Plant Circular RNA Database

Detail information of Csa3G170010_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa3G170010_circ_g.2
					
						ID in PlantcircBase
						csa_circ_001623
					
						Alias
						Chr3:11289514_11290363
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 11289514-11290363  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa3G170010						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa3G170010_circ_g.3 Csa3G170010_circ_g.4 Csa3G170010_circ_g.5 Csa3G170010_circ_g.6 Csa3G170010_circ_g.7 Csa3G170010_circ_g.8 Csa3G170010_circ_g.9 Csa3G170010_circ_g.10 						
					
						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  
						
							GT-AG							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
						Csa3G170010.1:2

General Information
CircRNA Name	Csa3G170010_circ_g.2
ID in PlantcircBase	csa_circ_001623
Alias	Chr3:11289514_11290363
Organism	Cucumis sativus
Position	chrChr3: 11289514-11290363 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa3G170010
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa3G170010_circ_g.3 Csa3G170010_circ_g.4 Csa3G170010_circ_g.5 Csa3G170010_circ_g.6 Csa3G170010_circ_g.7 Csa3G170010_circ_g.8 Csa3G170010_circ_g.9 Csa3G170010_circ_g.10
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	GT-AG 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	Csa3G170010.1:2

			
						 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  
						
							CTTAAACATGAATGTTGACAGTGTTTCCATCTATCTAAATATGGAGGATGGATCTCAGCTTGCA
ATGCTCGTGCAGGAGAGCTTTTTGCTTGACCTCAAGgtccatataattcttggtgatgatgatc
tttcagtcaaaacaaaactgcattcgttgcatattaaggatgaacttcaaggccacttatcaac
aaattcac

									
								

					

						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: 762
Transcript exons: 11289514-11289954,11290043-11290363
GTCCATATAATTCTTGGTGATGATGATCTTTCAGTCAAAACAAAACTGCATTCGTTGCATATTA
AGGATGAACTTCAAGGCCACTTATCAACAAATTCACAGTATTTAGCACGCTCTGTGCTATCAAA
TGAGAAATTATCTTCTTCTCCTGAAACATTTGATCCTGATGGGATACAAACAGCTAGTGCAATC
ACTGAAGAGGACGATAGTTTTAAGGATGCATTGCCTGATTTTTTGTCTCTATCTGATGTTGGAA
ATTACGAGTCCTCTGGACGTGAATCGACTGAGACCATATTTAATGAAAATGATATAGGAAAAGG
GAAGGGCATATCCAGTGACATATTTTATGAGGCAGAGGACAGCGAAGATTCAAACTTTGTGGCT
GTAACCTTCCTGACGAGGGGCTCAGATTCCCCTGATTACGATGGTATAGACACTCAGATGAGTA
TTCGCATGTCAAAAATGGAATTCTACTGCAACAGACCCACTCTTGTTGCATTAATTGGTTTTGG
TTTGGATATAAGTTCCTCAAATTATGTGGAAGCTAACACAGACTTGCCCAGCTCTTTGGAAGAT
AAGCTTGTTATGGATAAAGAAAAGGCAGAAGAAAAAGGCCGCGTAAAAGGATTGCTAGGATATG
GAAAAAGTCGTGTCGTATTCTACTTAAACATGAATGTTGACAGTGTTTCCATCTATCTAAATAT
GGAGGATGGATCTCAGCTTGCAATGCTCGTGCAGGAGAGCTTTTTGCTTGACCTCAAG
						
					

						Genomic sequence
						
							GTCCATATAATTCTTGGTGATGATGATCTTTCAGTCAAAACAAAACTGCATTCGTTGCATATTA
AGGATGAACTTCAAGGCCACTTATCAACAAATTCACAGTATTTAGCACGCTCTGTGCTATCAAA
TGAGAAATTATCTTCTTCTCCTGAAACATTTGATCCTGATGGGATACAAACAGCTAGTGCAATC
ACTGAAGAGGACGATAGTTTTAAGGATGCATTGCCTGATTTTTTGTCTCTATCTGATGTTGGAA
ATTACGAGTCCTCTGGACGTGAATCGACTGAGACCATATTTAATGAAAATGATATAGGAAAAGG
GAAGGGCATATCCAGTGACATATTTTATGAGGCAGAGGACAGCGAAGATTCAAACTTTGTGGCT
GTAACCTTCCTGACGAGGGGCTCAGATTCCCCTGATTACGATGGTATAGACACTCAGGTACTAT
TATGATAGTGGTGATAGTTGATTATTTTTTCCAACATCATGTTTTGTTACGATACTGACTAACA
TATATGAAACATTTCAGATGAGTATTCGCATGTCAAAAATGGAATTCTACTGCAACAGACCCAC
TCTTGTTGCATTAATTGGTTTTGGTTTGGATATAAGTTCCTCAAATTATGTGGAAGCTAACACA
GACTTGCCCAGCTCTTTGGAAGATAAGCTTGTTATGGATAAAGAAAAGGCAGAAGAAAAAGGCC
GCGTAAAAGGATTGCTAGGATATGGAAAAAGTCGTGTCGTATTCTACTTAAACATGAATGTTGA
CAGTGTTTCCATCTATCTAAATATGGAGGATGGATCTCAGCTTGCAATGCTCGTGCAGGAGAGC
TTTTTGCTTGACCTCAAG
						
					

			
		

Sequences
Splice junction sequence	CTTAAACATGAATGTTGACAGTGTTTCCATCTATCTAAATATGGAGGATGGATCTCAGCTTGCA ATGCTCGTGCAGGAGAGCTTTTTGCTTGACCTCAAGgtccatataattcttggtgatgatgatc tttcagtcaaaacaaaactgcattcgttgcatattaaggatgaacttcaaggccacttatcaac aaattcac
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: 762 Transcript exons: 11289514-11289954,11290043-11290363 GTCCATATAATTCTTGGTGATGATGATCTTTCAGTCAAAACAAAACTGCATTCGTTGCATATTA AGGATGAACTTCAAGGCCACTTATCAACAAATTCACAGTATTTAGCACGCTCTGTGCTATCAAA TGAGAAATTATCTTCTTCTCCTGAAACATTTGATCCTGATGGGATACAAACAGCTAGTGCAATC ACTGAAGAGGACGATAGTTTTAAGGATGCATTGCCTGATTTTTTGTCTCTATCTGATGTTGGAA ATTACGAGTCCTCTGGACGTGAATCGACTGAGACCATATTTAATGAAAATGATATAGGAAAAGG GAAGGGCATATCCAGTGACATATTTTATGAGGCAGAGGACAGCGAAGATTCAAACTTTGTGGCT GTAACCTTCCTGACGAGGGGCTCAGATTCCCCTGATTACGATGGTATAGACACTCAGATGAGTA TTCGCATGTCAAAAATGGAATTCTACTGCAACAGACCCACTCTTGTTGCATTAATTGGTTTTGG TTTGGATATAAGTTCCTCAAATTATGTGGAAGCTAACACAGACTTGCCCAGCTCTTTGGAAGAT AAGCTTGTTATGGATAAAGAAAAGGCAGAAGAAAAAGGCCGCGTAAAAGGATTGCTAGGATATG GAAAAAGTCGTGTCGTATTCTACTTAAACATGAATGTTGACAGTGTTTCCATCTATCTAAATAT GGAGGATGGATCTCAGCTTGCAATGCTCGTGCAGGAGAGCTTTTTGCTTGACCTCAAG
Genomic sequence	GTCCATATAATTCTTGGTGATGATGATCTTTCAGTCAAAACAAAACTGCATTCGTTGCATATTA AGGATGAACTTCAAGGCCACTTATCAACAAATTCACAGTATTTAGCACGCTCTGTGCTATCAAA TGAGAAATTATCTTCTTCTCCTGAAACATTTGATCCTGATGGGATACAAACAGCTAGTGCAATC ACTGAAGAGGACGATAGTTTTAAGGATGCATTGCCTGATTTTTTGTCTCTATCTGATGTTGGAA ATTACGAGTCCTCTGGACGTGAATCGACTGAGACCATATTTAATGAAAATGATATAGGAAAAGG GAAGGGCATATCCAGTGACATATTTTATGAGGCAGAGGACAGCGAAGATTCAAACTTTGTGGCT GTAACCTTCCTGACGAGGGGCTCAGATTCCCCTGATTACGATGGTATAGACACTCAGGTACTAT TATGATAGTGGTGATAGTTGATTATTTTTTCCAACATCATGTTTTGTTACGATACTGACTAACA TATATGAAACATTTCAGATGAGTATTCGCATGTCAAAAATGGAATTCTACTGCAACAGACCCAC TCTTGTTGCATTAATTGGTTTTGGTTTGGATATAAGTTCCTCAAATTATGTGGAAGCTAACACA GACTTGCCCAGCTCTTTGGAAGATAAGCTTGTTATGGATAAAGAAAAGGCAGAAGAAAAAGGCC GCGTAAAAGGATTGCTAGGATATGGAAAAAGTCGTGTCGTATTCTACTTAAACATGAATGTTGA CAGTGTTTCCATCTATCTAAATATGGAGGATGGATCTCAGCTTGCAATGCTCGTGCAGGAGAGC TTTTTGCTTGACCTCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.996392922

Conservation Information
Conserved circRNAs	NA
PMCS	0.996392922

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11290044-11290360(+)
11290312-11289520(+)
						
						Potential amino acid sequence
						
							MSIRMSKMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLL
GYGKSRVVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLKVHIILGDDDLSVKTKLHSLHI
KDELQGHLSTNSQYLARSVLSNEKLSSSPETFDPDGIQTASAITEEDDSFKDALPDFLSLSDVG
NYESSGRESTETIFNENDIGKGKGISSDIFYEAEDSEDSNFVAVTFLTRGSDSPDYDGIDTQMS
IRMSKMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLLGY
GKSRVVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLKVHIILGDDDLSVKTKLHSLHIKD
ELQGHLSTNSQYLARSVLSNEKLSSSPETFDPDGIQTASAITEEDDSFKDALPDFLSLSDVGNY
ESSGRESTETIFNENDIGKGKGISSDIFYEAEDSEDSNFVAVTFLTRGSDSPDYDGIDTQMSIR
MSKMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLLGYGK
SRVVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLKVHIILGDDDLSVKTKLHSLHIKDEL
QGHLSTNSQYLARSVLSNEKLSSSPETFDPDGIQTASAITEEDDSFKDALPDFLSLSDVGNYES
SGRESTETIFNENDIGKGKGISSDIFYEAEDSEDSNFVAVTFLTRGSDSPDYDGIDTQMSIRMS
KMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLLGYGKSR
VVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLK
MDLSLQCSCRRAFCLTSRSI*
						
						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	11290044-11290360(+) 11290312-11289520(+)
Potential amino acid sequence	MSIRMSKMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLL GYGKSRVVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLKVHIILGDDDLSVKTKLHSLHI KDELQGHLSTNSQYLARSVLSNEKLSSSPETFDPDGIQTASAITEEDDSFKDALPDFLSLSDVG NYESSGRESTETIFNENDIGKGKGISSDIFYEAEDSEDSNFVAVTFLTRGSDSPDYDGIDTQMS IRMSKMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLLGY GKSRVVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLKVHIILGDDDLSVKTKLHSLHIKD ELQGHLSTNSQYLARSVLSNEKLSSSPETFDPDGIQTASAITEEDDSFKDALPDFLSLSDVGNY ESSGRESTETIFNENDIGKGKGISSDIFYEAEDSEDSNFVAVTFLTRGSDSPDYDGIDTQMSIR MSKMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLLGYGK SRVVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLKVHIILGDDDLSVKTKLHSLHIKDEL QGHLSTNSQYLARSVLSNEKLSSSPETFDPDGIQTASAITEEDDSFKDALPDFLSLSDVGNYES SGRESTETIFNENDIGKGKGISSDIFYEAEDSEDSNFVAVTFLTRGSDSPDYDGIDTQMSIRMS KMEFYCNRPTLVALIGFGLDISSSNYVEANTDLPSSLEDKLVMDKEKAEEKGRVKGLLGYGKSR VVFYLNMNVDSVSIYLNMEDGSQLAMLVQESFLLDLK MDLSLQCSCRRAFCLTSRSI*
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 Csa3G170010_circ_g.2

Address

Any questions?

Supported by