Plant Circular RNA Database

Detail information of Csa3G116870_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa3G116870_circ_g.2
					
						ID in PlantcircBase
						csa_circ_001452
					
						Alias
						Chr3:6340696_6347405
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 6340696-6347405  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Csa3G116870						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa3G116870_circ_g.1 Csa3G116870_circ_g.3 						
					
						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  
						
							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
						Csa3G116870.1:7

General Information
CircRNA Name	Csa3G116870_circ_g.2
ID in PlantcircBase	csa_circ_001452
Alias	Chr3:6340696_6347405
Organism	Cucumis sativus
Position	chrChr3: 6340696-6347405 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	Find_circ
Parent gene	Csa3G116870
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa3G116870_circ_g.1 Csa3G116870_circ_g.3
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	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	Csa3G116870.1:7

			
						 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  
						
							CCTTAACAAAGCCATCTACAAATATACTTGTTTGGTGAATCATAGTTCCATCCTTCTCAAATAA
GAAGAGTTGTCCTGTTACTGTGAGAATGACAAGAACctgtttaagttgaaaagctctggaattc
gagaaatgaccactgcccgaaattcagtttgttcagaattgccaagctccagtaatgttctgtt
gataaagg

									
								

					

						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: 1877
Transcript exons: 6340696-6340886,6341419-6342104,6342297-6342352,6343929-
6344071,6345526-6345627,6345706-6345770,6346772-6347405
CTGTTTAAGTTGAAAAGCTCTGGAATTCGAGAAATGACCACTGCCCGAAATTCAGTTTGTTCAG
AATTGCCAAGCTCCAGTAATGTTCTGTTGATAAAGGTGAAGGTGTGAATGGGTTCGTCTACATC
TTTCATATAGCTATCCAAAGCTGATGAATACTGATGTGTGATGCTATGAATCAGGCCACAAACC
TGGAAAAATTGTGCTTTCTCACACATCCTTAACACAGAAGACGGATTCCAATGGGTCTCTGGTA
TCACCTCCAGTAGGGAAAGTACTTGCTTTTCCCTTTTTCTTGAAAGTACACTATTTGCAGTAAC
ACGAGGCAGAAAATCAGACACTGTTTCTGGAATATCGCTATTGGATATCAGGTGTTCCAAAATC
TGACCAACCACATCTTTAGAGACTGTAGCCTTTCCACAAGCAACATAAGTGGCAATAAAGTCGA
ACAAATGAATTAGTTCTTTCTTTGAAGGCCAATCGTCAACCAATGTAATATTATCACCAGCTGG
GGACTCATCTGTTTCACAGATAGCCTTATCGAGAACATGAACAAGAGCATCCACTACATTTTGA
ATTAGAAAGTTCTTTCTTCCAGAAATTGAGTTCTTTTCTTCTTGTAGCTGCATACTTGTATCAA
CTGGGCCATCTAGAGAAGAAATGGCTTTGAGGATTTCACCTTCAACAAAAGCACATCTCAAAAC
ATCTAAAGTGGCTTCAGTATCCAACTCTAAGAGAGGATACAGATTTAAACATCCAACTTCAGAT
GATTTATTTGAAATCGATCTTGTATCCACTGCATCAGAATTCTCCAACAAAAACTGTAGTAGTT
CATCTCTAAGAGATTGCACGCGTGAATGAGCAAGAGTTCCTTGGCCTGGTGGAAAAGCAAGTCC
TGAAAAGCAATACTTCAAATAAACTAGTGTCTTGTACCCAAGGGAAGAAGCATGTTTGCTCTTA
CTGGTTCGCAGCACTGCTAACAGCTCCTCTAAAGGCGTCCTGAAATCATCTAATCCTTTGTTGA
AAAGATATACCAATGCACTATACAATCCATGATCCCGGCATAACCTGACAACCTGATTAAAATC
TAAGGAAGAAATATCCATGTGAAGAACACACTGTTCTACACGCTGCAACCATCCTTTGTGGCTA
TAATGCTCTACCAAAGCTTGCATAATCTCCGGAGGCAGCGATCCAAGCATGTCCTTTAAAATAT
ATGGTTCTAGAAGCTCCAAAAATGTATCTCTCTGTTGAACCCCCACAAATTTGGAGAAAATTTC
ATCAAAGAGAATATCAGTCCTCGAGATGTGGACACAAAACTCAACTGCAACTCCACCAACACGA
TTGTATTGCTCTTTTATTTCAGAATGTGCAGAATGGCTTTCAATCGTCATATCATCCAGTTTTT
CATTCTTTTCAATTTGGTTACAGAAAGCCACTGATATATATGAAAACACCTCATCCACGTATGA
TAACAGCAACTCAATCAGAAAGGGCATTACCAACTCCTGCAAAGATTCCAACGACCTGGGGAGA
TCGATAACACCATGAGCATGGCCGTCATAAATGGTTATTGCCATGCTAAGAGCACTCATCCAGT
CCCCTGCTTTCCGTAGAACCTGAACCCGCTCCTTCCATGGAAGGAGACGGGAAATAACAAGATG
CATAGGTCCCAATACATATATAGAAGCTCCTCTAACAGCCACGCAATTGTGATATGCCTTCTCA
GGGTTGCCCAAAATGTTAGCAAAGTGGGTGTGATATGCAATGAAATCTTCCTTAACAAAGCCAT
CTACAAATATACTTGTTTGGTGAATCATAGTTCCATCCTTCTCAAATAAGAAGAGTTGTCCTGT
TACTGTGAGAATGACAAGAAC
						
					

						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	CCTTAACAAAGCCATCTACAAATATACTTGTTTGGTGAATCATAGTTCCATCCTTCTCAAATAA GAAGAGTTGTCCTGTTACTGTGAGAATGACAAGAACctgtttaagttgaaaagctctggaattc gagaaatgaccactgcccgaaattcagtttgttcagaattgccaagctccagtaatgttctgtt gataaagg
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: 1877 Transcript exons: 6340696-6340886,6341419-6342104,6342297-6342352,6343929- 6344071,6345526-6345627,6345706-6345770,6346772-6347405 CTGTTTAAGTTGAAAAGCTCTGGAATTCGAGAAATGACCACTGCCCGAAATTCAGTTTGTTCAG AATTGCCAAGCTCCAGTAATGTTCTGTTGATAAAGGTGAAGGTGTGAATGGGTTCGTCTACATC TTTCATATAGCTATCCAAAGCTGATGAATACTGATGTGTGATGCTATGAATCAGGCCACAAACC TGGAAAAATTGTGCTTTCTCACACATCCTTAACACAGAAGACGGATTCCAATGGGTCTCTGGTA TCACCTCCAGTAGGGAAAGTACTTGCTTTTCCCTTTTTCTTGAAAGTACACTATTTGCAGTAAC ACGAGGCAGAAAATCAGACACTGTTTCTGGAATATCGCTATTGGATATCAGGTGTTCCAAAATC TGACCAACCACATCTTTAGAGACTGTAGCCTTTCCACAAGCAACATAAGTGGCAATAAAGTCGA ACAAATGAATTAGTTCTTTCTTTGAAGGCCAATCGTCAACCAATGTAATATTATCACCAGCTGG GGACTCATCTGTTTCACAGATAGCCTTATCGAGAACATGAACAAGAGCATCCACTACATTTTGA ATTAGAAAGTTCTTTCTTCCAGAAATTGAGTTCTTTTCTTCTTGTAGCTGCATACTTGTATCAA CTGGGCCATCTAGAGAAGAAATGGCTTTGAGGATTTCACCTTCAACAAAAGCACATCTCAAAAC ATCTAAAGTGGCTTCAGTATCCAACTCTAAGAGAGGATACAGATTTAAACATCCAACTTCAGAT GATTTATTTGAAATCGATCTTGTATCCACTGCATCAGAATTCTCCAACAAAAACTGTAGTAGTT CATCTCTAAGAGATTGCACGCGTGAATGAGCAAGAGTTCCTTGGCCTGGTGGAAAAGCAAGTCC TGAAAAGCAATACTTCAAATAAACTAGTGTCTTGTACCCAAGGGAAGAAGCATGTTTGCTCTTA CTGGTTCGCAGCACTGCTAACAGCTCCTCTAAAGGCGTCCTGAAATCATCTAATCCTTTGTTGA AAAGATATACCAATGCACTATACAATCCATGATCCCGGCATAACCTGACAACCTGATTAAAATC TAAGGAAGAAATATCCATGTGAAGAACACACTGTTCTACACGCTGCAACCATCCTTTGTGGCTA TAATGCTCTACCAAAGCTTGCATAATCTCCGGAGGCAGCGATCCAAGCATGTCCTTTAAAATAT ATGGTTCTAGAAGCTCCAAAAATGTATCTCTCTGTTGAACCCCCACAAATTTGGAGAAAATTTC ATCAAAGAGAATATCAGTCCTCGAGATGTGGACACAAAACTCAACTGCAACTCCACCAACACGA TTGTATTGCTCTTTTATTTCAGAATGTGCAGAATGGCTTTCAATCGTCATATCATCCAGTTTTT CATTCTTTTCAATTTGGTTACAGAAAGCCACTGATATATATGAAAACACCTCATCCACGTATGA TAACAGCAACTCAATCAGAAAGGGCATTACCAACTCCTGCAAAGATTCCAACGACCTGGGGAGA TCGATAACACCATGAGCATGGCCGTCATAAATGGTTATTGCCATGCTAAGAGCACTCATCCAGT CCCCTGCTTTCCGTAGAACCTGAACCCGCTCCTTCCATGGAAGGAGACGGGAAATAACAAGATG CATAGGTCCCAATACATATATAGAAGCTCCTCTAACAGCCACGCAATTGTGATATGCCTTCTCA GGGTTGCCCAAAATGTTAGCAAAGTGGGTGTGATATGCAATGAAATCTTCCTTAACAAAGCCAT CTACAAATATACTTGTTTGGTGAATCATAGTTCCATCCTTCTCAAATAAGAAGAGTTGTCCTGT TACTGTGAGAATGACAAGAAC
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
						0.97550601

Conservation Information
Conserved circRNAs	NA
PMCS	0.97550601

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6347350-6347386(-)
						
						Potential amino acid sequence
						
							MIHQTSIFVDGFVKEDFIAYHTHFANILGNPEKAYHNCVAVRGASIYVLGPMHLVISRLLPWKE
RVQVLRKAGDWMSALSMAITIYDGHAHGVIDLPRSLESLQELVMPFLIELLLSYVDEVFSYISV
AFCNQIEKNEKLDDMTIESHSAHSEIKEQYNRVGGVAVEFCVHISRTDILFDEIFSKFVGVQQR
DTFLELLEPYILKDMLGSLPPEIMQALVEHYSHKGWLQRVEQCVLHMDISSLDFNQVVRLCRDH
GLYSALVYLFNKGLDDFRTPLEELLAVLRTSKSKHASSLGYKTLVYLKYCFSGLAFPPGQGTLA
HSRVQSLRDELLQFLLENSDAVDTRSISNKSSEVGCLNLYPLLELDTEATLDVLRCAFVEGEIL
KAISSLDGPVDTSMQLQEEKNSISGRKNFLIQNVVDALVHVLDKAICETDESPAGDNITLVDDW
PSKKELIHLFDFIATYVACGKATVSKDVVGQILEHLISNSDIPETVSDFLPRVTANSVLSRKRE
KQVLSLLEVIPETHWNPSSVLRMCEKAQFFQVCGLIHSITHQYSSALDSYMKDVDEPIHTFTFI
NRTLLELGNSEQTEFRAVVISRIPELFNLNRFLSFSQ*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6347350-6347386(-)
Potential amino acid sequence	MIHQTSIFVDGFVKEDFIAYHTHFANILGNPEKAYHNCVAVRGASIYVLGPMHLVISRLLPWKE RVQVLRKAGDWMSALSMAITIYDGHAHGVIDLPRSLESLQELVMPFLIELLLSYVDEVFSYISV AFCNQIEKNEKLDDMTIESHSAHSEIKEQYNRVGGVAVEFCVHISRTDILFDEIFSKFVGVQQR DTFLELLEPYILKDMLGSLPPEIMQALVEHYSHKGWLQRVEQCVLHMDISSLDFNQVVRLCRDH GLYSALVYLFNKGLDDFRTPLEELLAVLRTSKSKHASSLGYKTLVYLKYCFSGLAFPPGQGTLA HSRVQSLRDELLQFLLENSDAVDTRSISNKSSEVGCLNLYPLLELDTEATLDVLRCAFVEGEIL KAISSLDGPVDTSMQLQEEKNSISGRKNFLIQNVVDALVHVLDKAICETDESPAGDNITLVDDW PSKKELIHLFDFIATYVACGKATVSKDVVGQILEHLISNSDIPETVSDFLPRVTANSVLSRKRE KQVLSLLEVIPETHWNPSSVLRMCEKAQFFQVCGLIHSITHQYSSALDSYMKDVDEPIHTFTFI NRTLLELGNSEQTEFRAVVISRIPELFNLNRFLSFSQ*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						He et al., 2020

circRNA

Detail information of Csa3G116870_circ_g.2

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