Plant Circular RNA Database

Detail information of Csa4G052620_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa4G052620_circ_g.1
					
						ID in PlantcircBase
						csa_circ_002371
					
						Alias
						Chr4:4390046_4391853
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr4: 4390046-4391853  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Csa4G052620						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa4G052620_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						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  
						
							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
						Csa4G052620.1:5

General Information
CircRNA Name	Csa4G052620_circ_g.1
ID in PlantcircBase	csa_circ_002371
Alias	Chr4:4390046_4391853
Organism	Cucumis sativus
Position	chrChr4: 4390046-4391853 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	Find_circ
Parent gene	Csa4G052620
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa4G052620_circ_g.2
Support reads	NA
Tissues	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	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	Csa4G052620.1:5

			
						 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  
						
							TGTTCCAGAAAATTCCTCTTGTGACGTCTGCACGCCGACCTGGCGATGCTGAAATTGTATACGC
ATCGACATACAAAGCAGAAAAGGAGTTGAACTGGAActtgtcttctcgtcgtcagccaccgtat
atggttggccgaaggaggtaccatgtacagaagagtttcccctttctgcagcaaacccgtatgg
acgaacca

									
								

					

						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
						
							CTTGTCTTCTCGTCGTCAGCCACCGTATATGGTTGGCCGAAGGAGGTACCATGTACAGAAGAGT
TTCCCCTTTCTGCAGCAAACCCGTATGGACGAACCAAGGTATACAACTCCTATTATTTAGTGGG
CACTATAGTTGATCATTAGTTTTGTCTAAGTTTTAACTGTTGACCATCACACACAAGAAATTCC
CATCTATTCACTTTTGCACCGTTGCTGTTTTCTTCTTTTTCTTGGTATTGACTGCTATTACATG
TGGACTTGATTCTCTTTCAGCTTCTCATAGAAGAAATCTGCCGTGACATATACCGTTCAGACTC
TGAATGGAAAATCATATTGCTAAGATATTTCAATCCAGTGGGTGCCCACCCCAGTGGCTATATT
GGTGAGGATCCCCGTGGAATCCCAAACAACCTCATGCCCTTTGTACAGCAAGTTGCTGTTGGCA
GGCGTCCTGCCTTGACAGTCTATGGAACTGACTATTCAACAAAAGATGGAACCGGAGTAAGTTC
ATCGTAGGAACACTATATAACCTTGTTCTTTGCTGGATTGCTGGTTTTTCTTGCTGTGCTTGAT
ATCCGTAGTCTGAGGCTTCCAATAATTTTCTCTTCCTAATGTATACAAGTGAATTTTATGGAGA
AAGATGATTATTGAAAGATCTATTGTCCTCTGCAGGTACGTGATTATATTCATGTTGTTGATTT
AGCTGATGGACACATTGCTGCATTGCGCAAGTTAGATGCGGCTGGTATAGGTAATACACTCAAT
ATCAGGCTCTTTGCTTGTGCCTTGTGGTGACTGGTAATGCATAGTAGATTTTCCTGATCCTTTT
TAGTTCTTATTTATGTTTAAGAACCATTATGGAGGATACTTGGTATATTTACCCCAAATTTATA
TTTTGAGCTTTAATAACACTCATAATGCCACGAGAATGCCGAGGATACTAAGGAAAATTCCTAC
ATTACATGAGAGAGTAATATTTAGAGCTAGTTTATAATAATGTTTTGGGTTAAACAGAAAAGTC
TCAGGTTCAATACTTTGTGGCCTAAAATGTTGGCTACTGCCCTGTTAAATTAATACAACTTTGG
GCACTAAAGCATTATTTGCCGGCAAGGAAGCAATTTATTTGTGTTCAAATTTTCTTGCAACTCT
CTGATTTCTTCTTTCAAGATTTTTCTTCTTTTAATAACCACAATAGCTAATAATGACAAATGAA
AATTATATCATCCAAGAGTTTGAACGGTATATGTCATGAATATCATGATAGGTTGTGAAGTTTA
CAATTTGGGAACTGGAAAGGGTACATCAGTCTTGGAGATGGTTTCAGCTTTTGAAAAAGCATCT
GGAAAGGTATTTTTTACTCTACTTCTTTTGCGTTTGTTTCCAAGAAACTTGGTAGAATTAAGGG
TGTTCGTGGTTATAAGTAATGTGCTCCTGGTTTCAATGCCTTCCTCTGACTATGGTATACTAGG
CTTAATTTAAATGAAAATAATGGGATTCATATCTAGGATTTTAGTTTTCAGATTAGAGATGCTA
CCATGATTCCAAATACTATCCCCCATCCTCAACAGTCGTCACCTTTCACTGACACTTCCACCAC
GAGTTCTTGTCCTCTTGAACTCCCTAAAACTTATCAAGTCTTTGAGTGCTTCTTTATTCAATCA
TGACTCTACTTCACCTCCCATCTGAATTTACTGGTTAATTTCTCTGTTCCAGAAAATTCCTCTT
GTGACGTCTGCACGCCGACCTGGCGATGCTGAAATTGTATACGCATCGACATACAAAGCAGAAA
AGGAGTTGAACTGGAA
						
					

			
		

Sequences
Splice junction sequence	TGTTCCAGAAAATTCCTCTTGTGACGTCTGCACGCCGACCTGGCGATGCTGAAATTGTATACGC ATCGACATACAAAGCAGAAAAGGAGTTGAACTGGAActtgtcttctcgtcgtcagccaccgtat atggttggccgaaggaggtaccatgtacagaagagtttcccctttctgcagcaaacccgtatgg acgaacca
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	CTTGTCTTCTCGTCGTCAGCCACCGTATATGGTTGGCCGAAGGAGGTACCATGTACAGAAGAGT TTCCCCTTTCTGCAGCAAACCCGTATGGACGAACCAAGGTATACAACTCCTATTATTTAGTGGG CACTATAGTTGATCATTAGTTTTGTCTAAGTTTTAACTGTTGACCATCACACACAAGAAATTCC CATCTATTCACTTTTGCACCGTTGCTGTTTTCTTCTTTTTCTTGGTATTGACTGCTATTACATG TGGACTTGATTCTCTTTCAGCTTCTCATAGAAGAAATCTGCCGTGACATATACCGTTCAGACTC TGAATGGAAAATCATATTGCTAAGATATTTCAATCCAGTGGGTGCCCACCCCAGTGGCTATATT GGTGAGGATCCCCGTGGAATCCCAAACAACCTCATGCCCTTTGTACAGCAAGTTGCTGTTGGCA GGCGTCCTGCCTTGACAGTCTATGGAACTGACTATTCAACAAAAGATGGAACCGGAGTAAGTTC ATCGTAGGAACACTATATAACCTTGTTCTTTGCTGGATTGCTGGTTTTTCTTGCTGTGCTTGAT ATCCGTAGTCTGAGGCTTCCAATAATTTTCTCTTCCTAATGTATACAAGTGAATTTTATGGAGA AAGATGATTATTGAAAGATCTATTGTCCTCTGCAGGTACGTGATTATATTCATGTTGTTGATTT AGCTGATGGACACATTGCTGCATTGCGCAAGTTAGATGCGGCTGGTATAGGTAATACACTCAAT ATCAGGCTCTTTGCTTGTGCCTTGTGGTGACTGGTAATGCATAGTAGATTTTCCTGATCCTTTT TAGTTCTTATTTATGTTTAAGAACCATTATGGAGGATACTTGGTATATTTACCCCAAATTTATA TTTTGAGCTTTAATAACACTCATAATGCCACGAGAATGCCGAGGATACTAAGGAAAATTCCTAC ATTACATGAGAGAGTAATATTTAGAGCTAGTTTATAATAATGTTTTGGGTTAAACAGAAAAGTC TCAGGTTCAATACTTTGTGGCCTAAAATGTTGGCTACTGCCCTGTTAAATTAATACAACTTTGG GCACTAAAGCATTATTTGCCGGCAAGGAAGCAATTTATTTGTGTTCAAATTTTCTTGCAACTCT CTGATTTCTTCTTTCAAGATTTTTCTTCTTTTAATAACCACAATAGCTAATAATGACAAATGAA AATTATATCATCCAAGAGTTTGAACGGTATATGTCATGAATATCATGATAGGTTGTGAAGTTTA CAATTTGGGAACTGGAAAGGGTACATCAGTCTTGGAGATGGTTTCAGCTTTTGAAAAAGCATCT GGAAAGGTATTTTTTACTCTACTTCTTTTGCGTTTGTTTCCAAGAAACTTGGTAGAATTAAGGG TGTTCGTGGTTATAAGTAATGTGCTCCTGGTTTCAATGCCTTCCTCTGACTATGGTATACTAGG CTTAATTTAAATGAAAATAATGGGATTCATATCTAGGATTTTAGTTTTCAGATTAGAGATGCTA CCATGATTCCAAATACTATCCCCCATCCTCAACAGTCGTCACCTTTCACTGACACTTCCACCAC GAGTTCTTGTCCTCTTGAACTCCCTAAAACTTATCAAGTCTTTGAGTGCTTCTTTATTCAATCA TGACTCTACTTCACCTCCCATCTGAATTTACTGGTTAATTTCTCTGTTCCAGAAAATTCCTCTT GTGACGTCTGCACGCCGACCTGGCGATGCTGAAATTGTATACGCATCGACATACAAAGCAGAAA AGGAGTTGAACTGGAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13107011

Conservation Information
Conserved circRNAs	NA
PMCS	0.13107011

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							4390464-4390328(+)
						
						Potential amino acid sequence
						
							MPFVQQVAVGRRPALTVYGTDYSTKDGTGVRDYIHVVDLADGHIAALRKLDAAGIGCEVYNLGT
GKGTSVLEMVSAFEKASGKKIPLVTSARRPGDAEIVYASTYKAEKELNWNLSSRRQPPYMVGRR
RYHVQKSFPFLQQTRMDEPSFS*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	4390464-4390328(+)
Potential amino acid sequence	MPFVQQVAVGRRPALTVYGTDYSTKDGTGVRDYIHVVDLADGHIAALRKLDAAGIGCEVYNLGT GKGTSVLEMVSAFEKASGKKIPLVTSARRPGDAEIVYASTYKAEKELNWNLSSRRQPPYMVGRR RYHVQKSFPFLQQTRMDEPSFS*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						He et al., 2020

circRNA

Detail information of Csa4G052620_circ_g.1

Address

Any questions?

Supported by