Plant Circular RNA Database

Detail information of Csa4G187320_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa4G187320_circ_g.2
					
						ID in PlantcircBase
						csa_circ_002503
					
						Alias
						Chr4:9122113_9122851
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr4: 9122113-9122851  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa4G187320						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa4G187320_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
						Csa4G187320.1:2

General Information
CircRNA Name	Csa4G187320_circ_g.2
ID in PlantcircBase	csa_circ_002503
Alias	Chr4:9122113_9122851
Organism	Cucumis sativus
Position	chrChr4: 9122113-9122851 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa4G187320
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa4G187320_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	Csa4G187320.1:2

			
						 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  
						
							GAAGAGATGATGGCAATGGCACCTCATTGGGTGGAATATATCTGAGAATCAAAACCGATACAGC
CACTGTGGCAAATGCAAAAAGAGTACCAACACTAACcttggaaggcgcagattcgtagctgcat
aggtaagtagtagtgccccaacgcatgtgaacaagatggcccatccagcaaattttcgtcgatt
cttgtcat

						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
						
							CTTGGAAGGCGCAGATTCGTAGCTGCATAGGTAAGTAGTAGTGCCCCAACGCATGTGAACAAGA
TGGCCCATCCAGCAAATTTTCGTCGATTCTTGTCATTCAGAGTGTCTACAACAATTAAACATAA
TGGAAAATAAGAACACAACAGATTTTGAAAAAGCTTTTCTGTAAGTAAAAACATTAGTAACTCT
ACAGTCTTCAAAAAATCTTTTATAAAAGCCGATAACCATATTTTAGTGCAATATTCTTTTGGAG
CTTAAACACATGGAACCAAAAGAAAAGAAAGCCATCCAAGTTATTACATCCCTCCCATTTTCCT
TAAAATGGGAAAATAATTCTAAAAAAATGTTTCAAAATTATGAGCCTCAAGCCTAGGTGAGATA
AGCTGCTCCTTATGATACTGGCACCAATGAACAACCACATTGTAACAGACCAGATACTAAAGTA
AGAGCAATCATGAAACTTACAACCACGTCGAGTGAGATAGCTGCCGATTATTGGGATGTCAACT
GATGAATCCACTTTCGAAAGTAAGGGTCTACTAACACTGTCCTTTGTAGAATTGATCTCGGTAT
CTTGTCCATCAACAACATCAGCACTTGTATGAATTGGTAGGGACAGTGGATCAAATGACTCATG
AAGAGATGATGGCAATGGCACCTCATTGGGTGGAATATATCTGAGAATCAAAACCGATACAGCC
ACTGTGGCAAATGCAAAAAGAGTACCAACACTAAC

Sequences
Splice junction sequence	GAAGAGATGATGGCAATGGCACCTCATTGGGTGGAATATATCTGAGAATCAAAACCGATACAGC CACTGTGGCAAATGCAAAAAGAGTACCAACACTAACcttggaaggcgcagattcgtagctgcat aggtaagtagtagtgccccaacgcatgtgaacaagatggcccatccagcaaattttcgtcgatt cttgtcat
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	CTTGGAAGGCGCAGATTCGTAGCTGCATAGGTAAGTAGTAGTGCCCCAACGCATGTGAACAAGA TGGCCCATCCAGCAAATTTTCGTCGATTCTTGTCATTCAGAGTGTCTACAACAATTAAACATAA TGGAAAATAAGAACACAACAGATTTTGAAAAAGCTTTTCTGTAAGTAAAAACATTAGTAACTCT ACAGTCTTCAAAAAATCTTTTATAAAAGCCGATAACCATATTTTAGTGCAATATTCTTTTGGAG CTTAAACACATGGAACCAAAAGAAAAGAAAGCCATCCAAGTTATTACATCCCTCCCATTTTCCT TAAAATGGGAAAATAATTCTAAAAAAATGTTTCAAAATTATGAGCCTCAAGCCTAGGTGAGATA AGCTGCTCCTTATGATACTGGCACCAATGAACAACCACATTGTAACAGACCAGATACTAAAGTA AGAGCAATCATGAAACTTACAACCACGTCGAGTGAGATAGCTGCCGATTATTGGGATGTCAACT GATGAATCCACTTTCGAAAGTAAGGGTCTACTAACACTGTCCTTTGTAGAATTGATCTCGGTAT CTTGTCCATCAACAACATCAGCACTTGTATGAATTGGTAGGGACAGTGGATCAAATGACTCATG AAGAGATGATGGCAATGGCACCTCATTGGGTGGAATATATCTGAGAATCAAAACCGATACAGCC ACTGTGGCAAATGCAAAAAGAGTACCAACACTAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.110202921

Conservation Information
Conserved circRNAs	NA
PMCS	0.110202921

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							9122214-9122849(-)
9122186-9122802(-)
						
						Potential amino acid sequence
						
							MTRIDENLLDGPSCSHALGHYYLPMQLRICAFQG*
MGHLVHMRWGTTTYLCSYESAPSKVSVGTLFAFATVAVSVLILRYIPPNEVPLPSSLHESFDPL
SLPIHTSADVVDGQDTEINSTKDSVSRPLLSKVDSSVDIPIIGSYLTRRGYTLNDKNRRKFAGW
AILFTCVGALLLTYAATNLRLPRLVLVLFLHLPQWLYRF*
						
						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	9122214-9122849(-) 9122186-9122802(-)
Potential amino acid sequence	MTRIDENLLDGPSCSHALGHYYLPMQLRICAFQG* MGHLVHMRWGTTTYLCSYESAPSKVSVGTLFAFATVAVSVLILRYIPPNEVPLPSSLHESFDPL SLPIHTSADVVDGQDTEINSTKDSVSRPLLSKVDSSVDIPIIGSYLTRRGYTLNDKNRRKFAGW AILFTCVGALLLTYAATNLRLPRLVLVLFLHLPQWLYRF*
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 Csa4G187320_circ_g.2

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