Plant Circular RNA Database

Detail information of Csa7G336540_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa7G336540_circ_g.2
					
						ID in PlantcircBase
						csa_circ_004584
					
						Alias
						Chr7:12025558_12033071
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr7: 12025558-12033071  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa7G336540						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa7G336540_circ_g.1 Csa7G336540_circ_g.3 						
					
						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
						Csa7G336540.2:9
Csa7G336540.1:9

General Information
CircRNA Name	Csa7G336540_circ_g.2
ID in PlantcircBase	csa_circ_004584
Alias	Chr7:12025558_12033071
Organism	Cucumis sativus
Position	chrChr7: 12025558-12033071 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa7G336540
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa7G336540_circ_g.1 Csa7G336540_circ_g.3
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	Csa7G336540.2:9 Csa7G336540.1:9

			
						 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  
						
							CAGATTCAACGTTGATAGATAGAGATTCGATGTCTTCTGGAACTTCAAACTCGACAGACCCATC
ATCTTTCACAGTAGTTACTCTGTGCAACAATTTAATcacagccttgcatttaggaaaaagccaa
tcatgagggcaattgtccaacaaatataagaagtccttcggttctgcagctgggagggaagaca
taaattca

						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	CAGATTCAACGTTGATAGATAGAGATTCGATGTCTTCTGGAACTTCAAACTCGACAGACCCATC ATCTTTCACAGTAGTTACTCTGTGCAACAATTTAATcacagccttgcatttaggaaaaagccaa tcatgagggcaattgtccaacaaatataagaagtccttcggttctgcagctgggagggaagaca taaattca
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
						0.094646172

Conservation Information
Conserved circRNAs	NA
PMCS	0.094646172

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							12032908-12025560(-)
						
					

						Potential amino acid sequence
						
							MQIVILIVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYM
VRNKGFLPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGL
KLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVT
YLSGSQFSESDVPHVYLWSPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPV
YIGFGSLPVQDPEKMTQIIIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKC
KAVIKLLHRVTTVKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVIL
IVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGF
LPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHI
FFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQ
FSESDVPHVYLWSPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPVYIGFGS
LPVQDPEKMTQIIIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKCKAVIKL
LHRVTTVKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRG
DVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPS
EILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPW
TPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDV
PHVYLWSPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPVYIGFGSLPVQDP
EKMTQIIIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKCKAVIKLLHRVTT
VKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRGDVQPFI
PIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPSEILIQR
NQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPWTPTSEF
PHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDVPHVYLW
SPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPVYIGFGSLPVQDPEKMTQI
IIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKCKAV
						
					

						Sponge-miRNAs
						
							PC-5p-22000 						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						responsive to salt stress in root (acting as miRNA sponges)
					

			
		

Functional Information
Coding potential	Y
Potential coding position	12032908-12025560(-)
Potential amino acid sequence	MQIVILIVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYM VRNKGFLPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGL KLPLHIFFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVT YLSGSQFSESDVPHVYLWSPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPV YIGFGSLPVQDPEKMTQIIIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKC KAVIKLLHRVTTVKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVIL IVGTRGDVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGF LPSWPSEILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHI FFTMPWTPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQ FSESDVPHVYLWSPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPVYIGFGS LPVQDPEKMTQIIIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKCKAVIKL LHRVTTVKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRG DVQPFIPIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPS EILIQRNQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPW TPTSEFPHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDV PHVYLWSPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPVYIGFGSLPVQDP EKMTQIIIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKCKAVIKLLHRVTT VKDDGSVEFEVPEDIESLSINVESEEIFTNVDDEPLDTSDFQYIRPMQIVILIVGTRGDVQPFI PIGKRLQDYGHRVRLATHPNFKEFVLLAGLEFYPLGGDPKELAAYMVRNKGFLPSWPSEILIQR NQMKEIIYSLLPACKDPDMDTGIPFEADAIIANRTAYGHTHVAEGLKLPLHIFFTMPWTPTSEF PHPLSRVKQQAGYRLSYQIVDSLIWLGLRDIINDFRKKKLQIRPVTYLSGSQFSESDVPHVYLW SPYIVPKPKDWGPKIDVVGYCFLDLSSNYEPPESLVKWLEAGDKPVYIGFGSLPVQDPEKMTQI IIQALETTKQRGIINEGWGGLGKSAEPKDFLYLLDNCPHDWLFPKCKAV
Sponge-miRNAs	PC-5p-22000
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to salt stress in root (acting as miRNA sponges)

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa7G336540_circ_g.2

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