Plant Circular RNA Database

Detail information of Csa1G050140_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa1G050140_circ_g.1
					
						ID in PlantcircBase
						csa_circ_000195
					
						Alias
						Chr1:5753317_5755836
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr1: 5753317-5755836  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2;Find_circ
					
						Parent gene
						
							Csa1G050140						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						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
						Csa1G050140.1:3

General Information
CircRNA Name	Csa1G050140_circ_g.1
ID in PlantcircBase	csa_circ_000195
Alias	Chr1:5753317_5755836
Organism	Cucumis sativus
Position	chrChr1: 5753317-5755836 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2;Find_circ
Parent gene	Csa1G050140
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	NA
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	Csa1G050140.1:3

			
						 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  
						
							CTCCCCCACAAACATCATGGCGCCATCAAGTTCAATATTATTAGAAGCTTTTGCTTCTACTAGA
GAAAGGAATTGATTGGTAATCTGCTTGAAGAACGAGaagcttgctgctcaatcgtggctgattg
aacaaactcctttttggaccacacttctaccagacgctgcacagtcattaagaggctgctatta
ttattgcc

									
								

					

						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: 626
Transcript exons: 5753317-5753531,5753994-5754270,5755703-5755836
AAGCTTGCTGCTCAATCGTGGCTGATTGAACAAACTCCTTTTTGGACCACACTTCTACCAGACG
CTGCACAGTCATTAAGAGGCTGCTATTATTATTGCCTTTCTTGAGACAATTGGCATCAGGCGGG
CATTCTAGAATAGCAAACTGTAGAACCCAGCGCAGGCAATGAATGGGGAATACTTTCCAGACCA
AAAATTTGTCAACGAAAATGGACCTTACTGACATTCGTAATCTTAGACTACGATGAAAAAGTAG
CCAAAGCACCCAGTAGGCATCAACATCACTTTCACATGTAGCAGCTAGCTGATGTAAAAGCTGC
TCAGAAAATCTTTCAACAGCATAATTATCTTTAATTGTTTCCATTATCTTCAACCAGAACTGGG
AATTGGGGTTTGATTCAAATACATCAGCGACAGCTGAATGAATATTCAACATTACAACATCATG
GACGTGCTTCACAATACGTGGAAGTAATTCATTTAGTAACAAGTCTGTAGATCCACGTCGACAA
ATGCGAGAAAATGTCTCCCCCACAAACATCATGGCGCCATCAAGTTCAATATTATTAGAAGCTT
TTGCTTCTACTAGAGAAAGGAATTGATTGGTAATCTGCTTGAAGAACGAG
						
					

						Genomic sequence
						
							AAGCTTGCTGCTCAATCGTGGCTGATTGAACAAACTCCTTTTTGGACCACACTTCTACCAGACG
CTGCACAGTCATTAAGAGGCTGCTATTATTATTGCCTTTCTTGAGACAATTGGCATCAGGCGGG
CATTCTAGAATAGCAAACTGTAGAACCCAGCGCAGGCAATGAATGGGGAATACTTTCCAGACCA
AAAATTTGTCAACGAAAATGGACCTACAAAAGTAGGTTAGAAATAATCAAAGGGCTCAGTTAGA
CCAAAATCAACCAGACCCCTCAAAGAACTGTTATGCTTTTAAGATGGAAAAAAATACATTTTTA
AGCAGCCTTTGCTGGCTAGCTTAGTCAAATTTATAGTTGTTAGTTTGTTGCTTTTTCAAAGATT
TGCAGTTAGGTCTTGCGTGTACATTTAATGACAGATTAGGACAAATCAATTCATTTAAATAAAG
AGGTTAAGTTCAACCACCTGTTGCAAGAACTAGAAACCAATACACTCCTAGTTATACATATCAA
GAATGATATTAATTGATAAATGAATCGGTAGACATAATTAACTTGTAAAAAGAATTGTCAAATA
CATGATCTGAAGACATATCTAATGTAATTCCTTTTTCCCCTTCTTTAGGTGAAGGAAGGTGGGG
AAAACATGAATTGGATCTGTGGATCTAGATAACTGACCTTACTGACATTCGTAATCTTAGACTA
CGATGAAAAAGTAGCCAAAGCACCCAGTAGGCATCAACATCACTTTCACATGTAGCAGCTAGCT
GATGTAAAAGCTGCTCAGAAAATCTTTCAACAGCATAATTATCTTTAATTGTTTCCATTATCTT
CAACCAGAACTGGGAATTGGGGTTTGATTCAAATACATCAGCGACAGCTGAATGAATATTCAAC
ATTACAACATCATGGACGTGCTTCACAATACGTGGAAGTAATTCATTTAGTAACAAGTCTGCCA
AAACAGAAAAACCAAATAATTTGGTATGTATCCTGTGTGATGAAATAAACTTAACAGAGCATAA
ACGAATACCTGAAAGATGATTAAGTATACCGATTACACATACATAAACAGCATTGACAATCTAA
TTCCATTCCAATTTGATGATTTTTAGCTATATTTAGTTTTATCTAAAAGGAGATATACCGATAG
ACCTCCTATCATATACAAATATAGTAGGAGAGAAAAGAAGAATCAGAAGTAGCACGTGTATAGA
ATAGCACGTGAGAGTTAGTGGGGAAGGGATTAGAAGTTAGTATAAATAATTGAGTAGGAAGGGC
GGGAAAGGGAGTTAGCATCTTGTGAGAGAAAGGAATTACTCTGCTCTACCTTAAGAGATAGGTT
AGCAGTGGCATTAAGGTTGATCTTGTATTCAGGAACTCGTTCCTATTCTATTTATCAATAATAT
TCATATTTCACACCAATTGGATTTCCATCATATACAGATTAACATACGGATAATCCTAAAAATA
ATGGCTTTTGGCAGCCTTTTAATTATGTCATAACTCATAAGGGTTCACGCAAGGTGAGTATTTT
ATCAGTCATAAATGAAAATCATCCTATTGCTTGGATATCAGGGTTCGCACAAGGTTAGTAGCAT
CATCCTTTCATGTCATACTATACTATGACATGAAACGCTGCTTATCACTTGTATGAAATTCCTC
CTGCATTTGTGAATAATGAAGAACGTGGCAACTATAAAAGAAGATATAAAGAGACGTGCAGAAC
ACATCGCATTTCCTGCTTAGTTGATAGATTTATTATTGTCTCTAACAGTTGGATGGTGGCTTGA
TAAAGAAAGAGCCAAAGGACAGGCCCCTTATCACGGAATGTGGGATAGAAAAGCACCTCCTCCA
TCATCAAATAACACCCTTTGTTCTAGGCCAAGAAAATGAACATTAAGAGCTTCCAAGATAAATA
AAGCTTTAGACATATTAGCCTCATTTCCTTCCTATGTATAATAGTCACCTTAAGTCTTAACTAC
TGGCACAAAGCTGATGTACATCAATCAAACTAACAAAAAACCACAAAGGATCAAAGAGCATTAA
AGCGAGACAAATCAGCAACTTCATCTTCATTCTTATTGCTTATGCCTAGGAAATGGTTGATGGT
TAAAAAAAATTAGAAAGAAAAAAGTCCATTTTCAACTTCATATAGAAAGAACTATAAAAAATAG
GGACTTCCTAGCTGAAATCAAGAAGCATGAAGGCAACTTAGGCATTGGTAAGAATAAAAACTGG
TGTGCCAATTGTCGAGGACATAAATAGTTGAACAGCTTTCAAACCAAGACTGACTCTTCATGAA
ATTATAAGTTTTTATAAAATAAGCATTAGGAGAAAAATGGAGGGAAAAAAAACCCCTACTACTA
CACATTAATCTTGCTGACCTGTAGATCCACGTCGACAAATGCGAGAAAATGTCTCCCCCACAAA
CATCATGGCGCCATCAAGTTCAATATTATTAGAAGCTTTTGCTTCTACTAGAGAAAGGAATTGA
TTGGTAATCTGCTTGAAGAACGAG
						
					

			
		

Sequences
Splice junction sequence	CTCCCCCACAAACATCATGGCGCCATCAAGTTCAATATTATTAGAAGCTTTTGCTTCTACTAGA GAAAGGAATTGATTGGTAATCTGCTTGAAGAACGAGaagcttgctgctcaatcgtggctgattg aacaaactcctttttggaccacacttctaccagacgctgcacagtcattaagaggctgctatta ttattgcc
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: 626 Transcript exons: 5753317-5753531,5753994-5754270,5755703-5755836 AAGCTTGCTGCTCAATCGTGGCTGATTGAACAAACTCCTTTTTGGACCACACTTCTACCAGACG CTGCACAGTCATTAAGAGGCTGCTATTATTATTGCCTTTCTTGAGACAATTGGCATCAGGCGGG CATTCTAGAATAGCAAACTGTAGAACCCAGCGCAGGCAATGAATGGGGAATACTTTCCAGACCA AAAATTTGTCAACGAAAATGGACCTTACTGACATTCGTAATCTTAGACTACGATGAAAAAGTAG CCAAAGCACCCAGTAGGCATCAACATCACTTTCACATGTAGCAGCTAGCTGATGTAAAAGCTGC TCAGAAAATCTTTCAACAGCATAATTATCTTTAATTGTTTCCATTATCTTCAACCAGAACTGGG AATTGGGGTTTGATTCAAATACATCAGCGACAGCTGAATGAATATTCAACATTACAACATCATG GACGTGCTTCACAATACGTGGAAGTAATTCATTTAGTAACAAGTCTGTAGATCCACGTCGACAA ATGCGAGAAAATGTCTCCCCCACAAACATCATGGCGCCATCAAGTTCAATATTATTAGAAGCTT TTGCTTCTACTAGAGAAAGGAATTGATTGGTAATCTGCTTGAAGAACGAG
Genomic sequence	AAGCTTGCTGCTCAATCGTGGCTGATTGAACAAACTCCTTTTTGGACCACACTTCTACCAGACG CTGCACAGTCATTAAGAGGCTGCTATTATTATTGCCTTTCTTGAGACAATTGGCATCAGGCGGG CATTCTAGAATAGCAAACTGTAGAACCCAGCGCAGGCAATGAATGGGGAATACTTTCCAGACCA AAAATTTGTCAACGAAAATGGACCTACAAAAGTAGGTTAGAAATAATCAAAGGGCTCAGTTAGA CCAAAATCAACCAGACCCCTCAAAGAACTGTTATGCTTTTAAGATGGAAAAAAATACATTTTTA AGCAGCCTTTGCTGGCTAGCTTAGTCAAATTTATAGTTGTTAGTTTGTTGCTTTTTCAAAGATT TGCAGTTAGGTCTTGCGTGTACATTTAATGACAGATTAGGACAAATCAATTCATTTAAATAAAG AGGTTAAGTTCAACCACCTGTTGCAAGAACTAGAAACCAATACACTCCTAGTTATACATATCAA GAATGATATTAATTGATAAATGAATCGGTAGACATAATTAACTTGTAAAAAGAATTGTCAAATA CATGATCTGAAGACATATCTAATGTAATTCCTTTTTCCCCTTCTTTAGGTGAAGGAAGGTGGGG AAAACATGAATTGGATCTGTGGATCTAGATAACTGACCTTACTGACATTCGTAATCTTAGACTA CGATGAAAAAGTAGCCAAAGCACCCAGTAGGCATCAACATCACTTTCACATGTAGCAGCTAGCT GATGTAAAAGCTGCTCAGAAAATCTTTCAACAGCATAATTATCTTTAATTGTTTCCATTATCTT CAACCAGAACTGGGAATTGGGGTTTGATTCAAATACATCAGCGACAGCTGAATGAATATTCAAC ATTACAACATCATGGACGTGCTTCACAATACGTGGAAGTAATTCATTTAGTAACAAGTCTGCCA AAACAGAAAAACCAAATAATTTGGTATGTATCCTGTGTGATGAAATAAACTTAACAGAGCATAA ACGAATACCTGAAAGATGATTAAGTATACCGATTACACATACATAAACAGCATTGACAATCTAA TTCCATTCCAATTTGATGATTTTTAGCTATATTTAGTTTTATCTAAAAGGAGATATACCGATAG ACCTCCTATCATATACAAATATAGTAGGAGAGAAAAGAAGAATCAGAAGTAGCACGTGTATAGA ATAGCACGTGAGAGTTAGTGGGGAAGGGATTAGAAGTTAGTATAAATAATTGAGTAGGAAGGGC GGGAAAGGGAGTTAGCATCTTGTGAGAGAAAGGAATTACTCTGCTCTACCTTAAGAGATAGGTT AGCAGTGGCATTAAGGTTGATCTTGTATTCAGGAACTCGTTCCTATTCTATTTATCAATAATAT TCATATTTCACACCAATTGGATTTCCATCATATACAGATTAACATACGGATAATCCTAAAAATA ATGGCTTTTGGCAGCCTTTTAATTATGTCATAACTCATAAGGGTTCACGCAAGGTGAGTATTTT ATCAGTCATAAATGAAAATCATCCTATTGCTTGGATATCAGGGTTCGCACAAGGTTAGTAGCAT CATCCTTTCATGTCATACTATACTATGACATGAAACGCTGCTTATCACTTGTATGAAATTCCTC CTGCATTTGTGAATAATGAAGAACGTGGCAACTATAAAAGAAGATATAAAGAGACGTGCAGAAC ACATCGCATTTCCTGCTTAGTTGATAGATTTATTATTGTCTCTAACAGTTGGATGGTGGCTTGA TAAAGAAAGAGCCAAAGGACAGGCCCCTTATCACGGAATGTGGGATAGAAAAGCACCTCCTCCA TCATCAAATAACACCCTTTGTTCTAGGCCAAGAAAATGAACATTAAGAGCTTCCAAGATAAATA AAGCTTTAGACATATTAGCCTCATTTCCTTCCTATGTATAATAGTCACCTTAAGTCTTAACTAC TGGCACAAAGCTGATGTACATCAATCAAACTAACAAAAAACCACAAAGGATCAAAGAGCATTAA AGCGAGACAAATCAGCAACTTCATCTTCATTCTTATTGCTTATGCCTAGGAAATGGTTGATGGT TAAAAAAAATTAGAAAGAAAAAAGTCCATTTTCAACTTCATATAGAAAGAACTATAAAAAATAG GGACTTCCTAGCTGAAATCAAGAAGCATGAAGGCAACTTAGGCATTGGTAAGAATAAAAACTGG TGTGCCAATTGTCGAGGACATAAATAGTTGAACAGCTTTCAAACCAAGACTGACTCTTCATGAA ATTATAAGTTTTTATAAAATAAGCATTAGGAGAAAAATGGAGGGAAAAAAAACCCCTACTACTA CACATTAATCTTGCTGACCTGTAGATCCACGTCGACAAATGCGAGAAAATGTCTCCCCCACAAA CATCATGGCGCCATCAAGTTCAATATTATTAGAAGCTTTTGCTTCTACTAGAGAAAGGAATTGA TTGGTAATCTGCTTGAAGAACGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.092129653

Conservation Information
Conserved circRNAs	NA
PMCS	1.092129653

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5755756-5755798(-)
						
						Potential amino acid sequence
						
							MMFVGETFSRICRRGSTDLLLNELLPRIVKHVHDVVMLNIHSAVADVFESNPNSQFWLKIMETI
KDNYAVERFSEQLLHQLAATCESDVDAYWVLWLLFHRSLRLRMSVRSIFVDKFLVWKVFPIHCL
RWVLQFAILECPPDANCLKKGNNNSSLLMTVQRLVEVWSKKEFVQSATIEQQASRSSSRLPINS
FL*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5755756-5755798(-)
Potential amino acid sequence	MMFVGETFSRICRRGSTDLLLNELLPRIVKHVHDVVMLNIHSAVADVFESNPNSQFWLKIMETI KDNYAVERFSEQLLHQLAATCESDVDAYWVLWLLFHRSLRLRMSVRSIFVDKFLVWKVFPIHCL RWVLQFAILECPPDANCLKKGNNNSSLLMTVQRLVEVWSKKEFVQSATIEQQASRSSSRLPINS FL*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhu et al., 2019;He et al., 2020

circRNA

Detail information of Csa1G050140_circ_g.1

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