Plant Circular RNA Database

Detail information of AT3G02540_circ_g.5

			
						 General Information
					
						CircRNA Name
						AT3G02540_circ_g.5
					
						ID in PlantcircBase
						ath_circ_019331
					
						Alias
						3:533912-535466
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 533912-535466  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G02540						
					
						Parent gene annotation
						
							Ubiquitin receptor RAD23c
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G02540_circ_g.1 AT3G02540_circ_g.2 AT3G02540_circ_g.3 AT3G02540_circ_g.4 AT3G02540_circ_g.6 AT3G02540_circ_g.7 AT3G02540_circ_g.8 AT3G02540_circ_g.9 AT3G02540_circ_g.10 AT3G02540_circ_g.11 AT3G02540_circ_g.12 AT3G02540_circ_g.13 AT3G02540_circ_g.14 AT3G02540_circ_g.15 AT3G02540_circ_g.16 AT3G02540_circ_g.17 						
					
						Support reads
						1/1
					
						Tissues
						seedling;flower
					
						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
						AT3G02540.3:7
AT3G02540.2:7
AT3G02540.1:7

General Information
CircRNA Name	AT3G02540_circ_g.5
ID in PlantcircBase	ath_circ_019331
Alias	3:533912-535466
Organism	Arabidpsis thaliana
Position	chr3: 533912-535466 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G02540
Parent gene annotation	Ubiquitin receptor RAD23c
Parent gene strand	-
Alternative splicing	AT3G02540_circ_g.1 AT3G02540_circ_g.2 AT3G02540_circ_g.3 AT3G02540_circ_g.4 AT3G02540_circ_g.6 AT3G02540_circ_g.7 AT3G02540_circ_g.8 AT3G02540_circ_g.9 AT3G02540_circ_g.10 AT3G02540_circ_g.11 AT3G02540_circ_g.12 AT3G02540_circ_g.13 AT3G02540_circ_g.14 AT3G02540_circ_g.15 AT3G02540_circ_g.16 AT3G02540_circ_g.17
Support reads	1/1
Tissues	seedling;flower
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	AT3G02540.3:7 AT3G02540.2:7 AT3G02540.1:7

			
						 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  
						
							CATCTTTAAGCACTTTACCTTGGTGAATAAGCATCTGTTTTGCAGCAGGATACACATCTGCGCC
CTGCACACTCTCTATGTTCTTCTTCACATCAACAACctgttggctgttgcgcaagaagtcaagt
gttccagcaccaggatttcctccaacatttggcaagccctgtcagagataaagagcagatttta
gctgcaca

									
								

					

						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: 828
Transcript exons: 533912-533977,534072-534218,534384-534561,534645-534800,
534919-534986,535149-535199,535305-535466
CTGTTGGCTGTTGCGCAAGAAGTCAAGTGTTCCAGCACCAGGATTTCCTCCAACATTTGGCAAG
CCCTGTGGGAAGAGATCTAACGGATTTGCATTAGGACCACTTGCGGGTGCTGCTGCAGGTTGTT
GAGTCTGTGCTGGAGGATTTGCAGGCTGTCCGGCACTAGCTGGAGGACGGGCAACTGGTGGAAC
TTCAGCTTGCTCAGGGATCCCAGTATAAAGATATTCCACAGCTCTTTCAGGGTTGTTAAATGCA
GCACGAAGTGCAAGGACAACAGTCTCACGATCCCAGGTTCCTCCACCCATGTCAAGAATCTGCT
GAATGGTACTCTCTAAATTACTTCCAGCGGCTAGATTTGATGCTGCTTGTCCGTAAACATCACC
TTGACTTCCCACAGGAGCTGAGTCTGGTGCAGGAGTGCTTGATGATATAGTAGCAGGTACAGGT
TCAGGTATAGGGGTAGTCACAGTTTCAGTTGCAGCTACAGGTGCAGGTGTCGGTGTCGGTGCAG
GTGGTGGTGGACGTGTTGGTGCAGGTGCCACTGGTGCTGATACAGAAGCTGGAGTCTGAGGGGA
AATTGAAGGCTGTGATGTTGAGGGAGGTATCGACTTGGCCTGCGATGTGCCAGCAGATGCACTA
GATGCTGCAGCTGAAGCAGGTTTACTCTTGTTCATCATAATGACAATAAAACTGTTCTCAGCAA
CTTTGTTTTCCTCAATAGTTGTCTCATCTTTAAGCACTTTACCTTGGTGAATAAGCATCTGTTT
TGCAGCAGGATACACATCTGCGCCCTGCACACTCTCTATGTTCTTCTTCACATCAACAAC
						
					

						Genomic sequence
						
							CTGTTGGCTGTTGCGCAAGAAGTCAAGTGTTCCAGCACCAGGATTTCCTCCAACATTTGGCAAG
CCCTGTCAGAGATAAAGAGCAGATTTTAGCTGCACACCCATCTATAATCAAGAGTTTAAATGAA
CCAAATCTGCTTTCTATCTCAAGGTGTATTACCTGTGGGAAGAGATCTAACGGATTTGCATTAG
GACCACTTGCGGGTGCTGCTGCAGGTTGTTGAGTCTGTGCTGGAGGATTTGCAGGCTGTCCGGC
ACTAGCTGGAGGACGGGCAACTGGTGGAACTTCAGCTTGCTCAGGGATCCCCTAAGACATGAAT
TTCGGTGTTTAAATATGTATTCTCTCACTTAGTAGGTAGCCAATCATAATAAAAAGGAAATCTA
TTCTCGGCATAGTGATTGATTAGTGACCAAAATCTGCCTCTTAAGTTGCATGACGGTACGAAAA
TAGAGAGAAAATAATTGAACTCACAGTATAAAGATATTCCACAGCTCTTTCAGGGTTGTTAAAT
GCAGCACGAAGTGCAAGGACAACAGTCTCACGATCCCAGGTTCCTCCACCCATGTCAAGAATCT
GCTGAATGGTACTCTCTAAATTACTTCCAGCGGCTAGATTTGATGCTGCTTGTCCGTAAACATC
ACCTTGACTTCTATTTTAATCAAAACAAATAGGAAACAGAATAAGAGTAGGTCAATTTCTGAGC
TGCGCAGAAGACTGAAACGAGATGCTAACCCCACAGGAGCTGAGTCTGGTGCAGGAGTGCTTGA
TGATATAGTAGCAGGTACAGGTTCAGGTATAGGGGTAGTCACAGTTTCAGTTGCAGCTACAGGT
GCAGGTGTCGGTGTCGGTGCAGGTGGTGGTGGACGTGTTGGTGCAGGTGCCACTGGTCTGCACA
GTTTTCAAATTGGGGGCAAAATATTGAAATTAGTTGTAGAATGTAGCCACAGTTTTTTCAGATA
GATTCTAGGAATTTTTCAAACAGAGAGTACTTGTCTCGAAAACTCACGCTGATACAGAAGCTGG
AGTCTGAGGGGAAATTGAAGGCTGTGATGTTGAGGGAGGTATCGACTTGGCCTAAACCAACACC
AAAGTTAGATCATTCAACAAACAAGAAAATACATAGAAGCATTTGACACTTTCGTTTCATTAGT
TGCAGAGGCAAGAAGTTTTTCCAAAAATCCCAAGTTGCAGCATCTGAGCCTTTATAATGATGTC
ATAACAACAGAACCAACTCACCTGCGATGTGCCAGCAGATGCACTAGATGCTGCAGCTGAAGCA
GGTTTACTCTATTACATGTTTAGCACCAGAGAGCATAAATCAGAATCGGGTAATCAAAGAGCTA
AACAGAAAACAACAGAATTACTTATTTATTCCCCAGATCCAAAACGTACCTTGTTCATCATAAT
GACAATAAAACTGTTCTCAGCAACTTTGTTTTCCTCAATAGTTGTCTCATCTTTAAGCACTTTA
CCTTGGTGAATAAGCATCTGTTTTGCAGCAGGATACACATCTGCGCCCTGCACACTCTCTATGT
TCTTCTTCACATCAACAAC
						
					

			
		

Sequences
Splice junction sequence	CATCTTTAAGCACTTTACCTTGGTGAATAAGCATCTGTTTTGCAGCAGGATACACATCTGCGCC CTGCACACTCTCTATGTTCTTCTTCACATCAACAACctgttggctgttgcgcaagaagtcaagt gttccagcaccaggatttcctccaacatttggcaagccctgtcagagataaagagcagatttta gctgcaca
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: 828 Transcript exons: 533912-533977,534072-534218,534384-534561,534645-534800, 534919-534986,535149-535199,535305-535466 CTGTTGGCTGTTGCGCAAGAAGTCAAGTGTTCCAGCACCAGGATTTCCTCCAACATTTGGCAAG CCCTGTGGGAAGAGATCTAACGGATTTGCATTAGGACCACTTGCGGGTGCTGCTGCAGGTTGTT GAGTCTGTGCTGGAGGATTTGCAGGCTGTCCGGCACTAGCTGGAGGACGGGCAACTGGTGGAAC TTCAGCTTGCTCAGGGATCCCAGTATAAAGATATTCCACAGCTCTTTCAGGGTTGTTAAATGCA GCACGAAGTGCAAGGACAACAGTCTCACGATCCCAGGTTCCTCCACCCATGTCAAGAATCTGCT GAATGGTACTCTCTAAATTACTTCCAGCGGCTAGATTTGATGCTGCTTGTCCGTAAACATCACC TTGACTTCCCACAGGAGCTGAGTCTGGTGCAGGAGTGCTTGATGATATAGTAGCAGGTACAGGT TCAGGTATAGGGGTAGTCACAGTTTCAGTTGCAGCTACAGGTGCAGGTGTCGGTGTCGGTGCAG GTGGTGGTGGACGTGTTGGTGCAGGTGCCACTGGTGCTGATACAGAAGCTGGAGTCTGAGGGGA AATTGAAGGCTGTGATGTTGAGGGAGGTATCGACTTGGCCTGCGATGTGCCAGCAGATGCACTA GATGCTGCAGCTGAAGCAGGTTTACTCTTGTTCATCATAATGACAATAAAACTGTTCTCAGCAA CTTTGTTTTCCTCAATAGTTGTCTCATCTTTAAGCACTTTACCTTGGTGAATAAGCATCTGTTT TGCAGCAGGATACACATCTGCGCCCTGCACACTCTCTATGTTCTTCTTCACATCAACAAC
Genomic sequence	CTGTTGGCTGTTGCGCAAGAAGTCAAGTGTTCCAGCACCAGGATTTCCTCCAACATTTGGCAAG CCCTGTCAGAGATAAAGAGCAGATTTTAGCTGCACACCCATCTATAATCAAGAGTTTAAATGAA CCAAATCTGCTTTCTATCTCAAGGTGTATTACCTGTGGGAAGAGATCTAACGGATTTGCATTAG GACCACTTGCGGGTGCTGCTGCAGGTTGTTGAGTCTGTGCTGGAGGATTTGCAGGCTGTCCGGC ACTAGCTGGAGGACGGGCAACTGGTGGAACTTCAGCTTGCTCAGGGATCCCCTAAGACATGAAT TTCGGTGTTTAAATATGTATTCTCTCACTTAGTAGGTAGCCAATCATAATAAAAAGGAAATCTA TTCTCGGCATAGTGATTGATTAGTGACCAAAATCTGCCTCTTAAGTTGCATGACGGTACGAAAA TAGAGAGAAAATAATTGAACTCACAGTATAAAGATATTCCACAGCTCTTTCAGGGTTGTTAAAT GCAGCACGAAGTGCAAGGACAACAGTCTCACGATCCCAGGTTCCTCCACCCATGTCAAGAATCT GCTGAATGGTACTCTCTAAATTACTTCCAGCGGCTAGATTTGATGCTGCTTGTCCGTAAACATC ACCTTGACTTCTATTTTAATCAAAACAAATAGGAAACAGAATAAGAGTAGGTCAATTTCTGAGC TGCGCAGAAGACTGAAACGAGATGCTAACCCCACAGGAGCTGAGTCTGGTGCAGGAGTGCTTGA TGATATAGTAGCAGGTACAGGTTCAGGTATAGGGGTAGTCACAGTTTCAGTTGCAGCTACAGGT GCAGGTGTCGGTGTCGGTGCAGGTGGTGGTGGACGTGTTGGTGCAGGTGCCACTGGTCTGCACA GTTTTCAAATTGGGGGCAAAATATTGAAATTAGTTGTAGAATGTAGCCACAGTTTTTTCAGATA GATTCTAGGAATTTTTCAAACAGAGAGTACTTGTCTCGAAAACTCACGCTGATACAGAAGCTGG AGTCTGAGGGGAAATTGAAGGCTGTGATGTTGAGGGAGGTATCGACTTGGCCTAAACCAACACC AAAGTTAGATCATTCAACAAACAAGAAAATACATAGAAGCATTTGACACTTTCGTTTCATTAGT TGCAGAGGCAAGAAGTTTTTCCAAAAATCCCAAGTTGCAGCATCTGAGCCTTTATAATGATGTC ATAACAACAGAACCAACTCACCTGCGATGTGCCAGCAGATGCACTAGATGCTGCAGCTGAAGCA GGTTTACTCTATTACATGTTTAGCACCAGAGAGCATAAATCAGAATCGGGTAATCAAAGAGCTA AACAGAAAACAACAGAATTACTTATTTATTCCCCAGATCCAAAACGTACCTTGTTCATCATAAT GACAATAAAACTGTTCTCAGCAACTTTGTTTTCCTCAATAGTTGTCTCATCTTTAAGCACTTTA CCTTGGTGAATAAGCATCTGTTTTGCAGCAGGATACACATCTGCGCCCTGCACACTCTCTATGT TCTTCTTCACATCAACAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.200166765

Conservation Information
Conserved circRNAs	NA
PMCS	0.200166765

			
						 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 AT3G02540_circ_g.5

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