Plant Circular RNA Database

Detail information of Csa1G027520_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa1G027520_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000101
					
						Alias
						Chr1:3046979_3055990
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 3046979-3055990  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa1G027520						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa1G027520_circ_g.2 Chr1_circ_ig.20 Chr1_circ_ig.21 Csa1G028020_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						leaf,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  
						
							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
						Csa1G027520.1:3

General Information
CircRNA Name	Csa1G027520_circ_g.1
ID in PlantcircBase	csa_circ_000101
Alias	Chr1:3046979_3055990
Organism	Cucumis sativus
Position	chrChr1: 3046979-3055990 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa1G027520
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa1G027520_circ_g.2 Chr1_circ_ig.20 Chr1_circ_ig.21 Csa1G028020_circ_g.1
Support reads	NA
Tissues	leaf,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	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	Csa1G027520.1:3

			
						 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  
						
							AAACAGAATCTTTGAAAAATAAATTAAGGAAAATTAGCTGAACTGTACCAGAAAGGTGATCCCT
CAGCGTGCCATTTGACATAAATTCATAAGCCAACATctccctaacgatgttcttgccatgtgag
attgggtgcctcccagtcaaaagctccaaaaacacaacaccaaggctataaacatcactcttat
ctgtcaat

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAACAGAATCTTTGAAAAATAAATTAAGGAAAATTAGCTGAACTGTACCAGAAAGGTGATCCCT CAGCGTGCCATTTGACATAAATTCATAAGCCAACATctccctaacgatgttcttgccatgtgag attgggtgcctcccagtcaaaagctccaaaaacacaacaccaaggctataaacatcactcttat ctgtcaat
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.096892311

Conservation Information
Conserved circRNAs	NA
PMCS	0.096892311

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3055992-3046981(-)
						
						Potential amino acid sequence
						
							MLAYEFMSNGTLRDHLSVNSAEPLSFATRLKAALGAAKGILYLHTEADPPIFHRDIKSSNILLD
SKYVAKVADFGLSRLAPLPNAEGDVPAHVSTVVKGTPGYLDPEYFLTHKLTDKSDVYSLGVVFL
ELLTGRHPISHGKNIVREMLAYEFMSNGTLRDHLSVNSAEPLSFATRLKAALGAAKGILYLHTE
ADPPIFHRDIKSSNILLDSKYVAKVADFGLSRLAPLPNAEGDVPAHVSTVVKGTPGYLDPEYFL
THKLTDKSDVYSLGVVFLELLTGRHPISHGKNIVREMLAYEFMSNGTLRDHLSVNSAEPLSFAT
RLKAALGAAKGILYLHTEADPPIFHRDIKSSNILLDSKYVAKVADFGLSRLAPLPNAEGDVPAH
VSTVVKGTPGYLDPEYFLTHKLTDKSDVYSLGVVFLELLTGRHPISHGKNIVREMLAYEFMSNG
TLRDHLSVNSAEPLSFATRLKAALGAAKGILYLHTEADPPIFHRDIKSSNILLDSKYVAKVADF
GLSRLAPLPNAEGDVPAHVSTVVKGTPGYLDPEYFLTHKLTDKSDVYSLGVVFLELLTGRHPIS
HGKNIVRE
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to salt stress in root

Functional Information
Coding potential	Y
Potential coding position	3055992-3046981(-)
Potential amino acid sequence	MLAYEFMSNGTLRDHLSVNSAEPLSFATRLKAALGAAKGILYLHTEADPPIFHRDIKSSNILLD SKYVAKVADFGLSRLAPLPNAEGDVPAHVSTVVKGTPGYLDPEYFLTHKLTDKSDVYSLGVVFL ELLTGRHPISHGKNIVREMLAYEFMSNGTLRDHLSVNSAEPLSFATRLKAALGAAKGILYLHTE ADPPIFHRDIKSSNILLDSKYVAKVADFGLSRLAPLPNAEGDVPAHVSTVVKGTPGYLDPEYFL THKLTDKSDVYSLGVVFLELLTGRHPISHGKNIVREMLAYEFMSNGTLRDHLSVNSAEPLSFAT RLKAALGAAKGILYLHTEADPPIFHRDIKSSNILLDSKYVAKVADFGLSRLAPLPNAEGDVPAH VSTVVKGTPGYLDPEYFLTHKLTDKSDVYSLGVVFLELLTGRHPISHGKNIVREMLAYEFMSNG TLRDHLSVNSAEPLSFATRLKAALGAAKGILYLHTEADPPIFHRDIKSSNILLDSKYVAKVADF GLSRLAPLPNAEGDVPAHVSTVVKGTPGYLDPEYFLTHKLTDKSDVYSLGVVFLELLTGRHPIS HGKNIVRE
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa1G027520_circ_g.1

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