Plant Circular RNA Database

Detail information of Chr3_circ_ig.13

			
						 General Information
					
						CircRNA Name
						Chr3_circ_ig.13
					
						ID in PlantcircBase
						csa_circ_001427
					
						Alias
						Chr3:5494709_5498674
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 5494709-5498674  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Chr3_circ_ig.12 Csa3G110620_circ_g.2 Chr3_circ_ig.14 Chr3_circ_ig.15 Chr3_circ_ig.16 Chr3_circ_ig.17 						
					
						Support reads
						NA
					
						Tissues
						leaf
					
						Exon boundary  
						
							NA-NA							"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
						NA

General Information
CircRNA Name	Chr3_circ_ig.13
ID in PlantcircBase	csa_circ_001427
Alias	Chr3:5494709_5498674
Organism	Cucumis sativus
Position	chrChr3: 5494709-5498674 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	ag-circRNA
Identification method	Find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Chr3_circ_ig.12 Csa3G110620_circ_g.2 Chr3_circ_ig.14 Chr3_circ_ig.15 Chr3_circ_ig.16 Chr3_circ_ig.17
Support reads	NA
Tissues	leaf
Exon boundary	NA-NA "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	NA

			
						 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  
						
							ACTTTGTTCAAAGTCACAAATGAAACAGTATTCTCGTCGTTGTATTTGTAGTCACAGAACCAAA
GGGAGTAACCTTCTGGGTCATACATGTCCCAGAATCctttgattgcaacctcacggaagttaga
cttggtgttcgagtagagacatttccactcatccaaaatcatcgaactaggaggaagcaagtca
agaggatt

									
								

					

						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
						
							CTTTGATTGCAACCTCACGGAAGTTAGACTTGGTGTTCGAGTAGAGACATTTCCACTCATCCAA
AATCATCGAACTAGGAGGAAGCAAGTCAAGAGGATTTTTGGCCTTGGGCTTTGGTGCCTCCTCC
TCAGCAGGTGCTGCAGGCTTCTCTTCTTGTTTCTTGGGCTCAGCCTTCGCTTTGGCAGCTGCTG
CAGCCTCTTCAGGTGTTTTCACTGGTGGGACGGCGTCTGTCTGCTTTACCTCACCCATTATCTT
TTTGAAATTTGGTTGATTGACCAATGTCCAGAAGTACCTCTCAACGTGGGGAAACTCAGAAGTA
AAGCTTTTAGTCAATATATAGTTGAATCCCAAATAGAGATTGCATGTCAGAATGATATCAGCTA
GTGTCACGGAGTGTCCAACGAGGAATGTGTTTGAAGCAAGGTAGGAGTTCAAAGCACCGAAAGA
TCGTTTTAGAGCAGCATCAGCGGTTTCCTCTACCTTCATGAAGAGAATAATACCAAAGAAATAA
TTCATTCATAGGTATCAAAGGAATACTTACATGGTTTGAAAAGTGAATGAAAATGGATATATAT
ATATATAATAAAAGAAATAAAGTGAAAAGAAAGAAAAACTTCTTTGCAATCCAACTCACTTCTT
TTATTAATGCCCACAGATAAAGAATACAAAAGAAGAAAATAAACCTCAACCATTAACATCCACT
TTCAACCACAACTCAAAACAGAAATAAGAAAAAAGAAATCCAACTTACACCCGGATGGAAAGCA
GCATATCCAAATCTAGGCCTCAACTTAGTTGACACAGGAATATCAATTTCAAACGTGGAAAAAT
CAATCCATTGTTCAACATGTCCCTGAAAAGAATAGAAACGAAAGAATTGATTAGCAAACAGTTC
CTTTCTAATTGAAGAAAAGGGAAGAATCATAATCAAAACCAATTAAGAAAACGGATCTTTACAC
AATCAATGGAAGAAGAGCCAAATAAACCACTGTCCTTCAAGCGAGCAACTGAACCATTTAGAGA
GAAAAAAACATTAGCATAAAATAAAAACAAAAGGAAGAAGATTTCCATTTTAACTCATCTCCCC
AGTTATCAAGACTCTCCTAAGGAGAAACATGAAATAGTAATTACCATAGCGAGCTATAGCATTG
CTCTCAAAGATAGCACCATCTGGTGTTTCCAGAACAGGAACCTACAATATCAAACATTATTTTA
GAATATTCAAGCGCATATCAGTTGTAAACACTATCTCTCACACAGTCAGATTAACAGGCATCAC
CCGTAATATATGTTTACCTTCCCAATAGGATTCATTTTCAGATATTCAGGACTCTTGTTGGTCA
CGCCCATGGTAAAATCTTGGGAAAGATCAACCTTGACACCATTGTACTCCGCAGCTATTAAAGC
CTTGTAAGCATTTTTGTTAGTCTTCCAAGAATGCAAGACCTGCAAAATCAATACACATATACAT
CAAAGAACAAAATTACATTAGACCAGAAATCATCCATTTCTCCTATGCAACTTAACAAACGAGT
AATCAGACATTAAATTTATGTCCGTGCAATCGGAACATAAATCAATAGGCTATAGCATGCAAGA
AGCAATAAATGGCATGGATAACTAAGTTGAACATAATTCTAAAAAACTCCATCCATCACAGTAC
AAAAAAGAAGCAAGGATAAACACCAATCGTCAATAATGTAAATCAAATCAACTAATTCTTCAAT
CCTCCTACGCAATTCAACGTCAAAAACTTAAGAATTGCAAAAAGTAGAGAAATTAAGGAAATGC
GGCGGACATAAAAGAGTAATACTTTCGAAGATCGATTACTAAATTCCTCCAAAACTACTCAAAC
ACACTGTAAAAACATGGGATCCGGAATAAGTAGACGAAAATAAATCCAGTGGTTCAGAAATAAA
ATCGGCAGAAAAGAAAAAGAGCATAAAAAGATGGAGAGCGGAAGTAATGAGAGAGACTCACGAG
AGCCATCGGTTCGCGGAAGAAACGTTTCGCTCAAAAATCAGATCTGAATAAATAGGAAAGAAAA
CACAAGAGTTAGGAAGTGGAATAAGAGAATTAGTGATGATAAGGAAGAGATTGAAGGTGGAGAG
AATGATAGAGATGAAAGAAAGGGGAATAAGAAGAGGATGAAGATGAGAAAAAGGTAGAAGGAGA
GAGACCTGTGAGAGGGCGAGCGTTGTTCCGAGAGCAGGAAATGTGTTGGGAAGAGAGAGAGAAT
ATAAGGAGTGAGGGAATTAGGGTTTTGTAAAGGGTTTTTTTATATTATTATTATTTATTATTTA
TTTGTTTTATTTAATGCATGGCCCAAATTGAGAAGAAATATGAGTTTTGACCCAAATCTTTGAA
AATTAGGTTTTTTTTTTTTAATTTTAATTTTAACATTTATTGAAGTGCAAAATTGGGCACCAAA
AACCACTGTGTTCTCGTACACATGCACAATGGGTTTTACCTCTCTCTCTCTCTTTCTCTCTCTC
TCCCCCTCCCCTTTTATCACTCTATCAAACTACTTTTTGCTTTGCTTTCCAGCGTCTCATAAGA
TTTTGGGCAAACCAAGAAGAAGAAGAAAATCATCGCTATAGACCACAAACAAGAAGGGAAAAGA
AAAGAATAGAAAATCTCCAACTTCACTCATCCATGCCAAACTCAATTACCAATACTTTTTAAGA
AAATGAAGCATTTTTCATTTTAAGAAAGGTTCTTCTAGATTGATTGGATTTCATCTCATGTTTG
ATATAGACACAACTAAATTTTAAGATTACTCATTACTAACATATATTTGTGCTTTTACTCTTAC
TTAATTCATTGAAACGTGAATGACGAGGGAATAACTTATGGAAAAATAATATATTTCAAATTTT
CATTTTTTTTATAACAAAACTCCTTAAAATAAAATTTTTTAAAAAAAAACTAGCTTTCAAAACT
GTTTTCTTTAAGGTAAAAGCTCATTGAAATTGATATTTACTAAGAGTCCTTATTATTCTCAAAT
TACTATTGAAAGAAGTTGGTCGACAAATAATTGAAAGATGGTGAAAACATCACCATAAAAATCA
AAGAAAAGGAAATCAATGATGGCTCTTACACGCTTGAATGAATACAAAGAACTTAAATTTAACT
ATGTTATTTTTAGTTTTTCATGCAAGTTAACATTTAAAAACTCAAGGAATTATTTAGAGTTAAT
TAAGTATTTAGCTTAAATAAACTTATTTTATAAAATGATTTTTATTTAATAATTACATAAAAGT
GAACATGTACAAGTTGCTATACATTTTAAAATGGGAAAAGGTCAATCCATACTAATATGTTGCT
AATTATAAAGGGTGACAATCAGACCTATTTGAAAGGCTTTCCAAATATAAATATGATTTGATTA
CGATGGAGAATCGAGGCTGTTTACTTATCTGCTGGTATCTTTGTCCCCATAATGTTATCTTCGT
TATATCAATCGATAATGGTATTCGTAACAAAAATCTATTTGAAATGAAGGCAGAAAACAAAATC
TGACTAAAAAAAAGTCCACAGAAACATTTCTCTCAAAGTTAACTCTCTAATGTCCCCCAATAAT
AATTAAAAGTTTTGCGCTATTTCTCACTTAAAGCATTTGGCGTCCAAAAGAGCTTCACCCTCAA
ATGGTTCCTGATCTTCAATCATTTGGCTCACCCTCTCCTTCTGGGCTTCATCCGAGATATCCAC
CTTCTTCCACTCGTACAGCTCCATATCATAGCACTCATCAAGCACAAATTGTGGGATTTCTTTT
CCACGGAAAAGCCATAGTCCTGATAAGATCACAAGCATATTTCCAAGTGCGTACTTCCTAGCAA
TATCCATTCTCTGGAGGAATCCACCAACTTTGTTCAAAGTCACAAATGAAACAGTATTCTCGTC
GTTGTATTTGTAGTCACAGAACCAAAGGGAGTAACCTTCTGGGTCATACATGTCCCAGAATC
						
					

			
		

Sequences
Splice junction sequence	ACTTTGTTCAAAGTCACAAATGAAACAGTATTCTCGTCGTTGTATTTGTAGTCACAGAACCAAA GGGAGTAACCTTCTGGGTCATACATGTCCCAGAATCctttgattgcaacctcacggaagttaga cttggtgttcgagtagagacatttccactcatccaaaatcatcgaactaggaggaagcaagtca agaggatt
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	CTTTGATTGCAACCTCACGGAAGTTAGACTTGGTGTTCGAGTAGAGACATTTCCACTCATCCAA AATCATCGAACTAGGAGGAAGCAAGTCAAGAGGATTTTTGGCCTTGGGCTTTGGTGCCTCCTCC TCAGCAGGTGCTGCAGGCTTCTCTTCTTGTTTCTTGGGCTCAGCCTTCGCTTTGGCAGCTGCTG CAGCCTCTTCAGGTGTTTTCACTGGTGGGACGGCGTCTGTCTGCTTTACCTCACCCATTATCTT TTTGAAATTTGGTTGATTGACCAATGTCCAGAAGTACCTCTCAACGTGGGGAAACTCAGAAGTA AAGCTTTTAGTCAATATATAGTTGAATCCCAAATAGAGATTGCATGTCAGAATGATATCAGCTA GTGTCACGGAGTGTCCAACGAGGAATGTGTTTGAAGCAAGGTAGGAGTTCAAAGCACCGAAAGA TCGTTTTAGAGCAGCATCAGCGGTTTCCTCTACCTTCATGAAGAGAATAATACCAAAGAAATAA TTCATTCATAGGTATCAAAGGAATACTTACATGGTTTGAAAAGTGAATGAAAATGGATATATAT ATATATAATAAAAGAAATAAAGTGAAAAGAAAGAAAAACTTCTTTGCAATCCAACTCACTTCTT TTATTAATGCCCACAGATAAAGAATACAAAAGAAGAAAATAAACCTCAACCATTAACATCCACT TTCAACCACAACTCAAAACAGAAATAAGAAAAAAGAAATCCAACTTACACCCGGATGGAAAGCA GCATATCCAAATCTAGGCCTCAACTTAGTTGACACAGGAATATCAATTTCAAACGTGGAAAAAT CAATCCATTGTTCAACATGTCCCTGAAAAGAATAGAAACGAAAGAATTGATTAGCAAACAGTTC CTTTCTAATTGAAGAAAAGGGAAGAATCATAATCAAAACCAATTAAGAAAACGGATCTTTACAC AATCAATGGAAGAAGAGCCAAATAAACCACTGTCCTTCAAGCGAGCAACTGAACCATTTAGAGA GAAAAAAACATTAGCATAAAATAAAAACAAAAGGAAGAAGATTTCCATTTTAACTCATCTCCCC AGTTATCAAGACTCTCCTAAGGAGAAACATGAAATAGTAATTACCATAGCGAGCTATAGCATTG CTCTCAAAGATAGCACCATCTGGTGTTTCCAGAACAGGAACCTACAATATCAAACATTATTTTA GAATATTCAAGCGCATATCAGTTGTAAACACTATCTCTCACACAGTCAGATTAACAGGCATCAC CCGTAATATATGTTTACCTTCCCAATAGGATTCATTTTCAGATATTCAGGACTCTTGTTGGTCA CGCCCATGGTAAAATCTTGGGAAAGATCAACCTTGACACCATTGTACTCCGCAGCTATTAAAGC CTTGTAAGCATTTTTGTTAGTCTTCCAAGAATGCAAGACCTGCAAAATCAATACACATATACAT CAAAGAACAAAATTACATTAGACCAGAAATCATCCATTTCTCCTATGCAACTTAACAAACGAGT AATCAGACATTAAATTTATGTCCGTGCAATCGGAACATAAATCAATAGGCTATAGCATGCAAGA AGCAATAAATGGCATGGATAACTAAGTTGAACATAATTCTAAAAAACTCCATCCATCACAGTAC AAAAAAGAAGCAAGGATAAACACCAATCGTCAATAATGTAAATCAAATCAACTAATTCTTCAAT CCTCCTACGCAATTCAACGTCAAAAACTTAAGAATTGCAAAAAGTAGAGAAATTAAGGAAATGC GGCGGACATAAAAGAGTAATACTTTCGAAGATCGATTACTAAATTCCTCCAAAACTACTCAAAC ACACTGTAAAAACATGGGATCCGGAATAAGTAGACGAAAATAAATCCAGTGGTTCAGAAATAAA ATCGGCAGAAAAGAAAAAGAGCATAAAAAGATGGAGAGCGGAAGTAATGAGAGAGACTCACGAG AGCCATCGGTTCGCGGAAGAAACGTTTCGCTCAAAAATCAGATCTGAATAAATAGGAAAGAAAA CACAAGAGTTAGGAAGTGGAATAAGAGAATTAGTGATGATAAGGAAGAGATTGAAGGTGGAGAG AATGATAGAGATGAAAGAAAGGGGAATAAGAAGAGGATGAAGATGAGAAAAAGGTAGAAGGAGA GAGACCTGTGAGAGGGCGAGCGTTGTTCCGAGAGCAGGAAATGTGTTGGGAAGAGAGAGAGAAT ATAAGGAGTGAGGGAATTAGGGTTTTGTAAAGGGTTTTTTTATATTATTATTATTTATTATTTA TTTGTTTTATTTAATGCATGGCCCAAATTGAGAAGAAATATGAGTTTTGACCCAAATCTTTGAA AATTAGGTTTTTTTTTTTTAATTTTAATTTTAACATTTATTGAAGTGCAAAATTGGGCACCAAA AACCACTGTGTTCTCGTACACATGCACAATGGGTTTTACCTCTCTCTCTCTCTTTCTCTCTCTC TCCCCCTCCCCTTTTATCACTCTATCAAACTACTTTTTGCTTTGCTTTCCAGCGTCTCATAAGA TTTTGGGCAAACCAAGAAGAAGAAGAAAATCATCGCTATAGACCACAAACAAGAAGGGAAAAGA AAAGAATAGAAAATCTCCAACTTCACTCATCCATGCCAAACTCAATTACCAATACTTTTTAAGA AAATGAAGCATTTTTCATTTTAAGAAAGGTTCTTCTAGATTGATTGGATTTCATCTCATGTTTG ATATAGACACAACTAAATTTTAAGATTACTCATTACTAACATATATTTGTGCTTTTACTCTTAC TTAATTCATTGAAACGTGAATGACGAGGGAATAACTTATGGAAAAATAATATATTTCAAATTTT CATTTTTTTTATAACAAAACTCCTTAAAATAAAATTTTTTAAAAAAAAACTAGCTTTCAAAACT GTTTTCTTTAAGGTAAAAGCTCATTGAAATTGATATTTACTAAGAGTCCTTATTATTCTCAAAT TACTATTGAAAGAAGTTGGTCGACAAATAATTGAAAGATGGTGAAAACATCACCATAAAAATCA AAGAAAAGGAAATCAATGATGGCTCTTACACGCTTGAATGAATACAAAGAACTTAAATTTAACT ATGTTATTTTTAGTTTTTCATGCAAGTTAACATTTAAAAACTCAAGGAATTATTTAGAGTTAAT TAAGTATTTAGCTTAAATAAACTTATTTTATAAAATGATTTTTATTTAATAATTACATAAAAGT GAACATGTACAAGTTGCTATACATTTTAAAATGGGAAAAGGTCAATCCATACTAATATGTTGCT AATTATAAAGGGTGACAATCAGACCTATTTGAAAGGCTTTCCAAATATAAATATGATTTGATTA CGATGGAGAATCGAGGCTGTTTACTTATCTGCTGGTATCTTTGTCCCCATAATGTTATCTTCGT TATATCAATCGATAATGGTATTCGTAACAAAAATCTATTTGAAATGAAGGCAGAAAACAAAATC TGACTAAAAAAAAGTCCACAGAAACATTTCTCTCAAAGTTAACTCTCTAATGTCCCCCAATAAT AATTAAAAGTTTTGCGCTATTTCTCACTTAAAGCATTTGGCGTCCAAAAGAGCTTCACCCTCAA ATGGTTCCTGATCTTCAATCATTTGGCTCACCCTCTCCTTCTGGGCTTCATCCGAGATATCCAC CTTCTTCCACTCGTACAGCTCCATATCATAGCACTCATCAAGCACAAATTGTGGGATTTCTTTT CCACGGAAAAGCCATAGTCCTGATAAGATCACAAGCATATTTCCAAGTGCGTACTTCCTAGCAA TATCCATTCTCTGGAGGAATCCACCAACTTTGTTCAAAGTCACAAATGAAACAGTATTCTCGTC GTTGTATTTGTAGTCACAGAACCAAAGGGAGTAACCTTCTGGGTCATACATGTCCCAGAATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.001206507

Conservation Information
Conserved circRNAs	NA
PMCS	1.001206507

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						He et al., 2020

circRNA

Detail information of Chr3_circ_ig.13

Address

Any questions?

Supported by