Plant Circular RNA Database

Detail information of Csa2G402000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Csa2G402000_circ_g.1
					
						ID in PlantcircBase
						csa_circ_001256
					
						Alias
						Chr2:20570040_20572561
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr2: 20570040-20572561  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Csa2G402000						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						+
					
						Alternative splicing
						
							Csa2G402000_circ_g.2 Csa2G402000_circ_g.3 Csa2G402000_circ_g.4 						
					
						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
						Csa2G402000.1:4

General Information
CircRNA Name	Csa2G402000_circ_g.1
ID in PlantcircBase	csa_circ_001256
Alias	Chr2:20570040_20572561
Organism	Cucumis sativus
Position	chrChr2: 20570040-20572561 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	CIRI2
Parent gene	Csa2G402000
Parent gene annotation	NA
Parent gene strand	+
Alternative splicing	Csa2G402000_circ_g.2 Csa2G402000_circ_g.3 Csa2G402000_circ_g.4
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	Csa2G402000.1:4

			
						 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  
						
							ATTGGTGGTCGCAGAAGTGGATCCAATGATAAAAAATTCCAAAGCACTAAAGGATGTACAGCCT
GAGCTTGAAAAACTCCGACAGAAAGCAGTGTCTAAGgaatatattaaagaaagtgataacttag
tctcgcttcatgaacaaattcgcgactgcgacaacatcttatcacagatggaaactcttctcag
tggtttcc

									
								

					

						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: 411
Transcript exons: 20570040-20570141,20570557-20570640,20571980-20572060,20
572418-20572561
GAATATATTAAAGAAAGTGATAACTTAGTCTCGCTTCATGAACAAATTCGCGACTGCGACAACA
TCTTATCACAGATGGAAACTCTTCTCAGTGGTTTCCAGGCCGAAATTGGTTCTATTAGTGCAGA
CATTAAAGTCCTGCAGGAGAAGTCAATGGATATGGGTCTGAAGCTCAAGAATCGCAAGGTGGCA
GAATCAAAATTGGCAAAGTTTGTCGAAGAGATCATTGTCCCTCCAAGAATGATAGACATAATTG
TTGATGGAGAGGTTAATGATGAATATTTGAGGACTCTTGAGATTCTAAGTAAGAAATTGGTGGT
CGCAGAAGTGGATCCAATGATAAAAAATTCCAAAGCACTAAAGGATGTACAGCCTGAGCTTGAA
AAACTCCGACAGAAAGCAGTGTCTAAG
						
					

						Genomic sequence
						
							GAATATATTAAAGAAAGTGATAACTTAGTCTCGCTTCATGAACAAATTCGCGACTGCGACAACA
TCTTATCACAGATGGAAACTCTTCTCAGTGGTTTCCAGGTATTTCAGCTGCTTGTCTTGCACCC
TAGTAATATCTAACTTTTTAGTGAAGTGCAACAATCTGCTTGTATTAGCATGTAGCGTTTTTGT
GTCATTATATCCATCTCTGAAGTCTGAATTTCTACCTGATTCCTGTTTTCTTAAGTTGCATTTG
ATTCCTCAGGATGATCGTCAATCCTCATTAGATGATATACTGTGGGGCTTTAGGCTATCTTTCT
CAGATTTGAATGCACATGGAATTACACTGACCTTGAATTTAATTTCAATTGTTCATTTATATCA
TCTTAAATGAGTTCATTGGGACTGTTCTCCCCACCTCCCCACTAAAAATGACATCGTTTCTTCC
ATTTACATTTGTTCATTCTAGATATTCTTCCAATGAATTAATATATTTATGTTTTAAAAAAAAT
TTCAGGCCGAAATTGGTTCTATTAGTGCAGACATTAAAGTCCTGCAGGAGAAGTCAATGGATAT
GGGTCTGAAGCTCAAGAATCGCAAGGTATTCTTGATTGGATGAAGAAACTTCATTACATTGGTA
ATTTGAAAAAACTGAAGAATCAAGTCTTTGGATCTCAATAGGCGTTACAATGGCTTGCTTACTT
ATAATATCCATTGCTGTTCAATTTCGCTCGTATCAGATGCATTCTTTTTTTCCAGAAGCTTTAA
AGAAATTTTTGTGATTAAAAGTATTACTATATTATATAAAATGCCAAGGCATAGGAAGAAGTGA
AATTCAGGTGCTATGATAATTTTATTATGGCATTTTGGAGTTTTTAACTATCATATTTTGATAA
CATTAGTGTTCTCCTTTTCTTTTTATCTCCCATAATGAGTTTTTTGCAACTTTGTTTATTCATC
AATAAGACTGTCATTGATTTAGTTTCATTTAGTGAGCAAAACATAATTAGCATTGGTGTGAAAA
TCTTCACTTATATTTCTTTCCCTTGAATTTTCTGCATTTTAACAAAAACGTTTCTTGAGAAACT
TATCATAACTTAATGTTGGAGAAGTTGAAAGTCCCACATTGGAAATCCAAGGAGACTCATACTC
CATATAAGATAGTTGAGTTACTCCTCTCATTGCCAATTGGTTTTGAGATGGAACCCCATACTAT
CAAATTAACACTAAACACTTGCCATAAAATACCAAGAGATGGTAAAGTATTTTACCTTTGATAT
TACGGTGTTCCTCACTTGCTTATTTTAGAAATCCTTTCCATTCTTGGCATTTCTTTTCAGGTGG
GGACGAGCACATTGTTTCTAAAATATTATGCACTTTCTCATTGTGCACTCAAGAAGTTGTTAAT
GAAAATTGTTGTTTTCATTTTTTTTTAAATAGTATGTGCTTTCTCACCGCGTACTCTAGAAGTT
GTTAATGAGACCTTTTTGGGCTTAGCTCTCCTTCCCTCTTGTAATTTCATATCATCTACGAAAT
GACAAATTTTCTCATAAGAAAAGTTGGTTTTGAAAAGTTTCTTTTTTCTGCCTTTCTTTTTCTT
TAATACTTCTGTAAGTGAGAATTCTTTTTGGGCAATGCATGTCGCGGTTGGTTTCTTTTGAAAA
GAAAGTTGCATGTTCATCTAGTTTGCTCATTGTTTTAACTCAGTAAATGCTTTTATGGATTCCT
GAAAGTTATCTTTCTTTCCTCTTTCTTTTTAATGCTTCTGTGGGTGAGACACCATGTGAATTCT
TGTAGCAGTTGCTTTCTGTTGAAAAGAGGAATTGTATCTTCGTTTAGTTTTACTCATTATTTTA
ACTCAGCATACTACATGCATCACTATTTTATCTTCCTACTCTATCATTTTTTTCTCATGTGCTA
GGCTCTACAATCTTATTCAGGTGGCAGAATCAAAATTGGCAAAGTTTGTCGAAGAGATCATTGT
CCCTCCAAGAATGATAGACATAATTGTTGATGGAGAGGTATTGTCGGTATCTGTACACTTCACT
CCCATTTGGAACTTGGCGTTGTTTTCTACTCATTTTCTTATTGTTCTTGCTCTAAATTAGTTTT
CGGTATCCTTTAATTTTTTCAAGTTTCTCCTGTATATCGTTCTTATTAATTCAGTTTTGTTTTC
CTGTTTAAAAATGCATATATATTTAGTAGTAATGAATAAATATCACTCATTCTAATAGAAGGGA
AAAAAATTACATGTTCTTCGATTTCGTTTGTCCTTGCATAATTTGTGGTACCTAATTTGAAATT
TCTTCATGCTTCCTTCTCTTTTTCTCATTGAAATGCCTATGTTGATATTCCAGTGAACTTTTTT
TCTTTCTCAGGTTAATGATGAATATTTGAGGACTCTTGAGATTCTAAGTAAGAAATTGGTGGTC
GCAGAAGTGGATCCAATGATAAAAAATTCCAAAGCACTAAAGGATGTACAGCCTGAGCTTGAAA
AACTCCGACAGAAAGCAGTGTCTAAG
						
					

			
		

Sequences
Splice junction sequence	ATTGGTGGTCGCAGAAGTGGATCCAATGATAAAAAATTCCAAAGCACTAAAGGATGTACAGCCT GAGCTTGAAAAACTCCGACAGAAAGCAGTGTCTAAGgaatatattaaagaaagtgataacttag tctcgcttcatgaacaaattcgcgactgcgacaacatcttatcacagatggaaactcttctcag tggtttcc
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: 411 Transcript exons: 20570040-20570141,20570557-20570640,20571980-20572060,20 572418-20572561 GAATATATTAAAGAAAGTGATAACTTAGTCTCGCTTCATGAACAAATTCGCGACTGCGACAACA TCTTATCACAGATGGAAACTCTTCTCAGTGGTTTCCAGGCCGAAATTGGTTCTATTAGTGCAGA CATTAAAGTCCTGCAGGAGAAGTCAATGGATATGGGTCTGAAGCTCAAGAATCGCAAGGTGGCA GAATCAAAATTGGCAAAGTTTGTCGAAGAGATCATTGTCCCTCCAAGAATGATAGACATAATTG TTGATGGAGAGGTTAATGATGAATATTTGAGGACTCTTGAGATTCTAAGTAAGAAATTGGTGGT CGCAGAAGTGGATCCAATGATAAAAAATTCCAAAGCACTAAAGGATGTACAGCCTGAGCTTGAA AAACTCCGACAGAAAGCAGTGTCTAAG
Genomic sequence	GAATATATTAAAGAAAGTGATAACTTAGTCTCGCTTCATGAACAAATTCGCGACTGCGACAACA TCTTATCACAGATGGAAACTCTTCTCAGTGGTTTCCAGGTATTTCAGCTGCTTGTCTTGCACCC TAGTAATATCTAACTTTTTAGTGAAGTGCAACAATCTGCTTGTATTAGCATGTAGCGTTTTTGT GTCATTATATCCATCTCTGAAGTCTGAATTTCTACCTGATTCCTGTTTTCTTAAGTTGCATTTG ATTCCTCAGGATGATCGTCAATCCTCATTAGATGATATACTGTGGGGCTTTAGGCTATCTTTCT CAGATTTGAATGCACATGGAATTACACTGACCTTGAATTTAATTTCAATTGTTCATTTATATCA TCTTAAATGAGTTCATTGGGACTGTTCTCCCCACCTCCCCACTAAAAATGACATCGTTTCTTCC ATTTACATTTGTTCATTCTAGATATTCTTCCAATGAATTAATATATTTATGTTTTAAAAAAAAT TTCAGGCCGAAATTGGTTCTATTAGTGCAGACATTAAAGTCCTGCAGGAGAAGTCAATGGATAT GGGTCTGAAGCTCAAGAATCGCAAGGTATTCTTGATTGGATGAAGAAACTTCATTACATTGGTA ATTTGAAAAAACTGAAGAATCAAGTCTTTGGATCTCAATAGGCGTTACAATGGCTTGCTTACTT ATAATATCCATTGCTGTTCAATTTCGCTCGTATCAGATGCATTCTTTTTTTCCAGAAGCTTTAA AGAAATTTTTGTGATTAAAAGTATTACTATATTATATAAAATGCCAAGGCATAGGAAGAAGTGA AATTCAGGTGCTATGATAATTTTATTATGGCATTTTGGAGTTTTTAACTATCATATTTTGATAA CATTAGTGTTCTCCTTTTCTTTTTATCTCCCATAATGAGTTTTTTGCAACTTTGTTTATTCATC AATAAGACTGTCATTGATTTAGTTTCATTTAGTGAGCAAAACATAATTAGCATTGGTGTGAAAA TCTTCACTTATATTTCTTTCCCTTGAATTTTCTGCATTTTAACAAAAACGTTTCTTGAGAAACT TATCATAACTTAATGTTGGAGAAGTTGAAAGTCCCACATTGGAAATCCAAGGAGACTCATACTC CATATAAGATAGTTGAGTTACTCCTCTCATTGCCAATTGGTTTTGAGATGGAACCCCATACTAT CAAATTAACACTAAACACTTGCCATAAAATACCAAGAGATGGTAAAGTATTTTACCTTTGATAT TACGGTGTTCCTCACTTGCTTATTTTAGAAATCCTTTCCATTCTTGGCATTTCTTTTCAGGTGG GGACGAGCACATTGTTTCTAAAATATTATGCACTTTCTCATTGTGCACTCAAGAAGTTGTTAAT GAAAATTGTTGTTTTCATTTTTTTTTAAATAGTATGTGCTTTCTCACCGCGTACTCTAGAAGTT GTTAATGAGACCTTTTTGGGCTTAGCTCTCCTTCCCTCTTGTAATTTCATATCATCTACGAAAT GACAAATTTTCTCATAAGAAAAGTTGGTTTTGAAAAGTTTCTTTTTTCTGCCTTTCTTTTTCTT TAATACTTCTGTAAGTGAGAATTCTTTTTGGGCAATGCATGTCGCGGTTGGTTTCTTTTGAAAA GAAAGTTGCATGTTCATCTAGTTTGCTCATTGTTTTAACTCAGTAAATGCTTTTATGGATTCCT GAAAGTTATCTTTCTTTCCTCTTTCTTTTTAATGCTTCTGTGGGTGAGACACCATGTGAATTCT TGTAGCAGTTGCTTTCTGTTGAAAAGAGGAATTGTATCTTCGTTTAGTTTTACTCATTATTTTA ACTCAGCATACTACATGCATCACTATTTTATCTTCCTACTCTATCATTTTTTTCTCATGTGCTA GGCTCTACAATCTTATTCAGGTGGCAGAATCAAAATTGGCAAAGTTTGTCGAAGAGATCATTGT CCCTCCAAGAATGATAGACATAATTGTTGATGGAGAGGTATTGTCGGTATCTGTACACTTCACT CCCATTTGGAACTTGGCGTTGTTTTCTACTCATTTTCTTATTGTTCTTGCTCTAAATTAGTTTT CGGTATCCTTTAATTTTTTCAAGTTTCTCCTGTATATCGTTCTTATTAATTCAGTTTTGTTTTC CTGTTTAAAAATGCATATATATTTAGTAGTAATGAATAAATATCACTCATTCTAATAGAAGGGA AAAAAATTACATGTTCTTCGATTTCGTTTGTCCTTGCATAATTTGTGGTACCTAATTTGAAATT TCTTCATGCTTCCTTCTCTTTTTCTCATTGAAATGCCTATGTTGATATTCCAGTGAACTTTTTT TCTTTCTCAGGTTAATGATGAATATTTGAGGACTCTTGAGATTCTAAGTAAGAAATTGGTGGTC GCAGAAGTGGATCCAATGATAAAAAATTCCAAAGCACTAAAGGATGTACAGCCTGAGCTTGAAA AACTCCGACAGAAAGCAGTGTCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.483348695

Conservation Information
Conserved circRNAs	NA
PMCS	0.483348695

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20570116-20572558(+)
20572516-20570064(+)
						
						Potential amino acid sequence
						
							METLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRKVAESKLAKFVEEIIVPPRMIDIIVDGE
VNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPELEKLRQKAVSKEYIKESDNLVSLHEQI
RDCDNILSQMETLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRKVAESKLAKFVEEIIVPPR
MIDIIVDGEVNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPELEKLRQKAVSKEYIKESD
NLVSLHEQIRDCDNILSQMETLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRKVAESKLAKF
VEEIIVPPRMIDIIVDGEVNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPELEKLRQKAV
SKEYIKESDNLVSLHEQIRDCDNILSQMETLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRK
VAESKLAKFVEEIIVPPRMIDIIVDGEVNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPE
LEKLRQKAVSK
MYSLSLKNSDRKQCLRNILKKVIT*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20570116-20572558(+) 20572516-20570064(+)
Potential amino acid sequence	METLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRKVAESKLAKFVEEIIVPPRMIDIIVDGE VNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPELEKLRQKAVSKEYIKESDNLVSLHEQI RDCDNILSQMETLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRKVAESKLAKFVEEIIVPPR MIDIIVDGEVNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPELEKLRQKAVSKEYIKESD NLVSLHEQIRDCDNILSQMETLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRKVAESKLAKF VEEIIVPPRMIDIIVDGEVNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPELEKLRQKAV SKEYIKESDNLVSLHEQIRDCDNILSQMETLLSGFQAEIGSISADIKVLQEKSMDMGLKLKNRK VAESKLAKFVEEIIVPPRMIDIIVDGEVNDEYLRTLEILSKKLVVAEVDPMIKNSKALKDVQPE LEKLRQKAVSK MYSLSLKNSDRKQCLRNILKKVIT*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhu et al., 2019

circRNA

Detail information of Csa2G402000_circ_g.1

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