Plant Circular RNA Database

Detail information of Csa1G629080_circ_g.4

			
						 General Information
					
						CircRNA Name
						Csa1G629080_circ_g.4
					
						ID in PlantcircBase
						csa_circ_000618
					
						Alias
						Chr1:24881078_24883786
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 24881078-24883786  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa1G629080						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa1G629080_circ_g.7 Csa1G629080_circ_g.8 Csa1G629080_circ_g.9 Csa1G629080_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  
						
							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
						Csa1G629080.1:5

General Information
CircRNA Name	Csa1G629080_circ_g.4
ID in PlantcircBase	csa_circ_000618
Alias	Chr1:24881078_24883786
Organism	Cucumis sativus
Position	chrChr1: 24881078-24883786 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa1G629080
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa1G629080_circ_g.7 Csa1G629080_circ_g.8 Csa1G629080_circ_g.9 Csa1G629080_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	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	Csa1G629080.1:5

			
						 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  
						
							AAGACACAAACAGATTTCATATATGAAGGAAAAAGCCATTGAAATCTTACTCTTCTTCTCCAGA
AGAATCTACCGACTCAATAGATGGCGTCTTTCTGGCaattgggagccatgattctgaacatgct
gatatcggtcacatgcatcagataaagaaccatagttgtgttggcgttgctgattcaactggtg
gtggagct

									
								

					

						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
						
							AATTGGGAGCCATGATTCTGAACATGCTGATATCGGTCACATGCATCAGATAAAGAACCATAGT
TGTGTTGGCGTTGCTGATTCAACTGGTGGTGGAGCTCAGCAACTTTCTGCTTTAACCGAGCCAC
ATCTGCTTCAGCAAGAGCAATCTCCTCAAGCTCAGCCCTTGTCTTCACATCAGTATAATCATGC
CTCATGAGAATGAATATGACCAATGGAGGTGAAAAAAAAAATTAAATGCCAAACATGCAGACAA
ACCTTCGAATCCATGCCCCGTGAATTATTAAATTGTCCAGAAGACATGCTTAGGCCAACTTCCA
GAGCAGCTCTAAGATCTCTTTCTGCTTGCAATTGCTCTTGTAATCTTGAAACCTACAAGGTCAT
TCAAACCCAAGAAATGTAATTTAAAAAACAAATATGCATTTGTTAGATACCTAGATTAGTATAG
GGTTAGGGGTGCGGTGCAAGGGTAATTGAATAAGATAGGAAGTTACTAGTAGTTATTGTCTAAA
GGTGGGTACTAGTAGCTATTGTGTAAGTATGGTTACTAGGGTGGTTACAACTTGTTATAAATAG
AGGGAGGGTAAGTGAGAGGAGGGAGTATCAGTTATTTTCGTGTGTAGGCTGTGAATCCTTGAGA
GGAGTACAGAGTGGATTGTTCTAGCTTTCTTACTGTATTTTGTGTGTGTAATTTCCAGATTGAT
AAATTATCAATCTGTAACTTCTTTTACCAAATTGAATAAAGAACAACTATATTAGTGTTCTATC
AGCATTTTTGTCTACGTTTCCTTGTTATATAAAAAAAAAGAAAATGGTACTATATCCACATAAA
TAACTTCCAAGCCCACTCCCATCACCAAACCAAATCTCACATACTAATAGTCGCAAACATTTTC
TAAAAGTAATTTGAAAGAACAGTTTTATAGTATTAAATATAGCTCCTCTCCTAAACTATACCAA
GGATTTATTAGAAAAATAAAGTTCAAGTAACAAGCATTCGCCACCCTGAAACGTACATCTTGTT
CAAGTGCCAACCGTCGTTCATGCAAAGCTTGTTTCCTTCTTTCCAAGCTGGCTTGTAAAATTGC
ATTGCCTCTAGCCTACACAATATGGATATTCAGTAAATACTCTAATCAACCACTGGATCTTTGG
ATAACAAAGTTAGAGAGTTTGACTACCTCCTTCGCAATCCTCTGTTGCAGGTCATTTTTTGTCA
TCTCAAGCCTCTGAATAGCAAGCCTACAAAAATAGTTGAAATTTATCTTCAGGGAATAGTTTTA
GTTCATGGTGAAGTAACATTCAGAAGGTGAGAAGAAAAACCCGTGGAACAAACCAAGAAGTAAA
AATATTCTAGAAAAAAATACAAAAAAGATGCAATTTGTAGAAAACAAGCCACTTTGGTTATCTA
CAGAGTTAGCTTTGCATTCTTGCAAAAAGTCAATTAATGAAACTTTGTGCAGTTATCGTGATGA
ATGTAGAGGAGATATTGTAACCTCAACTGGACCTTCAATTGCCCAATTGTATCTTGGTGTAGAC
CAAGAGAGATATTAACCAATTCAAAATTACTCTAACCCAACAGACCAGAATCCCAACTAATCAA
CATATAAATAACGACCAATCCACTTGAAAAACCTTCAAACAGCGAAACAAATAAAACAACCAAA
TAAAATAAGAGATTTGTCAGAAAATACAATAAAGTTGTTAAATAACTAATAGACCAAAAGGCTT
AAGCTGATGGATAAAGGTAAATTTAACATTCTCCCTCACTTGTGGACTTGAAATATGTGAAAGA
TCCAACGAGTGGAAATCATAATTGGTAAGGAAATAGCATTCTAGAGGTGGTAACACAGGACCTC
CTAGACCACGTCCTAGACCACTTGCTTTGATACCATAAAGACACGTTTGTTTCTTCTTATATTT
TATGCAAAGATACAACCCTCAGTTTTAAAAGGGGAAAATCATAGAAGGAAAAATGAATAACAAT
AATTGTTCTTCCAGATCATTAGTAGCCATCTTCTACAAATCATGTTTTGCAGCCATCATTGAAA
GACTCTTTGTCTACACCATTGTACCGCCGTTGTTTATTCCATGTTTGTTTATAGTTTTTTGGCT
TTACAGCACATGCTGACCATACTCTAGAAAGACTTTATTTTGTATCTTAGGACTATTTTTGTTT
GGATATGATGATAGCGCTAAGAGGAAGTCAACCTAGTTGAGATGTCCGGATGTGTCTATTGATC
CTATGGTCTCGTTATTGCTTAGCTCTTTGTGTAAACCTTTTTATACTTTGAGCTTATTATTTAT
CAATAAAGAGGTTGGTTTCCTTTTCAAGAAAATAACAATAATCATTCTTTCTCATCTTGTCATT
TAATAATTTTCTGTTTCATTTTAGCCAAAAGTCCAAAAGGTGAAAATTACAAAACAAGTCATAC
ACACCTTTTAACATGCCAAACCTCATTCTTCCATAACAATAACATAATTTATCCATCTTCAGTA
TGAAGAAAACGTAAAACGTGTGATGAATTTAAACAGCCAATTAACTTCATCATAGAACTTATTT
GACGAGCTAATATGCAAAAAAAAATTCAGATTGAGCTCATACAGATCGCAAGACACAAACAGAT
TTCATATATGAAGGAAAAAGCCATTGAAATCTTACTCTTCTTCTCCAGAAGAATCTACCGACTC
AATAGATGGCGTCTTTCTGGC
						
					

			
		

Sequences
Splice junction sequence	AAGACACAAACAGATTTCATATATGAAGGAAAAAGCCATTGAAATCTTACTCTTCTTCTCCAGA AGAATCTACCGACTCAATAGATGGCGTCTTTCTGGCaattgggagccatgattctgaacatgct gatatcggtcacatgcatcagataaagaaccatagttgtgttggcgttgctgattcaactggtg gtggagct
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	AATTGGGAGCCATGATTCTGAACATGCTGATATCGGTCACATGCATCAGATAAAGAACCATAGT TGTGTTGGCGTTGCTGATTCAACTGGTGGTGGAGCTCAGCAACTTTCTGCTTTAACCGAGCCAC ATCTGCTTCAGCAAGAGCAATCTCCTCAAGCTCAGCCCTTGTCTTCACATCAGTATAATCATGC CTCATGAGAATGAATATGACCAATGGAGGTGAAAAAAAAAATTAAATGCCAAACATGCAGACAA ACCTTCGAATCCATGCCCCGTGAATTATTAAATTGTCCAGAAGACATGCTTAGGCCAACTTCCA GAGCAGCTCTAAGATCTCTTTCTGCTTGCAATTGCTCTTGTAATCTTGAAACCTACAAGGTCAT TCAAACCCAAGAAATGTAATTTAAAAAACAAATATGCATTTGTTAGATACCTAGATTAGTATAG GGTTAGGGGTGCGGTGCAAGGGTAATTGAATAAGATAGGAAGTTACTAGTAGTTATTGTCTAAA GGTGGGTACTAGTAGCTATTGTGTAAGTATGGTTACTAGGGTGGTTACAACTTGTTATAAATAG AGGGAGGGTAAGTGAGAGGAGGGAGTATCAGTTATTTTCGTGTGTAGGCTGTGAATCCTTGAGA GGAGTACAGAGTGGATTGTTCTAGCTTTCTTACTGTATTTTGTGTGTGTAATTTCCAGATTGAT AAATTATCAATCTGTAACTTCTTTTACCAAATTGAATAAAGAACAACTATATTAGTGTTCTATC AGCATTTTTGTCTACGTTTCCTTGTTATATAAAAAAAAAGAAAATGGTACTATATCCACATAAA TAACTTCCAAGCCCACTCCCATCACCAAACCAAATCTCACATACTAATAGTCGCAAACATTTTC TAAAAGTAATTTGAAAGAACAGTTTTATAGTATTAAATATAGCTCCTCTCCTAAACTATACCAA GGATTTATTAGAAAAATAAAGTTCAAGTAACAAGCATTCGCCACCCTGAAACGTACATCTTGTT CAAGTGCCAACCGTCGTTCATGCAAAGCTTGTTTCCTTCTTTCCAAGCTGGCTTGTAAAATTGC ATTGCCTCTAGCCTACACAATATGGATATTCAGTAAATACTCTAATCAACCACTGGATCTTTGG ATAACAAAGTTAGAGAGTTTGACTACCTCCTTCGCAATCCTCTGTTGCAGGTCATTTTTTGTCA TCTCAAGCCTCTGAATAGCAAGCCTACAAAAATAGTTGAAATTTATCTTCAGGGAATAGTTTTA GTTCATGGTGAAGTAACATTCAGAAGGTGAGAAGAAAAACCCGTGGAACAAACCAAGAAGTAAA AATATTCTAGAAAAAAATACAAAAAAGATGCAATTTGTAGAAAACAAGCCACTTTGGTTATCTA CAGAGTTAGCTTTGCATTCTTGCAAAAAGTCAATTAATGAAACTTTGTGCAGTTATCGTGATGA ATGTAGAGGAGATATTGTAACCTCAACTGGACCTTCAATTGCCCAATTGTATCTTGGTGTAGAC CAAGAGAGATATTAACCAATTCAAAATTACTCTAACCCAACAGACCAGAATCCCAACTAATCAA CATATAAATAACGACCAATCCACTTGAAAAACCTTCAAACAGCGAAACAAATAAAACAACCAAA TAAAATAAGAGATTTGTCAGAAAATACAATAAAGTTGTTAAATAACTAATAGACCAAAAGGCTT AAGCTGATGGATAAAGGTAAATTTAACATTCTCCCTCACTTGTGGACTTGAAATATGTGAAAGA TCCAACGAGTGGAAATCATAATTGGTAAGGAAATAGCATTCTAGAGGTGGTAACACAGGACCTC CTAGACCACGTCCTAGACCACTTGCTTTGATACCATAAAGACACGTTTGTTTCTTCTTATATTT TATGCAAAGATACAACCCTCAGTTTTAAAAGGGGAAAATCATAGAAGGAAAAATGAATAACAAT AATTGTTCTTCCAGATCATTAGTAGCCATCTTCTACAAATCATGTTTTGCAGCCATCATTGAAA GACTCTTTGTCTACACCATTGTACCGCCGTTGTTTATTCCATGTTTGTTTATAGTTTTTTGGCT TTACAGCACATGCTGACCATACTCTAGAAAGACTTTATTTTGTATCTTAGGACTATTTTTGTTT GGATATGATGATAGCGCTAAGAGGAAGTCAACCTAGTTGAGATGTCCGGATGTGTCTATTGATC CTATGGTCTCGTTATTGCTTAGCTCTTTGTGTAAACCTTTTTATACTTTGAGCTTATTATTTAT CAATAAAGAGGTTGGTTTCCTTTTCAAGAAAATAACAATAATCATTCTTTCTCATCTTGTCATT TAATAATTTTCTGTTTCATTTTAGCCAAAAGTCCAAAAGGTGAAAATTACAAAACAAGTCATAC ACACCTTTTAACATGCCAAACCTCATTCTTCCATAACAATAACATAATTTATCCATCTTCAGTA TGAAGAAAACGTAAAACGTGTGATGAATTTAAACAGCCAATTAACTTCATCATAGAACTTATTT GACGAGCTAATATGCAAAAAAAAATTCAGATTGAGCTCATACAGATCGCAAGACACAAACAGAT TTCATATATGAAGGAAAAAGCCATTGAAATCTTACTCTTCTTCTCCAGAAGAATCTACCGACTC AATAGATGGCGTCTTTCTGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13005654

Conservation Information
Conserved circRNAs	NA
PMCS	0.13005654

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24882296-24883758(-)
24881140-24883766(-)
						
						Potential amino acid sequence
						
							MTKNDLQQRIAKEARGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLS
MSSGQFNNSRGMDSKTRAELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQH
VQNHGSQLPERRHLLSR*
MVLYLMHVTDISMFRIMAPNCQKDAIY*
						
						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	24882296-24883758(-) 24881140-24883766(-)
Potential amino acid sequence	MTKNDLQQRIAKEARGNAILQASLERRKQALHERRLALEQDVSRLQEQLQAERDLRAALEVGLS MSSGQFNNSRGMDSKTRAELEEIALAEADVARLKQKVAELHHQLNQQRQHNYGSLSDACDRYQH VQNHGSQLPERRHLLSR* MVLYLMHVTDISMFRIMAPNCQKDAIY*
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 Csa1G629080_circ_g.4

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