Plant Circular RNA Database

Detail information of AT3G59340_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G59340_circ_g.2
					
						ID in PlantcircBase
						ath_circ_028266
					
						Alias
						Ath_circ_FC5070
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 21929798-21931203  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRI, circRNA_finder
					
						Parent gene
						
							AT3G59340						
					
						Parent gene annotation
						
							Solute carrier family 35 protein (DUF914)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.6 AT3G59310_circ_g.1 AT3G59310_circ_g.2 3_circ_ag.3 AT3G59310_circ_g.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 3_circ_ag.10 3_circ_ag.11 AT3G59320_circ_g.1 AT3G59340_circ_g.1 AT3G59340_circ_g.3 						
					
						Support reads
						5
					
						Tissues
						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
						AT3G59340.4:7
AT3G59340.1:6
AT3G59340.3:7
AT3G59340.2:7

General Information
CircRNA Name	AT3G59340_circ_g.2
ID in PlantcircBase	ath_circ_028266
Alias	Ath_circ_FC5070
Organism	Arabidpsis thaliana
Position	chr3: 21929798-21931203 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRI, circRNA_finder
Parent gene	AT3G59340
Parent gene annotation	Solute carrier family 35 protein (DUF914)
Parent gene strand	-
Alternative splicing	3_circ_ag.6 AT3G59310_circ_g.1 AT3G59310_circ_g.2 3_circ_ag.3 AT3G59310_circ_g.4 3_circ_ag.5 3_circ_ag.6 3_circ_ag.7 3_circ_ag.8 3_circ_ag.9 3_circ_ag.10 3_circ_ag.11 AT3G59320_circ_g.1 AT3G59340_circ_g.1 AT3G59340_circ_g.3
Support reads	5
Tissues	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	AT3G59340.4:7 AT3G59340.1:6 AT3G59340.3:7 AT3G59340.2:7

			
						 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  
						
							ACGGCAGATCAGAAAGGATTTGTTGTTGCTGTCACTACCTACCGTTGACATTTTTTAAGCTTTT
CTTTTTCTCCTTCTCTTTTCCCTCCATTCAACTAAGacctgaatggcactaataatggctccaa
aaagtcccatgaaggtcatcaactcaactgtgtctgcattcttcacaagaaactcctataacaa
atgaacaa

									
								

					

						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: 728
Transcript exons: 21929798-21929880,21929952-21930028,21930113-21930307,21
930467-21930524,21930678-21930772,21930901-21931062,2193
1146-21931203
ACCTGAATGGCACTAATAATGGCTCCAAAAAGTCCCATGAAGGTCATCAACTCAACTGTGTCTG
CATTCTTCACAAGAAACTCCTCGGTGGTATTACTGACAGCATATAAAGTTGCTCCAGCTAGAAC
AAGAAAATCTCCTTTAACAGGATTACTTCCACCTGCTCGACTTCCTGCGTGAACGTCAGAGAAG
AGTACCATGACAACACCAGCAATACAGATAAATACACCACTGATCTTCATTAATCTGTATTTTG
TTTTCAGGAACATCCAAGTTAAGACCAACACACAAGGGATCGCCCAGCAATCAAGTAGCATGAT
ACTCGTAATCGATGTGTACTGATTCGCCTTCACCACAAGAAAATTGCCTTCCACGTCAACTAAA
GCAAGGAGGAAATAGTGATACCACTTCCCCTTAATTGTTGGTCTCCGATAGAGCATGATACCTC
CATAGACGACTGCCAGTAATGTATAACTGAGGAACGTTTGTGACGTTGGAGCATTTATTCCTTT
TCTGGCGAGCTCAGAGGATGTGAAGGCATTAGAAGTACATAGAAGTGAGAGGATCTGTCCCAAG
CCAAGTCCAATTAAAGTCTTCTTTGTTTTGTTCATCTCATTGAAATCGAAACCCATTGCCATTA
TTGCAGAAGAAGCTGAGATCTTCGGTGAATCGTTGACATTTTTTAAGCTTTTCTTTTTCTCCTT
CTCTTTTCCCTCCATTCAACTAAG
						
					

						Genomic sequence
						
							ACCTGAATGGCACTAATAATGGCTCCAAAAAGTCCCATGAAGGTCATCAACTCAACTGTGTCTG
CATTCTTCACAAGAAACTCCTATAACAAATGAACAATAAATTTTACATTTTTGCGGGATATAAC
AATTTCTTGTTGTAGCACTTGCTTACCTCGGTGGTATTACTGACAGCATATAAAGTTGCTCCAG
CTAGAACAAGAAAATCTCCTTTAACAGGATTACTTCCACCTAAAAAAACGCAACCATTATCATA
AGCGTAGATTGAGTTTTACTTGCGTGACAAGTAACGAATGATTAGTTTCTACCATTTACCTGCT
CGACTTCCTGCGTGAACGTCAGAGAAGAGTACCATGACAACACCAGCAATACAGATAAATACAC
CACTGATCTTCATTAATCTGTATTTTGTTTTCAGGAACATCCAAGTTAAGACCAACACACAAGG
GATCGCCCAGCAATCAAGTAGCATGATACTCGTAATCGATGTGTACTGATTCGCCTTCACCACT
GTTAAACCAAAGCAATAATGAAGTTTTATTCAAAATCTCACTACAACAGCAACCAAAATGTAAT
GGAAGTATATACAGTTTCTAAGAAAACTTGTCTCCAAAATAACTTCAGATCAGTGCTCAAGCCA
AAGAAGACTGTGTCAATAAGAAAACTGACCAAGAAAATTGCCTTCCACGTCAACTAAAGCAAGG
AGGAAATAGTGATACCACTTCCCCTACAAGAGTATTTGCATTGAAGATTTTAGTAGCACATACT
AGTTACGTTATAAGCACTCAATAGTGCATGTAATCTTGAAAAAAACTCTCATTACACCAAAAAG
AGAAATTAGCAGTAAGTAACACAAAGTGAAACCAAATTCAATACTGACCTTAATTGTTGGTCTC
CGATAGAGCATGATACCTCCATAGACGACTGCCAGTAATGTATAACTGAGGAACGTTTGTGACG
TTGGAGCATTTATTCCTATAAGATTTCAAAATTTTAAACCATGAATGTATAAACCATAAAGATC
ATAAATCTATATGATCGATCGAATCTTAAAGCTAGCATAAACGAGATGCATGCATTAAAAAAAA
TAGAAACAGTAAAACCTTTTCTGGCGAGCTCAGAGGATGTGAAGGCATTAGAAGTACATAGAAG
TGAGAGGATCTGTCCCAAGCCAAGTCCAATTAAAGTCTTCTTTGTTTTGTTCATCTCATTGAAA
TCGAAACCCATTGCCATTATTGCAGAAGAAGCTGAGATCTTCGGTGAATCTATAAATTACAGAC
ATTCAAATACAATAAGAGATTCGCAGACGGCAGATCAGAAAGGATTTGTTGTTGCTGTCACTAC
CTACCGTTGACATTTTTTAAGCTTTTCTTTTTCTCCTTCTCTTTTCCCTCCATTCAACTAAG
						
					

			
		

Sequences
Splice junction sequence	ACGGCAGATCAGAAAGGATTTGTTGTTGCTGTCACTACCTACCGTTGACATTTTTTAAGCTTTT CTTTTTCTCCTTCTCTTTTCCCTCCATTCAACTAAGacctgaatggcactaataatggctccaa aaagtcccatgaaggtcatcaactcaactgtgtctgcattcttcacaagaaactcctataacaa atgaacaa
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: 728 Transcript exons: 21929798-21929880,21929952-21930028,21930113-21930307,21 930467-21930524,21930678-21930772,21930901-21931062,2193 1146-21931203 ACCTGAATGGCACTAATAATGGCTCCAAAAAGTCCCATGAAGGTCATCAACTCAACTGTGTCTG CATTCTTCACAAGAAACTCCTCGGTGGTATTACTGACAGCATATAAAGTTGCTCCAGCTAGAAC AAGAAAATCTCCTTTAACAGGATTACTTCCACCTGCTCGACTTCCTGCGTGAACGTCAGAGAAG AGTACCATGACAACACCAGCAATACAGATAAATACACCACTGATCTTCATTAATCTGTATTTTG TTTTCAGGAACATCCAAGTTAAGACCAACACACAAGGGATCGCCCAGCAATCAAGTAGCATGAT ACTCGTAATCGATGTGTACTGATTCGCCTTCACCACAAGAAAATTGCCTTCCACGTCAACTAAA GCAAGGAGGAAATAGTGATACCACTTCCCCTTAATTGTTGGTCTCCGATAGAGCATGATACCTC CATAGACGACTGCCAGTAATGTATAACTGAGGAACGTTTGTGACGTTGGAGCATTTATTCCTTT TCTGGCGAGCTCAGAGGATGTGAAGGCATTAGAAGTACATAGAAGTGAGAGGATCTGTCCCAAG CCAAGTCCAATTAAAGTCTTCTTTGTTTTGTTCATCTCATTGAAATCGAAACCCATTGCCATTA TTGCAGAAGAAGCTGAGATCTTCGGTGAATCGTTGACATTTTTTAAGCTTTTCTTTTTCTCCTT CTCTTTTCCCTCCATTCAACTAAG
Genomic sequence	ACCTGAATGGCACTAATAATGGCTCCAAAAAGTCCCATGAAGGTCATCAACTCAACTGTGTCTG CATTCTTCACAAGAAACTCCTATAACAAATGAACAATAAATTTTACATTTTTGCGGGATATAAC AATTTCTTGTTGTAGCACTTGCTTACCTCGGTGGTATTACTGACAGCATATAAAGTTGCTCCAG CTAGAACAAGAAAATCTCCTTTAACAGGATTACTTCCACCTAAAAAAACGCAACCATTATCATA AGCGTAGATTGAGTTTTACTTGCGTGACAAGTAACGAATGATTAGTTTCTACCATTTACCTGCT CGACTTCCTGCGTGAACGTCAGAGAAGAGTACCATGACAACACCAGCAATACAGATAAATACAC CACTGATCTTCATTAATCTGTATTTTGTTTTCAGGAACATCCAAGTTAAGACCAACACACAAGG GATCGCCCAGCAATCAAGTAGCATGATACTCGTAATCGATGTGTACTGATTCGCCTTCACCACT GTTAAACCAAAGCAATAATGAAGTTTTATTCAAAATCTCACTACAACAGCAACCAAAATGTAAT GGAAGTATATACAGTTTCTAAGAAAACTTGTCTCCAAAATAACTTCAGATCAGTGCTCAAGCCA AAGAAGACTGTGTCAATAAGAAAACTGACCAAGAAAATTGCCTTCCACGTCAACTAAAGCAAGG AGGAAATAGTGATACCACTTCCCCTACAAGAGTATTTGCATTGAAGATTTTAGTAGCACATACT AGTTACGTTATAAGCACTCAATAGTGCATGTAATCTTGAAAAAAACTCTCATTACACCAAAAAG AGAAATTAGCAGTAAGTAACACAAAGTGAAACCAAATTCAATACTGACCTTAATTGTTGGTCTC CGATAGAGCATGATACCTCCATAGACGACTGCCAGTAATGTATAACTGAGGAACGTTTGTGACG TTGGAGCATTTATTCCTATAAGATTTCAAAATTTTAAACCATGAATGTATAAACCATAAAGATC ATAAATCTATATGATCGATCGAATCTTAAAGCTAGCATAAACGAGATGCATGCATTAAAAAAAA TAGAAACAGTAAAACCTTTTCTGGCGAGCTCAGAGGATGTGAAGGCATTAGAAGTACATAGAAG TGAGAGGATCTGTCCCAAGCCAAGTCCAATTAAAGTCTTCTTTGTTTTGTTCATCTCATTGAAA TCGAAACCCATTGCCATTATTGCAGAAGAAGCTGAGATCTTCGGTGAATCTATAAATTACAGAC ATTCAAATACAATAAGAGATTCGCAGACGGCAGATCAGAAAGGATTTGTTGTTGCTGTCACTAC CTACCGTTGACATTTTTTAAGCTTTTCTTTTTCTCCTTCTCTTTTCCCTCCATTCAACTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.178655588

Conservation Information
Conserved circRNAs	NA
PMCS	0.178655588

			
						 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
						Chu et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G59340_circ_g.2

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