Plant Circular RNA Database

Detail information of Csa4G009870_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa4G009870_circ_g.1
					
						ID in PlantcircBase
						csa_circ_002292
					
						Alias
						Chr4:1460831_1462443
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr4: 1460831-1462443  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa4G009870						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa4G009870_circ_g.2 Csa4G009870_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  
						
							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
						Csa4G009870.1:3

General Information
CircRNA Name	Csa4G009870_circ_g.1
ID in PlantcircBase	csa_circ_002292
Alias	Chr4:1460831_1462443
Organism	Cucumis sativus
Position	chrChr4: 1460831-1462443 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa4G009870
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa4G009870_circ_g.2 Csa4G009870_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	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	Csa4G009870.1:3

			
						 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  
						
							GATAGAATTCCTGGAATTGACATAAGTTTAAAAGATGGAGACAAGTGGATGTTTGCTGGCCATG
AAGTGCATGTAATGGAAACACCCGGTCATACTCGAGgttaggagcgtatgtgtttggccgagtg
tgaaacagctttcttttagaaaagacctattatatggagttatgcgacttttatctactccatt
gaaaacgt

									
								

					

						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: 508
Transcript exons: 1460831-1461010,1461544-1461747,1462320-1462443
GTTAGGAGCGTATGTGTTTGGCCGAGTGTGAAACAGCTTTCTTTTAGAAAAGACCTATTATATG
GAGTTATGCGACTTTTATCTACTCCATTGAAAACGTTGCGTGGAGCTAGTCGTTCGCTTAAAGT
TGCTCAGTTTTGCAGTGTTGTCAACATGTCTTCCACTTTGCAAATTGAATTGGTACCTTGTCTT
CGTGACAACTATGCATACCTCTTACATGATGTTGATACCGGCACAGTTGGTGTTGTTGATCCAT
CTGAAGCTCTACCAGTTATAGATGCTTTAAGCAAGAAGAACAGAAATTTGACATATATACTTAA
TACTCATCATCATCATGATCACACTGGTGGGAACGAAGAATTAAAAGCAAGGTATGGAGCAAAG
GTAATTGGGTCTGGAATAGACAGCGATAGAATTCCTGGAATTGACATAAGTTTAAAAGATGGAG
ACAAGTGGATGTTTGCTGGCCATGAAGTGCATGTAATGGAAACACCCGGTCATACTCGAG
						
					

						Genomic sequence
						
							GTTAGGAGCGTATGTGTTTGGCCGAGTGTGAAACAGCTTTCTTTTAGAAAAGACCTATTATATG
GAGTTATGCGACTTTTATCTACTCCATTGAAAACGTTGCGTGGAGCTAGTCGTTCGCTTAAAGT
TGCTCAGTTTTGCAGTGTTGTCAACATGTCTTCCACTTTGCAAATTGAATTGGTAAGCTGTTAT
GAGATCTGGAAATTGGTTTTAGGGTGTCAATGACATCAGTTCTTTTTATCCATTATGGTCTTCC
TGTGGTGGTCAGTTTGTGATAACTTTCCTGGTTTATCATTTTCTTCTCTAAATTCATGCTTTGG
TTATAAAACATTTTCACCTGAGAGAATTTCTAATTGTGATATGAACTATGAAGAGGGCGTTCAA
GGTCCATATTGCAGTTTATTGTTTCTTTCCAAAGTTAGATTAGTTCAAACAAGGGTATATATTA
CTTACCACTTTAGCCTGCTCAGCTACACAACATATAGTTCTTCTTCCGACTTCCGAGTCAATTT
GAGTCAGGTGGCTACAAATTATATTCAGGGAGGCATTAGACGTGTTCATTTTGGGCTTCCACGC
TTAATTAATCATTTGTAAGGATGCCGGTTGTCCTCTATCATTCTAGGCTGTACATCCCTAATAA
CTGCTTAGCTTAGTCACTTCCAGCCTACACATTCATTAAAATCATTTCTTTTCCTCTACTCCCT
CTTTCATAGGTACCTTGTCTTCGTGACAACTATGCATACCTCTTACATGATGTTGATACCGGCA
CAGTTGGTGTTGTTGATCCATCTGAAGCTCTACCAGTTATAGATGCTTTAAGCAAGAAGAACAG
AAATTTGACATATATACTTAATACTCATCATCATCATGATCACACTGGTGGGAACGAAGAATTA
AAAGCAAGGTATGGAGCAAAGGTATGAATTTAATTCTTTTGCATTGCAATTGAATCAATATTCT
AGTTGGCCCTAGCTTTATCCTATAAATGTTGTATGTTTGATCCCTAAGGGTTGGTCATAGAGTG
ATAGAGGTAAGAACCTATGGACACATCCTAGAGGCCTGAGTCACCAGACTCCTTGAGGCATCAT
GTGCGAATTTTAGTTCTTGATGTCAAAAGAATTTTAGTTTATTAATAGTCTCTATTTCTCATCC
TTTTCTCTAGTAAACATAGTGAGGTGAATGCTTTATTATTGTAAAACACGGATATTTATTGTCA
TGAGAAATACATACCTTGTGATGTGCAAGAAATTTTATATACTTCATTACGGATTACCAAGTAT
TTTGAACATTTTGACTTGTTTTGAATTAAATACTTTCCTAAATTGTCCTTTAAATTAAGGCTTG
GATTGAAAATGAAATGAATCAAGGCATTGATGCTGGCATATGTTATTTAGTAGTCTCTGAAATA
ATTTTATCCTTGAGTTAGTGGTTTACATTTCTATTTTATAGAATTTCTGTCAAATTTTTATCCC
CTTTCTGCTGGTTGTAGGTAATTGGGTCTGGAATAGACAGCGATAGAATTCCTGGAATTGACAT
AAGTTTAAAAGATGGAGACAAGTGGATGTTTGCTGGCCATGAAGTGCATGTAATGGAAACACCC
GGTCATACTCGAG
						
					

			
		

Sequences
Splice junction sequence	GATAGAATTCCTGGAATTGACATAAGTTTAAAAGATGGAGACAAGTGGATGTTTGCTGGCCATG AAGTGCATGTAATGGAAACACCCGGTCATACTCGAGgttaggagcgtatgtgtttggccgagtg tgaaacagctttcttttagaaaagacctattatatggagttatgcgacttttatctactccatt gaaaacgt
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: 508 Transcript exons: 1460831-1461010,1461544-1461747,1462320-1462443 GTTAGGAGCGTATGTGTTTGGCCGAGTGTGAAACAGCTTTCTTTTAGAAAAGACCTATTATATG GAGTTATGCGACTTTTATCTACTCCATTGAAAACGTTGCGTGGAGCTAGTCGTTCGCTTAAAGT TGCTCAGTTTTGCAGTGTTGTCAACATGTCTTCCACTTTGCAAATTGAATTGGTACCTTGTCTT CGTGACAACTATGCATACCTCTTACATGATGTTGATACCGGCACAGTTGGTGTTGTTGATCCAT CTGAAGCTCTACCAGTTATAGATGCTTTAAGCAAGAAGAACAGAAATTTGACATATATACTTAA TACTCATCATCATCATGATCACACTGGTGGGAACGAAGAATTAAAAGCAAGGTATGGAGCAAAG GTAATTGGGTCTGGAATAGACAGCGATAGAATTCCTGGAATTGACATAAGTTTAAAAGATGGAG ACAAGTGGATGTTTGCTGGCCATGAAGTGCATGTAATGGAAACACCCGGTCATACTCGAG
Genomic sequence	GTTAGGAGCGTATGTGTTTGGCCGAGTGTGAAACAGCTTTCTTTTAGAAAAGACCTATTATATG GAGTTATGCGACTTTTATCTACTCCATTGAAAACGTTGCGTGGAGCTAGTCGTTCGCTTAAAGT TGCTCAGTTTTGCAGTGTTGTCAACATGTCTTCCACTTTGCAAATTGAATTGGTAAGCTGTTAT GAGATCTGGAAATTGGTTTTAGGGTGTCAATGACATCAGTTCTTTTTATCCATTATGGTCTTCC TGTGGTGGTCAGTTTGTGATAACTTTCCTGGTTTATCATTTTCTTCTCTAAATTCATGCTTTGG TTATAAAACATTTTCACCTGAGAGAATTTCTAATTGTGATATGAACTATGAAGAGGGCGTTCAA GGTCCATATTGCAGTTTATTGTTTCTTTCCAAAGTTAGATTAGTTCAAACAAGGGTATATATTA CTTACCACTTTAGCCTGCTCAGCTACACAACATATAGTTCTTCTTCCGACTTCCGAGTCAATTT GAGTCAGGTGGCTACAAATTATATTCAGGGAGGCATTAGACGTGTTCATTTTGGGCTTCCACGC TTAATTAATCATTTGTAAGGATGCCGGTTGTCCTCTATCATTCTAGGCTGTACATCCCTAATAA CTGCTTAGCTTAGTCACTTCCAGCCTACACATTCATTAAAATCATTTCTTTTCCTCTACTCCCT CTTTCATAGGTACCTTGTCTTCGTGACAACTATGCATACCTCTTACATGATGTTGATACCGGCA CAGTTGGTGTTGTTGATCCATCTGAAGCTCTACCAGTTATAGATGCTTTAAGCAAGAAGAACAG AAATTTGACATATATACTTAATACTCATCATCATCATGATCACACTGGTGGGAACGAAGAATTA AAAGCAAGGTATGGAGCAAAGGTATGAATTTAATTCTTTTGCATTGCAATTGAATCAATATTCT AGTTGGCCCTAGCTTTATCCTATAAATGTTGTATGTTTGATCCCTAAGGGTTGGTCATAGAGTG ATAGAGGTAAGAACCTATGGACACATCCTAGAGGCCTGAGTCACCAGACTCCTTGAGGCATCAT GTGCGAATTTTAGTTCTTGATGTCAAAAGAATTTTAGTTTATTAATAGTCTCTATTTCTCATCC TTTTCTCTAGTAAACATAGTGAGGTGAATGCTTTATTATTGTAAAACACGGATATTTATTGTCA TGAGAAATACATACCTTGTGATGTGCAAGAAATTTTATATACTTCATTACGGATTACCAAGTAT TTTGAACATTTTGACTTGTTTTGAATTAAATACTTTCCTAAATTGTCCTTTAAATTAAGGCTTG GATTGAAAATGAAATGAATCAAGGCATTGATGCTGGCATATGTTATTTAGTAGTCTCTGAAATA ATTTTATCCTTGAGTTAGTGGTTTACATTTCTATTTTATAGAATTTCTGTCAAATTTTTATCCC CTTTCTGCTGGTTGTAGGTAATTGGGTCTGGAATAGACAGCGATAGAATTCCTGGAATTGACAT AAGTTTAAAAGATGGAGACAAGTGGATGTTTGCTGGCCATGAAGTGCATGTAATGGAAACACCC GGTCATACTCGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.50259425

Conservation Information
Conserved circRNAs	NA
PMCS	0.50259425

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1460901-1460832(+)
						
						Potential amino acid sequence
						
							MRLLSTPLKTLRGASRSLKVAQFCSVVNMSSTLQIELVPCLRDNYAYLLHDVDTGTVGVVDPSE
ALPVIDALSKKNRNLTYILNTHHHHDHTGGNEELKARYGAKVIGSGIDSDRIPGIDISLKDGDK
WMFAGHEVHVMETPGHTRG*
						
						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	1460901-1460832(+)
Potential amino acid sequence	MRLLSTPLKTLRGASRSLKVAQFCSVVNMSSTLQIELVPCLRDNYAYLLHDVDTGTVGVVDPSE ALPVIDALSKKNRNLTYILNTHHHHDHTGGNEELKARYGAKVIGSGIDSDRIPGIDISLKDGDK WMFAGHEVHVMETPGHTRG*
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 Csa4G009870_circ_g.1

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