Plant Circular RNA Database

Detail information of Csa3G879460_circ_g.2

			
						 General Information
					
						CircRNA Name
						Csa3G879460_circ_g.2
					
						ID in PlantcircBase
						csa_circ_002172
					
						Alias
						Chr3:37028274_37034812
					
						Organism
						
							Cucumis sativus						
					
						Position
						
							chrChr3: 37028274-37034812  JBrowse»						
					
						Reference genome
						
							Cucumis sativus v1.5						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Find_circ
					
						Parent gene
						
							Csa3G879460						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						-
					
						Alternative splicing
						
							Csa3G879460_circ_g.3 Csa3G879460_circ_g.4 Csa3G879460_circ_g.5 						
					
						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
						Csa3G879460.1:7

General Information
CircRNA Name	Csa3G879460_circ_g.2
ID in PlantcircBase	csa_circ_002172
Alias	Chr3:37028274_37034812
Organism	Cucumis sativus
Position	chrChr3: 37028274-37034812 JBrowse»
Reference genome	Cucumis sativus v1.5
Type	e-circRNA
Identification method	Find_circ
Parent gene	Csa3G879460
Parent gene annotation	NA
Parent gene strand	-
Alternative splicing	Csa3G879460_circ_g.3 Csa3G879460_circ_g.4 Csa3G879460_circ_g.5
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	Csa3G879460.1:7

			
						 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  
						
							GGAATTAACAATAATATAATCATGGGAAATATTGATATCTCCTCGAGCATCCCTGAATGATCCT
TCAGCAAGTGGTGCAGTCCAATTAATGTTAAACCTCcattgtatccccattgcctccaccactt
gcatcaagagagccatgccagcagcctctgagttcagataagcctggaagagataaatcttcaa
gaacaatt

									
								

					

						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: 1339
Transcript exons: 37028274-37028405,37028592-37028657,37030666-37030941,37
032211-37032333,37032855-37032914,37033066-37033233,3703
4299-37034812
CATTGTATCCCCATTGCCTCCACCACTTGCATCAAGAGAGCCATGCCAGCAGCCTCTGAGTTCA
GATAAGCCTGGAAGAGATAAATCTTCAAGAACAATTTCATCTGATAGAATAAATTGTCTCCGTA
TCACCTCAATCAGATCTTGAACACTTTCGGTGTATAATCCAACAGCTTGCAAATTTTGTATAAA
AAAATCCTTGGATCTTGAGTGAACTGAAGGATCTGTACTTCGTGATAGAAGGCGGGCCAGTGGA
AGCATCTCAGCAACCTCAGCCTTAGGAACTTCCAGTCTCATCCTCCATCTTCCCATGGAGGATA
TGACACTGCTCAGATGGGAAGCCATTGCCTTTTTCAAAAATCCAGTACTTTCCTTATCGGTAAC
ATTTCGATCACGGCTTCCAGGAAGCACATATTCACCTTGAAGCTCATAACGGCTGTTGCTTTGC
TCTAGAATAGTTTTCTCGATGGTGATCACGTCTCCGCTCCACCTAGCAGCTATATCTAAAGCTT
CTCCCAACACGCCGCTAAATTTTGGGTCAAGTACTGATAAAACCCCATGACCTCTTCTTTTCTG
AAGATTAAGTTCAATTTCTGCCCTTTGTATTGCTCCCCTAAGTGAAGCCAGCTCCAAGTCATCT
AGCGGCAAATGACGTAACTCCAAATGTGCAGATCTAGATGGTTGGTAACGTGCATTGGCTTTTA
ACTGCCCCCGTTGAAGATTAAAAGAGAACAACTTCGACTTTCTAGAATTATCTGAGCTAGGCTT
CAACGACCCCACAATTTCTACTGAAAGACTTTCGTCTGGCCTACCTGTTGTCTCCAACTTGATT
GACTCACGAGTCATGCTCAATAGCCCAGCAAGCTTAGGGGCCAGAACCAATTGATTCAGCTTAA
GACCAGAAATTGAAACCTCGCCAGCAAGACCATCTTTATTCTCTTCATCAATTGGCTGCACCTG
CTGCTTACTCTTCTCATTACTAAAATCTTTACTAGAAGGTCTCAAAACTTTCCCCACAAACTTA
ACCCTTCCAGTTGCTTTTAGATGCATAGGCCTTGGAGATTCAAAAATATAAGACACTAAGCTCA
AGAACTCAAAACCACGCATATGTAAGTCCAACTCCACTCCATCAATAGTAAATGATGGAGTCCT
CTTTGCATCAAACACTTCTTCATCAAGCATAATCTTGTCAGAATACGATGTTTGCACTTTTGAG
AAGAGTTCAAAAGCAACAGAGGAGGAATTAACAATAATATAATCATGGGAAATATTGATATCTC
CTCGAGCATCCCTGAATGATCCTTCAGCAAGTGGTGCAGTCCAATTAATGTTAAACCTC
						
					

						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	GGAATTAACAATAATATAATCATGGGAAATATTGATATCTCCTCGAGCATCCCTGAATGATCCT TCAGCAAGTGGTGCAGTCCAATTAATGTTAAACCTCcattgtatccccattgcctccaccactt gcatcaagagagccatgccagcagcctctgagttcagataagcctggaagagataaatcttcaa gaacaatt
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: 1339 Transcript exons: 37028274-37028405,37028592-37028657,37030666-37030941,37 032211-37032333,37032855-37032914,37033066-37033233,3703 4299-37034812 CATTGTATCCCCATTGCCTCCACCACTTGCATCAAGAGAGCCATGCCAGCAGCCTCTGAGTTCA GATAAGCCTGGAAGAGATAAATCTTCAAGAACAATTTCATCTGATAGAATAAATTGTCTCCGTA TCACCTCAATCAGATCTTGAACACTTTCGGTGTATAATCCAACAGCTTGCAAATTTTGTATAAA AAAATCCTTGGATCTTGAGTGAACTGAAGGATCTGTACTTCGTGATAGAAGGCGGGCCAGTGGA AGCATCTCAGCAACCTCAGCCTTAGGAACTTCCAGTCTCATCCTCCATCTTCCCATGGAGGATA TGACACTGCTCAGATGGGAAGCCATTGCCTTTTTCAAAAATCCAGTACTTTCCTTATCGGTAAC ATTTCGATCACGGCTTCCAGGAAGCACATATTCACCTTGAAGCTCATAACGGCTGTTGCTTTGC TCTAGAATAGTTTTCTCGATGGTGATCACGTCTCCGCTCCACCTAGCAGCTATATCTAAAGCTT CTCCCAACACGCCGCTAAATTTTGGGTCAAGTACTGATAAAACCCCATGACCTCTTCTTTTCTG AAGATTAAGTTCAATTTCTGCCCTTTGTATTGCTCCCCTAAGTGAAGCCAGCTCCAAGTCATCT AGCGGCAAATGACGTAACTCCAAATGTGCAGATCTAGATGGTTGGTAACGTGCATTGGCTTTTA ACTGCCCCCGTTGAAGATTAAAAGAGAACAACTTCGACTTTCTAGAATTATCTGAGCTAGGCTT CAACGACCCCACAATTTCTACTGAAAGACTTTCGTCTGGCCTACCTGTTGTCTCCAACTTGATT GACTCACGAGTCATGCTCAATAGCCCAGCAAGCTTAGGGGCCAGAACCAATTGATTCAGCTTAA GACCAGAAATTGAAACCTCGCCAGCAAGACCATCTTTATTCTCTTCATCAATTGGCTGCACCTG CTGCTTACTCTTCTCATTACTAAAATCTTTACTAGAAGGTCTCAAAACTTTCCCCACAAACTTA ACCCTTCCAGTTGCTTTTAGATGCATAGGCCTTGGAGATTCAAAAATATAAGACACTAAGCTCA AGAACTCAAAACCACGCATATGTAAGTCCAACTCCACTCCATCAATAGTAAATGATGGAGTCCT CTTTGCATCAAACACTTCTTCATCAAGCATAATCTTGTCAGAATACGATGTTTGCACTTTTGAG AAGAGTTCAAAAGCAACAGAGGAGGAATTAACAATAATATAATCATGGGAAATATTGATATCTC CTCGAGCATCCCTGAATGATCCTTCAGCAAGTGGTGCAGTCCAATTAATGTTAAACCTC
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
						0.454042596

Conservation Information
Conserved circRNAs	NA
PMCS	0.454042596

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							37034657-37034806(-)
37028379-37034806(-)
						
						Potential amino acid sequence
						
							MLDEEVFDAKRTPSFTIDGVELDLHMRGFEFLSLVSYIFESPRPMHLKATGRVKFVGKVLRPSS
KDFSNEKSKQQVQPIDEENKDGLAGEVSISGLKLNQLVLAPKLAGLLSMTRESIKLETTGRPDE
SLSVEIVGSLKPSSDNSRKSKLFSFNLQRGQLKANARYQPSRSAHLELRHLPLDDLELASLRGA
IQRAEIELNLQKRRGHGVLSVLDPKFSGVLGEALDIAARWSGDVITIEKTILEQSNSRYELQGE
YVLPGSRDRNVTDKESTGFLKKAMASHLSSVISSMGRWRMRLEVPKAEVAEMLPLARLLSRSTD
PSVHSRSKDFFIQNLQAVGLYTESVQDLIEVIRRQFILSDEIVLEDLSLPGLSELRGCWHGSLD
ASGGGNGDTMEV*
MKLFLKIYLFQAYLNSEAAGMALLMQVVEAMGIQWRFNINWTAPLAEGSFRDARGDINISHDYI
IVNSSSVAFELFSKVQTSYSDKIMLDEEVFDAKRTPSFTIDGVELDLHMRGFEFLSLVSYIFES
PRPMHLKATGRVKFVGKVLRPSSKDFSNEKSKQQVQPIDEENKDGLAGEVSISGLKLNQLVLAP
KLAGLLSMTRESIKLETTGRPDESLSVEIVGSLKPSSDNSRKSKLFSFNLQRGQLKANARYQPS
RSAHLELRHLPLDDLELASLRGAIQRAEIELNLQKRRGHGVLSVLDPKFSGVLGEALDIAARWS
GDVITIEKTILEQSNSRYELQGEYVLPGSRDRNVTDKESTGFLKKAMASHLSSVISSMGRWRMR
LEVPKAEVAEMLPLARLLSRSTDPSVHSRSKDFFIQNLQAVGLYTESVQDLIEVIRRQFILSDE
IVLEDLSLPGLSELRGCWHGSLDASGGGNGDTMEV*
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	37034657-37034806(-) 37028379-37034806(-)
Potential amino acid sequence	MLDEEVFDAKRTPSFTIDGVELDLHMRGFEFLSLVSYIFESPRPMHLKATGRVKFVGKVLRPSS KDFSNEKSKQQVQPIDEENKDGLAGEVSISGLKLNQLVLAPKLAGLLSMTRESIKLETTGRPDE SLSVEIVGSLKPSSDNSRKSKLFSFNLQRGQLKANARYQPSRSAHLELRHLPLDDLELASLRGA IQRAEIELNLQKRRGHGVLSVLDPKFSGVLGEALDIAARWSGDVITIEKTILEQSNSRYELQGE YVLPGSRDRNVTDKESTGFLKKAMASHLSSVISSMGRWRMRLEVPKAEVAEMLPLARLLSRSTD PSVHSRSKDFFIQNLQAVGLYTESVQDLIEVIRRQFILSDEIVLEDLSLPGLSELRGCWHGSLD ASGGGNGDTMEV* MKLFLKIYLFQAYLNSEAAGMALLMQVVEAMGIQWRFNINWTAPLAEGSFRDARGDINISHDYI IVNSSSVAFELFSKVQTSYSDKIMLDEEVFDAKRTPSFTIDGVELDLHMRGFEFLSLVSYIFES PRPMHLKATGRVKFVGKVLRPSSKDFSNEKSKQQVQPIDEENKDGLAGEVSISGLKLNQLVLAP KLAGLLSMTRESIKLETTGRPDESLSVEIVGSLKPSSDNSRKSKLFSFNLQRGQLKANARYQPS RSAHLELRHLPLDDLELASLRGAIQRAEIELNLQKRRGHGVLSVLDPKFSGVLGEALDIAARWS GDVITIEKTILEQSNSRYELQGEYVLPGSRDRNVTDKESTGFLKKAMASHLSSVISSMGRWRMR LEVPKAEVAEMLPLARLLSRSTDPSVHSRSKDFFIQNLQAVGLYTESVQDLIEVIRRQFILSDE IVLEDLSLPGLSELRGCWHGSLDASGGGNGDTMEV*
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						He et al., 2020

circRNA

Detail information of Csa3G879460_circ_g.2

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