Plant Circular RNA Database

Detail information of AT1G35580_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G35580_circ_g.1
					
						ID in PlantcircBase
						ath_circ_005736
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 13123209-13124827  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT1G35580						
					
						Parent gene annotation
						
							Alkaline/neutral invertase CINV1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G35580_circ_g.2 AT1G35580_circ_g.3 AT1G35580_circ_g.4 AT1G35580_circ_g.5 AT1G35580_circ_g.6 						
					
						Support reads
						39
					
						Tissues
						whole_plant
					
						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
						AT1G35580.3:4
AT1G35580.2:4
AT1G35580.1:4

General Information
CircRNA Name	AT1G35580_circ_g.1
ID in PlantcircBase	ath_circ_005736
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 13123209-13124827 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT1G35580
Parent gene annotation	Alkaline/neutral invertase CINV1
Parent gene strand	-
Alternative splicing	AT1G35580_circ_g.2 AT1G35580_circ_g.3 AT1G35580_circ_g.4 AT1G35580_circ_g.5 AT1G35580_circ_g.6
Support reads	39
Tissues	whole_plant
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	AT1G35580.3:4 AT1G35580.2:4 AT1G35580.1:4

			
						 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  
						
							CAAAGCTCGAGTCAAATCAAGATCATCCATCTCAGATAAAGAACAGTGTGATCCTACAGCTCTT
AGTCCAACACCTTCCATTATAACACTAAACCAAGATctggccaagatccaccattgtggtagct
ccaccgtgtgttcttggggtcacagccagtaacgatgcgccactcatggccctcgaggcatgga
taacaaat

									
								

					

						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: 1376
Transcript exons: 13123209-13123576,13123657-13123847,13123939-13124370,13
124443-13124827
CTGGCCAAGATCCACCATTGTGGTAGCTCCACCGTGTGTTCTTGGGGTCACAGCCAGTAACGAT
GCGCCACTCATGGCCCTCGAGGCATGGATAACAAATCTTGAGAGGCATCTCACCTACAAGCTCT
GCCCACCGGTGCTCAAGGAGGTCCATAATGGCCATGGATTGATCTGGAGTGGCCAATGAAGAAA
GTATGGAGACACAATTACCGAGTGCGAACCACCGGAAATCCATATGGGCAGGTCCTACGTTTCC
CACAAAGTAGCCTCCACGGAGAGGCATGAAGTCGAAAACCCACTCGGGTATAGAATCAGGCATC
ACATTGAACTTGTTCACCGCCGTGTGAGAGTATTCCTCAGTCTTGAACCTGTAAATGTCATTGA
GGTTCTGATGATCAAGCCAGAAGTAATTGCGCATATGGAAGCTCAAGGCATGAAGTCGCTTAAC
GATCCTCTCAATGACCTCTCTGCCATCTCCATCGGGCTTTAACATCGACAAAGCAGATCTCAAA
GCCATGAAGAACAACGCTTGGATCTCAATGGGATACCCATAAACACCCATTCTTCGATCAATCA
TGGAACATCCATCAGCACAAAGCAGTGTAGGAAACGTGTCAAACCCTTCAGCTAAGCACAAAGA
CAAGATCAGTTTCATTCCCTTTTGACACTCTGGTGTCTCAGAGAGAGTCAAATCTCCAGTAGAT
TTGGTATAAGCACGAAGAAGAATAATCCACCAGAACCCTGAATCTACAGGAGCCACACGTCCAA
TAGCACTCTCACCGAAATCCGCAACAATGTTATCCGTTTCACGGATAGGATCATGAAGCACCTT
GAAACTTGCAGGCATCACACCTTCTCCTAACTTAAACCGATCCACACGTTTCTCCCAACCTTGC
AGCTGAAGTGTCTTAAGCAAAAAATGCTTCACTATATCCGGTTCTCCATTCATCAGAAACGCCA
ACGCACTCGGTACAAAATCCCTCACAAACACCTGATCATAGTTCAAGACTTCATCGGTAGTATT
ATCAACCGCGGCAAGAGTACCAACAGGTTGACCACGGAAGAAGACCATTGACCTTCTTAAAGCC
TCCCAAGCTTCAGCCATCATAGGATGAGGCTCAAAGGAGTTTCTAGCAGAAGAAAGAGGCGTAT
CAAGCACCGATCTACCTCGCGGCGAATCGTGTATACCGTCATGTCTACTGTAACCAGTCGATAG
CTCACTCATCGATCTTTCATCAAACGATCTCTTCCTTTCGATCTTCAATCTTGGTTTATCCAAA
GCTCGAGTCAAATCAAGATCATCCATCTCAGATAAAGAACAGTGTGATCCTACAGCTCTTAGTC
CAACACCTTCCATTATAACACTAAACCAAGAT
						
					

						Genomic sequence
						
							CTGGCCAAGATCCACCATTGTGGTAGCTCCACCGTGTGTTCTTGGGGTCACAGCCAGTAACGAT
GCGCCACTCATGGCCCTCGAGGCATGGATAACAAATCTTGAGAGGCATCTCACCTACAAGCTCT
GCCCACCGGTGCTCAAGGAGGTCCATAATGGCCATGGATTGATCTGGAGTGGCCAATGAAGAAA
GTATGGAGACACAATTACCGAGTGCGAACCACCGGAAATCCATATGGGCAGGTCCTACGTTTCC
CACAAAGTAGCCTCCACGGAGAGGCATGAAGTCGAAAACCCACTCGGGTATAGAATCAGGCATC
ACATTGAACTTGTTCACCGCCGTGTGAGAGTATTCCTCAGTCTTGAACCTTTTTAAACAAATGT
ACTATAAGTTATAGTGATCTTTTGTGACTCTACATATCATCTAAAGCAAATGAAATAACTATAC
CTGTAAATGTCATTGAGGTTCTGATGATCAAGCCAGAAGTAATTGCGCATATGGAAGCTCAAGG
CATGAAGTCGCTTAACGATCCTCTCAATGACCTCTCTGCCATCTCCATCGGGCTTTAACATCGA
CAAAGCAGATCTCAAAGCCATGAAGAACAACGCTTGGATCTCAATGGGATACCCATAAACACCC
TTCAAATACAGGAAAAAAAAGAAATCAATCTTAATAGCCAAACAAAACAAGAAACAACAATCAG
TTTCGATCAAAGATTGCTTTTAATACCATTCTTCGATCAATCATGGAACATCCATCAGCACAAA
GCAGTGTAGGAAACGTGTCAAACCCTTCAGCTAAGCACAAAGACAAGATCAGTTTCATTCCCTT
TTGACACTCTGGTGTCTCAGAGAGAGTCAAATCTCCAGTAGATTTGGTATAAGCACGAAGAAGA
ATAATCCACCAGAACCCTGAATCTACAGGAGCCACACGTCCAATAGCACTCTCACCGAAATCCG
CAACAATGTTATCCGTTTCACGGATAGGATCATGAAGCACCTTGAAACTTGCAGGCATCACACC
TTCTCCTAACTTAAACCGATCCACACGTTTCTCCCAACCTTGCAGCTGAAGTGTCTTAAGCAAA
AAATGCTTCACTATATCCGGTTCTCCATTCATCAGAAACGCCAACGCACTCGGTACAAAATCCC
TCACAAACACCTACAACAACCGCAAAAAAAACATTTTGAAACGTTTTGAGATAAAACCATGAAA
ACTTTTCGATAGTTTTACCTGATCATAGTTCAAGACTTCATCGGTAGTATTATCAACCGCGGCA
AGAGTACCAACAGGTTGACCACGGAAGAAGACCATTGACCTTCTTAAAGCCTCCCAAGCTTCAG
CCATCATAGGATGAGGCTCAAAGGAGTTTCTAGCAGAAGAAAGAGGCGTATCAAGCACCGATCT
ACCTCGCGGCGAATCGTGTATACCGTCATGTCTACTGTAACCAGTCGATAGCTCACTCATCGAT
CTTTCATCAAACGATCTCTTCCTTTCGATCTTCAATCTTGGTTTATCCAAAGCTCGAGTCAAAT
CAAGATCATCCATCTCAGATAAAGAACAGTGTGATCCTACAGCTCTTAGTCCAACACCTTCCAT
TATAACACTAAACCAAGAT
						
					

			
		

Sequences
Splice junction sequence	CAAAGCTCGAGTCAAATCAAGATCATCCATCTCAGATAAAGAACAGTGTGATCCTACAGCTCTT AGTCCAACACCTTCCATTATAACACTAAACCAAGATctggccaagatccaccattgtggtagct ccaccgtgtgttcttggggtcacagccagtaacgatgcgccactcatggccctcgaggcatgga taacaaat
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: 1376 Transcript exons: 13123209-13123576,13123657-13123847,13123939-13124370,13 124443-13124827 CTGGCCAAGATCCACCATTGTGGTAGCTCCACCGTGTGTTCTTGGGGTCACAGCCAGTAACGAT GCGCCACTCATGGCCCTCGAGGCATGGATAACAAATCTTGAGAGGCATCTCACCTACAAGCTCT GCCCACCGGTGCTCAAGGAGGTCCATAATGGCCATGGATTGATCTGGAGTGGCCAATGAAGAAA GTATGGAGACACAATTACCGAGTGCGAACCACCGGAAATCCATATGGGCAGGTCCTACGTTTCC CACAAAGTAGCCTCCACGGAGAGGCATGAAGTCGAAAACCCACTCGGGTATAGAATCAGGCATC ACATTGAACTTGTTCACCGCCGTGTGAGAGTATTCCTCAGTCTTGAACCTGTAAATGTCATTGA GGTTCTGATGATCAAGCCAGAAGTAATTGCGCATATGGAAGCTCAAGGCATGAAGTCGCTTAAC GATCCTCTCAATGACCTCTCTGCCATCTCCATCGGGCTTTAACATCGACAAAGCAGATCTCAAA GCCATGAAGAACAACGCTTGGATCTCAATGGGATACCCATAAACACCCATTCTTCGATCAATCA TGGAACATCCATCAGCACAAAGCAGTGTAGGAAACGTGTCAAACCCTTCAGCTAAGCACAAAGA CAAGATCAGTTTCATTCCCTTTTGACACTCTGGTGTCTCAGAGAGAGTCAAATCTCCAGTAGAT TTGGTATAAGCACGAAGAAGAATAATCCACCAGAACCCTGAATCTACAGGAGCCACACGTCCAA TAGCACTCTCACCGAAATCCGCAACAATGTTATCCGTTTCACGGATAGGATCATGAAGCACCTT GAAACTTGCAGGCATCACACCTTCTCCTAACTTAAACCGATCCACACGTTTCTCCCAACCTTGC AGCTGAAGTGTCTTAAGCAAAAAATGCTTCACTATATCCGGTTCTCCATTCATCAGAAACGCCA ACGCACTCGGTACAAAATCCCTCACAAACACCTGATCATAGTTCAAGACTTCATCGGTAGTATT ATCAACCGCGGCAAGAGTACCAACAGGTTGACCACGGAAGAAGACCATTGACCTTCTTAAAGCC TCCCAAGCTTCAGCCATCATAGGATGAGGCTCAAAGGAGTTTCTAGCAGAAGAAAGAGGCGTAT CAAGCACCGATCTACCTCGCGGCGAATCGTGTATACCGTCATGTCTACTGTAACCAGTCGATAG CTCACTCATCGATCTTTCATCAAACGATCTCTTCCTTTCGATCTTCAATCTTGGTTTATCCAAA GCTCGAGTCAAATCAAGATCATCCATCTCAGATAAAGAACAGTGTGATCCTACAGCTCTTAGTC CAACACCTTCCATTATAACACTAAACCAAGAT
Genomic sequence	CTGGCCAAGATCCACCATTGTGGTAGCTCCACCGTGTGTTCTTGGGGTCACAGCCAGTAACGAT GCGCCACTCATGGCCCTCGAGGCATGGATAACAAATCTTGAGAGGCATCTCACCTACAAGCTCT GCCCACCGGTGCTCAAGGAGGTCCATAATGGCCATGGATTGATCTGGAGTGGCCAATGAAGAAA GTATGGAGACACAATTACCGAGTGCGAACCACCGGAAATCCATATGGGCAGGTCCTACGTTTCC CACAAAGTAGCCTCCACGGAGAGGCATGAAGTCGAAAACCCACTCGGGTATAGAATCAGGCATC ACATTGAACTTGTTCACCGCCGTGTGAGAGTATTCCTCAGTCTTGAACCTTTTTAAACAAATGT ACTATAAGTTATAGTGATCTTTTGTGACTCTACATATCATCTAAAGCAAATGAAATAACTATAC CTGTAAATGTCATTGAGGTTCTGATGATCAAGCCAGAAGTAATTGCGCATATGGAAGCTCAAGG CATGAAGTCGCTTAACGATCCTCTCAATGACCTCTCTGCCATCTCCATCGGGCTTTAACATCGA CAAAGCAGATCTCAAAGCCATGAAGAACAACGCTTGGATCTCAATGGGATACCCATAAACACCC TTCAAATACAGGAAAAAAAAGAAATCAATCTTAATAGCCAAACAAAACAAGAAACAACAATCAG TTTCGATCAAAGATTGCTTTTAATACCATTCTTCGATCAATCATGGAACATCCATCAGCACAAA GCAGTGTAGGAAACGTGTCAAACCCTTCAGCTAAGCACAAAGACAAGATCAGTTTCATTCCCTT TTGACACTCTGGTGTCTCAGAGAGAGTCAAATCTCCAGTAGATTTGGTATAAGCACGAAGAAGA ATAATCCACCAGAACCCTGAATCTACAGGAGCCACACGTCCAATAGCACTCTCACCGAAATCCG CAACAATGTTATCCGTTTCACGGATAGGATCATGAAGCACCTTGAAACTTGCAGGCATCACACC TTCTCCTAACTTAAACCGATCCACACGTTTCTCCCAACCTTGCAGCTGAAGTGTCTTAAGCAAA AAATGCTTCACTATATCCGGTTCTCCATTCATCAGAAACGCCAACGCACTCGGTACAAAATCCC TCACAAACACCTACAACAACCGCAAAAAAAACATTTTGAAACGTTTTGAGATAAAACCATGAAA ACTTTTCGATAGTTTTACCTGATCATAGTTCAAGACTTCATCGGTAGTATTATCAACCGCGGCA AGAGTACCAACAGGTTGACCACGGAAGAAGACCATTGACCTTCTTAAAGCCTCCCAAGCTTCAG CCATCATAGGATGAGGCTCAAAGGAGTTTCTAGCAGAAGAAAGAGGCGTATCAAGCACCGATCT ACCTCGCGGCGAATCGTGTATACCGTCATGTCTACTGTAACCAGTCGATAGCTCACTCATCGAT CTTTCATCAAACGATCTCTTCCTTTCGATCTTCAATCTTGGTTTATCCAAAGCTCGAGTCAAAT CAAGATCATCCATCTCAGATAAAGAACAGTGTGATCCTACAGCTCTTAGTCCAACACCTTCCAT TATAACACTAAACCAAGAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.481807723

Conservation Information
Conserved circRNAs	NA
PMCS	0.481807723

			
						 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

circRNA

Detail information of AT1G35580_circ_g.1

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