Plant Circular RNA Database

Detail information of Csa1G651660_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa1G651660_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000650
					
						Alias
						Chr1:25794119_25796332
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 25794119-25796332  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa1G651660						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa1G651660_circ_g.2 Csa1G651660_circ_g.3 Csa1G651660_circ_g.4 Chr1_circ_ig.139 Csa1G651670_circ_g.1 Csa1G651670_circ_g.2 Csa1G651670_circ_g.3 Csa1G651670_circ_g.4 Csa1G651670_circ_g.5 Csa1G651670_circ_g.6 Csa1G651670_circ_g.7 Csa1G651670_circ_g.8 						
					
						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
						Csa1G651660.1:6

General Information
CircRNA Name	Csa1G651660_circ_g.1
ID in PlantcircBase	csa_circ_000650
Alias	Chr1:25794119_25796332
Organism	Cucumis sativus
Position	chrChr1: 25794119-25796332 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa1G651660
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa1G651660_circ_g.2 Csa1G651660_circ_g.3 Csa1G651660_circ_g.4 Chr1_circ_ig.139 Csa1G651670_circ_g.1 Csa1G651670_circ_g.2 Csa1G651670_circ_g.3 Csa1G651670_circ_g.4 Csa1G651670_circ_g.5 Csa1G651670_circ_g.6 Csa1G651670_circ_g.7 Csa1G651670_circ_g.8
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	Csa1G651660.1:6

			
						 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  
						
							TTTTCACTAGCTTTGTGGAGTACCTTCAACTTGAAAATGCTTACAACATTTTTATTCTAAATCT
CAAGCGTGACACAAAAAGGGCCAGATATGGATACCGctattagcagcaagaccccttgcatctt
cctctggaaatcgtaaaagtagaaagtcctctgtattctccttgtttaaccttaaagataaaag
caagtttt

									
								

					

						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: 707
Transcript exons: 25794119-25794242,25794365-25794427,25795407-25795508,25
795609-25795777,25795944-25796042,25796183-25796332
CTATTAGCAGCAAGACCCCTTGCATCTTCCTCTGGAAATCGTAAAAGTAGAAAGTCCTCTGTAT
TCTCCTTGTTTAACCTTAAAGATAAAAGCAAGTTTTGGAGTGAGACAGTCATACGTGGTGATTT
TGATGATCTGGAATCATCCACCACCGAGAAAATGAGTGTTGTTAACTACACAAAGGCAGGTAAC
GTAGCAAATTACTTAAAGCTTCTTGAAGTTGATTCCCTGTACCTTCCAGTCCCTGTGAATTTCA
TTTTTATAGGATTTGAAGGGAAAGGCAACCATGAATTCAAGCTGCATCCAGAAGAGCTTGAACG
TTGGTTCATCAAACTTGATCATATCTTTGAACATACACGGATTCCACAATTTAGGGAGGTGCTA
ACCCCGTTTTATAAGATGAGCATGGACAAAGTTTTGAGGCACCAACTACCCCTCATCAGTCACA
CAAACTACAATTTTTCTGTTCATGTAATACAAACGGGTGAGAAGGTTACTTCAATCTTTGAGCT
TGCAAGAAATGTCTTATCCCGCAAAGAAGATGTATCTAATAATGGGGATGGGAATGATGCTCTT
TGGCAAGTAGACGTGGACCTGATGGATGTACTTTTCACTAGCTTTGTGGAGTACCTTCAACTTG
AAAATGCTTACAACATTTTTATTCTAAATCTCAAGCGTGACACAAAAAGGGCCAGATATGGATA
CCG
						
					

						Genomic sequence
						
							CTATTAGCAGCAAGACCCCTTGCATCTTCCTCTGGAAATCGTAAAAGTAGAAAGTCCTCTGTAT
TCTCCTTGTTTAACCTTAAAGATAAAAGCAAGTTTTGGAGTGAGACAGTCATACGTGGTGGTAT
GTTCTACTTTCTTATATTTGTTACTTCAAAGCATATATACGTTCTCTAATCATGGTTATTGCGA
ATGGGTTGCCTTTTTGTTTTACTCTTTTGACACATTGTTTTTTCATTTGTTTAGATTTTGATGA
TCTGGAATCATCCACCACCGAGAAAATGAGTGTTGTTAACTACACAAAGGCAGGTAATTGCATT
GATCTAACCAGTGAAGACTTTCTGTTTTGTCAGTGTAATAAATATTGTGAGAGTTGGGGGCTTT
TGGCCCGTTTTTATGTTTATGTTACGTTAAAGATGGGAGTTGGTTAGACATCACATAAGTGGTG
GAGTGAGATACAAAATTGAATTTTTACTGGGATGAAAATCTAGTTGGGAGAGTGATAAGTCTTC
CAAAATCTCGAAGTTCTTAATGCAATACTCTTTAGTAATTAGTCCTATCACAACCCAGCAACAC
AACACTGATGCATTCATGCTGGATACAGAGCCATTTGAAATATCTTTTGACCTCCATTTGGGAA
GTAGCTCACCCTGCTGAATCCACATTCTTGAAATTGTTATTCATTTCCTTGCCTGTTTCTTCTT
ACAAATGAAAATGTAGAAAGTTTTTTTTTAAAATCTTCACACAGTGATATATGTTTTTGGAGAG
GAGGTCCTTTAGCTTGGTTGTTAGGTTTTACAGAATTTATTATTTCATCTTTTATCTTCCTTTT
AGCAAGTCTCCAATACCCGTGAAAGATGATCTAAGATAAATAAGTATTTTATGGCAACTACTTG
GATCTGGACTTGGTGTAAAATATCGTTTCTATTGTCATTTTGAGTGTTAGTGACTAGGATTTTT
ATTATATGTCTTTGTTCTTTGCTCTATATCTTTCTTTTTGCTCTTAGTATAATTCTCTTGACCG
AGGCTTGTTTCTGTTTAAAAGAAAATATATATGGTTGTTACTCATTTCATATATTATTATTTGA
ACTATTTTTTCTGTTTTGGTAATTTCCTAATCCTTCTTGGGTCTATGCTAAATCTCATTCTTTT
CTACATCTTGTTCTTCCATAAATTTTTATAGCGAAATTTCTTGAAGTCTCTACAGTAATATGAT
GTGAGAACCAATACATTGAAAAAGCAAGAGCACCATAAGAAGTCTCTTTTTCATGTCTATCTTC
TATTGCAGGTAACGTAGCAAATTACTTAAAGCTTCTTGAAGTTGATTCCCTGTACCTTCCAGTC
CCTGTGAATTTCATTTTTATAGGATTTGAAGGGAAAGGCAACCATGGTATGAAATGCTCTTGAA
TATGAACTTGTTTCATGGTTGGACTTTTATCTTTGGTTCGAAGTTGTTATATGGATGTTCTAAG
AGTTCTTTTTCTTGTTAGAATTCAAGCTGCATCCAGAAGAGCTTGAACGTTGGTTCATCAAACT
TGATCATATCTTTGAACATACACGGATTCCACAATTTAGGGAGGTGCTAACCCCGTTTTATAAG
ATGAGCATGGACAAAGTTTTGAGGCACCAACTACCCCTCATCAGTCACACAAACTACAAGTAAT
GCTTAACTGGTACTTTGTATATTATGGGAGCCTAAGTTGGTGTACTTTTTTGAGAAAGTTAGAT
TTCTTATTTTATGTTTGTCATAAGTTAGTAAATGACAATTTAGCTCTTGCGTACAAAGTTGAAA
TGAAATCCTTAATCTTCTCATGAAATCTTGCAGTTTTTCTGTTCATGTAATACAAACGGGTGAG
AAGGTTACTTCAATCTTTGAGCTTGCAAGAAATGTCTTATCCCGCAAAGAAGATGTATCTAATA
ATGGGTAACTTTTGTAGCATTGTACTTTTGTTAGTTTTATCATTTATTATCTCAATATATTCTC
ATTGTTGAAGCTATTTGAGCAATGTTGGCTTTTTTATTTTTCCAAATTTAAATTATTATTATTG
TATCTCATGGTTGCAGGGATGGGAATGATGCTCTTTGGCAAGTAGACGTGGACCTGATGGATGT
ACTTTTCACTAGCTTTGTGGAGTACCTTCAACTTGAAAATGCTTACAACATTTTTATTCTAAAT
CTCAAGCGTGACACAAAAAGGGCCAGATATGGATACCG
						
					

			
		

Sequences
Splice junction sequence	TTTTCACTAGCTTTGTGGAGTACCTTCAACTTGAAAATGCTTACAACATTTTTATTCTAAATCT CAAGCGTGACACAAAAAGGGCCAGATATGGATACCGctattagcagcaagaccccttgcatctt cctctggaaatcgtaaaagtagaaagtcctctgtattctccttgtttaaccttaaagataaaag caagtttt
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: 707 Transcript exons: 25794119-25794242,25794365-25794427,25795407-25795508,25 795609-25795777,25795944-25796042,25796183-25796332 CTATTAGCAGCAAGACCCCTTGCATCTTCCTCTGGAAATCGTAAAAGTAGAAAGTCCTCTGTAT TCTCCTTGTTTAACCTTAAAGATAAAAGCAAGTTTTGGAGTGAGACAGTCATACGTGGTGATTT TGATGATCTGGAATCATCCACCACCGAGAAAATGAGTGTTGTTAACTACACAAAGGCAGGTAAC GTAGCAAATTACTTAAAGCTTCTTGAAGTTGATTCCCTGTACCTTCCAGTCCCTGTGAATTTCA TTTTTATAGGATTTGAAGGGAAAGGCAACCATGAATTCAAGCTGCATCCAGAAGAGCTTGAACG TTGGTTCATCAAACTTGATCATATCTTTGAACATACACGGATTCCACAATTTAGGGAGGTGCTA ACCCCGTTTTATAAGATGAGCATGGACAAAGTTTTGAGGCACCAACTACCCCTCATCAGTCACA CAAACTACAATTTTTCTGTTCATGTAATACAAACGGGTGAGAAGGTTACTTCAATCTTTGAGCT TGCAAGAAATGTCTTATCCCGCAAAGAAGATGTATCTAATAATGGGGATGGGAATGATGCTCTT TGGCAAGTAGACGTGGACCTGATGGATGTACTTTTCACTAGCTTTGTGGAGTACCTTCAACTTG AAAATGCTTACAACATTTTTATTCTAAATCTCAAGCGTGACACAAAAAGGGCCAGATATGGATA CCG
Genomic sequence	CTATTAGCAGCAAGACCCCTTGCATCTTCCTCTGGAAATCGTAAAAGTAGAAAGTCCTCTGTAT TCTCCTTGTTTAACCTTAAAGATAAAAGCAAGTTTTGGAGTGAGACAGTCATACGTGGTGGTAT GTTCTACTTTCTTATATTTGTTACTTCAAAGCATATATACGTTCTCTAATCATGGTTATTGCGA ATGGGTTGCCTTTTTGTTTTACTCTTTTGACACATTGTTTTTTCATTTGTTTAGATTTTGATGA TCTGGAATCATCCACCACCGAGAAAATGAGTGTTGTTAACTACACAAAGGCAGGTAATTGCATT GATCTAACCAGTGAAGACTTTCTGTTTTGTCAGTGTAATAAATATTGTGAGAGTTGGGGGCTTT TGGCCCGTTTTTATGTTTATGTTACGTTAAAGATGGGAGTTGGTTAGACATCACATAAGTGGTG GAGTGAGATACAAAATTGAATTTTTACTGGGATGAAAATCTAGTTGGGAGAGTGATAAGTCTTC CAAAATCTCGAAGTTCTTAATGCAATACTCTTTAGTAATTAGTCCTATCACAACCCAGCAACAC AACACTGATGCATTCATGCTGGATACAGAGCCATTTGAAATATCTTTTGACCTCCATTTGGGAA GTAGCTCACCCTGCTGAATCCACATTCTTGAAATTGTTATTCATTTCCTTGCCTGTTTCTTCTT ACAAATGAAAATGTAGAAAGTTTTTTTTTAAAATCTTCACACAGTGATATATGTTTTTGGAGAG GAGGTCCTTTAGCTTGGTTGTTAGGTTTTACAGAATTTATTATTTCATCTTTTATCTTCCTTTT AGCAAGTCTCCAATACCCGTGAAAGATGATCTAAGATAAATAAGTATTTTATGGCAACTACTTG GATCTGGACTTGGTGTAAAATATCGTTTCTATTGTCATTTTGAGTGTTAGTGACTAGGATTTTT ATTATATGTCTTTGTTCTTTGCTCTATATCTTTCTTTTTGCTCTTAGTATAATTCTCTTGACCG AGGCTTGTTTCTGTTTAAAAGAAAATATATATGGTTGTTACTCATTTCATATATTATTATTTGA ACTATTTTTTCTGTTTTGGTAATTTCCTAATCCTTCTTGGGTCTATGCTAAATCTCATTCTTTT CTACATCTTGTTCTTCCATAAATTTTTATAGCGAAATTTCTTGAAGTCTCTACAGTAATATGAT GTGAGAACCAATACATTGAAAAAGCAAGAGCACCATAAGAAGTCTCTTTTTCATGTCTATCTTC TATTGCAGGTAACGTAGCAAATTACTTAAAGCTTCTTGAAGTTGATTCCCTGTACCTTCCAGTC CCTGTGAATTTCATTTTTATAGGATTTGAAGGGAAAGGCAACCATGGTATGAAATGCTCTTGAA TATGAACTTGTTTCATGGTTGGACTTTTATCTTTGGTTCGAAGTTGTTATATGGATGTTCTAAG AGTTCTTTTTCTTGTTAGAATTCAAGCTGCATCCAGAAGAGCTTGAACGTTGGTTCATCAAACT TGATCATATCTTTGAACATACACGGATTCCACAATTTAGGGAGGTGCTAACCCCGTTTTATAAG ATGAGCATGGACAAAGTTTTGAGGCACCAACTACCCCTCATCAGTCACACAAACTACAAGTAAT GCTTAACTGGTACTTTGTATATTATGGGAGCCTAAGTTGGTGTACTTTTTTGAGAAAGTTAGAT TTCTTATTTTATGTTTGTCATAAGTTAGTAAATGACAATTTAGCTCTTGCGTACAAAGTTGAAA TGAAATCCTTAATCTTCTCATGAAATCTTGCAGTTTTTCTGTTCATGTAATACAAACGGGTGAG AAGGTTACTTCAATCTTTGAGCTTGCAAGAAATGTCTTATCCCGCAAAGAAGATGTATCTAATA ATGGGTAACTTTTGTAGCATTGTACTTTTGTTAGTTTTATCATTTATTATCTCAATATATTCTC ATTGTTGAAGCTATTTGAGCAATGTTGGCTTTTTTATTTTTCCAAATTTAAATTATTATTATTG TATCTCATGGTTGCAGGGATGGGAATGATGCTCTTTGGCAAGTAGACGTGGACCTGATGGATGT ACTTTTCACTAGCTTTGTGGAGTACCTTCAACTTGAAAATGCTTACAACATTTTTATTCTAAAT CTCAAGCGTGACACAAAAAGGGCCAGATATGGATACCG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.477871872

Conservation Information
Conserved circRNAs	NA
PMCS	0.477871872

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25794401-25794122(+)
						
						Potential amino acid sequence
						
							MSVVNYTKAGNVANYLKLLEVDSLYLPVPVNFIFIGFEGKGNHEFKLHPEELERWFIKLDHIFE
HTRIPQFREVLTPFYKMSMDKVLRHQLPLISHTNYNFSVHVIQTGEKVTSIFELARNVLSRKED
VSNNGDGNDALWQVDVDLMDVLFTSFVEYLQLENAYNIFILNLKRDTKRARYGYRY*
						
						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	25794401-25794122(+)
Potential amino acid sequence	MSVVNYTKAGNVANYLKLLEVDSLYLPVPVNFIFIGFEGKGNHEFKLHPEELERWFIKLDHIFE HTRIPQFREVLTPFYKMSMDKVLRHQLPLISHTNYNFSVHVIQTGEKVTSIFELARNVLSRKED VSNNGDGNDALWQVDVDLMDVLFTSFVEYLQLENAYNIFILNLKRDTKRARYGYRY*
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 Csa1G651660_circ_g.1

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