1678523-1678595 CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG AGCTGGCTCAGGTGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCCCATTCGGGTGTCCG TACAAACACAGATTCTCCATTT Transcript length: 223 Transcript exons: 1678373-1678595 CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG AGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCCCATTC GGGTGTCCGTACAAACACAGATTCTCCATTT
Genomic sequence	CTCTCATTGCGATTAAGACGAGCGCCGAAGTAAGAAGAAACAGAGAGTAACCAACAATCACTGT GGACAGCAACTAAAGAGAGCCAATCTTTACGCTGCATACCATCTCTAGCGAAATTGATTCCAAG AGCTGGCTCAGGTAGCTCCGGAGGCACTTCCTCAGCTGGAAGATTCACTTCCCATGTCCCATTC GGGTGTCCGTACAAACACAGATTCTCCATTT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.696290861

Conservation Information
Conserved circRNAs	NA
PMCS	0.696290861

			
						 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 AT5G05610_circ_g.4

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