Plant Circular RNA Database

Detail information of AT5G09660_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G09660_circ_g.4
					
						ID in PlantcircBase
						ath_circ_037273
					
						Alias
						AT5G09660_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 2993978-2994285  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						PcircRNA_finder, CIRI2
					
						Parent gene
						
							AT5G09660						
					
						Parent gene annotation
						
							Malate dehydrogenase
							
						Parent gene strand
						-
					
						Alternative splicing
						
							5_circ_ag.29 AT5G09570_circ_g.1 AT5G09570_circ_g.2 AT5G09570_circ_g.3 AT5G09580_circ_g.1 AT5G09590_circ_g.1 AT5G09590_circ_g.2 AT5G09590_circ_g.3 AT5G09590_circ_g.4 AT5G09590_circ_g.5 AT5G09590_circ_g.6 AT5G09620_circ_g.1 AT5G09650_circ_g.1 AT5G09650_circ_g.2 AT5G09660_circ_g.1 AT5G09660_circ_g.2 AT5G09660_circ_g.3 AT5G09660_circ_g.5 AT5G09660_circ_g.6 AT5G09660_circ_g.7 AT5G09660_circ_g.8 AT5G09660_circ_g.9 AT5G09660_circ_g.10 AT5G09660_circ_g.11 AT5G09660_circ_g.12 AT5G09660_circ_g.13 AT5G09660_circ_g.14 AT5G09690_circ_g.1 AT5G09690_circ_g.2 AT5G09690_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 ENSRNA049493670_circ_g.1 ENSRNA049493670_circ_g.2 ENSRNA049493670_circ_g.3 ENSRNA049493670_circ_g.4 ENSRNA049493670_circ_g.5 ENSRNA049493670_circ_g.6 						
					
						Support reads
						49
					
						Tissues
						aerial, 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
						AT5G09660.4:2
AT5G09660.5:2
AT5G09660.2:2
AT5G09660.3:2
AT5G09660.1:2

General Information
CircRNA Name	AT5G09660_circ_g.4
ID in PlantcircBase	ath_circ_037273
Alias	AT5G09660_C1
Organism	Arabidpsis thaliana
Position	chr5: 2993978-2994285 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	PcircRNA_finder, CIRI2
Parent gene	AT5G09660
Parent gene annotation	Malate dehydrogenase
Parent gene strand	-
Alternative splicing	5_circ_ag.29 AT5G09570_circ_g.1 AT5G09570_circ_g.2 AT5G09570_circ_g.3 AT5G09580_circ_g.1 AT5G09590_circ_g.1 AT5G09590_circ_g.2 AT5G09590_circ_g.3 AT5G09590_circ_g.4 AT5G09590_circ_g.5 AT5G09590_circ_g.6 AT5G09620_circ_g.1 AT5G09650_circ_g.1 AT5G09650_circ_g.2 AT5G09660_circ_g.1 AT5G09660_circ_g.2 AT5G09660_circ_g.3 AT5G09660_circ_g.5 AT5G09660_circ_g.6 AT5G09660_circ_g.7 AT5G09660_circ_g.8 AT5G09660_circ_g.9 AT5G09660_circ_g.10 AT5G09660_circ_g.11 AT5G09660_circ_g.12 AT5G09660_circ_g.13 AT5G09660_circ_g.14 AT5G09690_circ_g.1 AT5G09690_circ_g.2 AT5G09690_circ_g.3 5_circ_ag.4 5_circ_ag.5 5_circ_ag.6 5_circ_ag.7 5_circ_ag.8 5_circ_ag.9 5_circ_ag.10 5_circ_ag.11 ENSRNA049493670_circ_g.1 ENSRNA049493670_circ_g.2 ENSRNA049493670_circ_g.3 ENSRNA049493670_circ_g.4 ENSRNA049493670_circ_g.5 ENSRNA049493670_circ_g.6
Support reads	49
Tissues	aerial, 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	AT5G09660.4:2 AT5G09660.5:2 AT5G09660.2:2 AT5G09660.3:2 AT5G09660.1:2

			
						 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  
						
							CAGCTCCAGCTTTTGCCTCCACAACTTCAGTTCCACCATTTTGAATCCGGTTTGTCAGGTACTC
AATTTCTTGAGGTGTGAAGCTGCTAGGAGGTTTAACctgtgaagcaacaaaagagcattctacg
acattcgcatctcctcttaacccgcgaaggcaagcatctgcaaacttggctgcagcatatgcct
atagtagt

						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: 210
Transcript exons: 2993978-2994067,2994166-2994285
CTGTGAAGCAACAAAAGAGCATTCTACGACATTCGCATCTCCTCTTAACCCGCGAAGGCAAGCA
TCTGCAAACTTGGCTGCAGCATATGCCATTGAAAGTGTTGCAGAACCAGCTCCAGCTTTTGCCT
CCACAACTTCAGTTCCACCATTTTGAATCCGGTTTGTCAGGTACTCAATTTCTTGAGGTGTGAA
GCTGCTAGGAGGTTTAAC
						
						Genomic sequence
						
							CTGTGAAGCAACAAAAGAGCATTCTACGACATTCGCATCTCCTCTTAACCCGCGAAGGCAAGCA
TCTGCAAACTTGGCTGCAGCATATGCCTATAGTAGTAGTACATTTCACATGGATTCAGTACACT
GTTCCAGAGAAATAAACAGGTGTAATGATGATGTATTAAAGTGATTTGGTTTGGTTTTACCATT
GAAAGTGTTGCAGAACCAGCTCCAGCTTTTGCCTCCACAACTTCAGTTCCACCATTTTGAATCC
GGTTTGTCAGGTACTCAATTTCTTGAGGTGTGAAGCTGCTAGGAGGTTTAAC

Sequences
Splice junction sequence	CAGCTCCAGCTTTTGCCTCCACAACTTCAGTTCCACCATTTTGAATCCGGTTTGTCAGGTACTC AATTTCTTGAGGTGTGAAGCTGCTAGGAGGTTTAACctgtgaagcaacaaaagagcattctacg acattcgcatctcctcttaacccgcgaaggcaagcatctgcaaacttggctgcagcatatgcct atagtagt
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: 210 Transcript exons: 2993978-2994067,2994166-2994285 CTGTGAAGCAACAAAAGAGCATTCTACGACATTCGCATCTCCTCTTAACCCGCGAAGGCAAGCA TCTGCAAACTTGGCTGCAGCATATGCCATTGAAAGTGTTGCAGAACCAGCTCCAGCTTTTGCCT CCACAACTTCAGTTCCACCATTTTGAATCCGGTTTGTCAGGTACTCAATTTCTTGAGGTGTGAA GCTGCTAGGAGGTTTAAC
Genomic sequence	CTGTGAAGCAACAAAAGAGCATTCTACGACATTCGCATCTCCTCTTAACCCGCGAAGGCAAGCA TCTGCAAACTTGGCTGCAGCATATGCCTATAGTAGTAGTACATTTCACATGGATTCAGTACACT GTTCCAGAGAAATAAACAGGTGTAATGATGATGTATTAAAGTGATTTGGTTTGGTTTTACCATT GAAAGTGTTGCAGAACCAGCTCCAGCTTTTGCCTCCACAACTTCAGTTCCACCATTTTGAATCC GGTTTGTCAGGTACTCAATTTCTTGAGGTGTGAAGCTGCTAGGAGGTTTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.357953903

Conservation Information
Conserved circRNAs	NA
PMCS	0.357953903

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2994169-2993980(-)
						
						Potential amino acid sequence
						
							MAYAAAKFADACLRGLRGDANVVECSFVASQVKPPSSFTPQEIEYLTNRIQNGGTEVVEAKAGA
GSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQVKPPSSFTPQEIEYLTNRIQNGGTEVV
EAKAGAGSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQVKPPSSFTPQEIEYLTNRIQN
GGTEVVEAKAGAGSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						response to drought stress

Functional Information
Coding potential	Y
Potential coding position	2994169-2993980(-)
Potential amino acid sequence	MAYAAAKFADACLRGLRGDANVVECSFVASQVKPPSSFTPQEIEYLTNRIQNGGTEVVEAKAGA GSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQVKPPSSFTPQEIEYLTNRIQNGGTEVV EAKAGAGSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQVKPPSSFTPQEIEYLTNRIQN GGTEVVEAKAGAGSATLSMAYAAAKFADACLRGLRGDANVVECSFVASQ(-)
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 AT5G09660_circ_g.4

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