Plant Circular RNA Database

Detail information of AT1G05960_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT1G05960_circ_g.7
					
						ID in PlantcircBase
						ath_circ_000918
					
						Alias
						AT1G05960_C4
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 1813386-1815085  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, CIRI2
					
						Parent gene
						
							AT1G05960						
					
						Parent gene annotation
						
							ARM repeat superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G05960_circ_g.8 AT1G05960_circ_g.9 AT1G05960_circ_g.10 AT1G05960_circ_g.11 						
					
						Support reads
						4/8
					
						Tissues
						seed, whole_plant/seedlings, 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
						AT1G05960.2:7
AT1G05960.1:6
AT1G05960.4:6
AT1G05960.3:6

General Information
CircRNA Name	AT1G05960_circ_g.7
ID in PlantcircBase	ath_circ_000918
Alias	AT1G05960_C4
Organism	Arabidpsis thaliana
Position	chr1: 1813386-1815085 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, CIRI2
Parent gene	AT1G05960
Parent gene annotation	ARM repeat superfamily protein
Parent gene strand	-
Alternative splicing	AT1G05960_circ_g.8 AT1G05960_circ_g.9 AT1G05960_circ_g.10 AT1G05960_circ_g.11
Support reads	4/8
Tissues	seed, whole_plant/seedlings, 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	AT1G05960.2:7 AT1G05960.1:6 AT1G05960.4:6 AT1G05960.3:6

			
						 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  
						
							CCTTGCCCTCAAAGAAGGACAGAAGAAACAGAGGTTACCACAGGCGGGCAAAACCCGTCTGGAC
ATAACCCCCATTTTCTTCTCCGCCTAATATCCCCCCcatatccaagtccattgatagttgggaa
tgctcaccaatgaaagatacctggtattaactattgattagtagcaaaagttccaagcagaaac
agttgtgg

									
								

					

						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: 643
Transcript exons: 1813386-1813433,1813927-1814055,1814144-1814258,1814447-
1814562,1814659-1814733,1814926-1815085
CATATCCAAGTCCATTGATAGTTGGGAATGCTCACCAATGAAAGATACCATGAATGCCAAAGCC
TGCATTCCTGCTGACCGTAATTGGAGTGATCTTTCATCATCACCCATTTCTTGAGCAAGTTGAC
AAAGTTTAGGGATTAGACCTTCTAAGTTGAACATGTGCGAATTCACAGTCTGTAAACTTATAAA
GTCGACAAGAGTATTGCAACCCAAGATCTGAACTTCTTCCTCTTTTGTTTGCTCCAAAAGAGTT
CTGACAATGCTTAGCAAACTACACGAAAAAAGAGGCATCTGCTCCTTACATGATGAAAGCAGTT
TCTTATAAATGCATAAGACGACTTTCACTGAACCAATATTTCCATTTCGCAATTCTTTGTAACA
TTTTTGCTCAAGGTACTCTGTAATCTTTGGAATTCGTAAAGGATTCCTAGACGCATACTCACAC
AGCTTGCCGATTTTTCTATCATTAGGCTCAGCTTCCTGATTACGAGGGAAGATTTCAGCGAGCA
TTTTCTTGTAGCGTTTAACGGGATGCCTAGACCTTGCCCTCAAAGAAGGACAGAAGAAACAGAG
GTTACCACAGGCGGGCAAAACCCGTCTGGACATAACCCCCATTTTCTTCTCCGCCTAATATCCC
CCC
Transcript length: 706
Transcript exons: 1813386-1813433,1813927-1814055,1814144-1814258,1814328-
1814390,1814447-1814562,1814659-1814733,1814926-1815085
CATATCCAAGTCCATTGATAGTTGGGAATGCTCACCAATGAAAGATACCATGAATGCCAAAGCC
TGCATTCCTGCTGACCGTAATTGGAGTGATCTTTCATCATCACCCATTTCTTGAGCAAGTTGAC
AAAGTTTAGGGATTAGACCTTCTAAGTTGAACATGTGCGAATTCACAGTCTGTAAACTTATAAA
GTCGACAAGAGTATTGCAACCCAAGATCTGAACTTCTTCCTCTTTTGTTTGCTCCAAAAGAGTT
CTGACAATGCTTAGCAAACTACACGAAAAAAGAGGCAGGAATTCGAAAGTAAATGATCGAGCAA
CAAGAAAGAAAAAAGTAAGCATTATTTCTGAAGATATCTGCTCCTTACATGATGAAAGCAGTTT
CTTATAAATGCATAAGACGACTTTCACTGAACCAATATTTCCATTTCGCAATTCTTTGTAACAT
TTTTGCTCAAGGTACTCTGTAATCTTTGGAATTCGTAAAGGATTCCTAGACGCATACTCACACA
GCTTGCCGATTTTTCTATCATTAGGCTCAGCTTCCTGATTACGAGGGAAGATTTCAGCGAGCAT
TTTCTTGTAGCGTTTAACGGGATGCCTAGACCTTGCCCTCAAAGAAGGACAGAAGAAACAGAGG
TTACCACAGGCGGGCAAAACCCGTCTGGACATAACCCCCATTTTCTTCTCCGCCTAATATCCCC
CC
						
					

						Genomic sequence
						
							CATATCCAAGTCCATTGATAGTTGGGAATGCTCACCAATGAAAGATACCTGGTATTAACTATTG
ATTAGTAGCAAAAGTTCCAAGCAGAAACAGTTGTGGACTTTGCACCACATAAGACGAAGGTCGA
AATAAAATAGGATTTCAACTAAAGAGAAACTAACAACAGAATTCCCTTTGAACTGAAATGGAAC
TAACTAGTAAAACTAAACAGGTTGACCATAAATTCTATACTAGCTGAATAAGGACTACCATGCT
TAAAATGTTTTCTTGAACAAGAAAAAAAACTCATTAATAAAAGTGTCCGTTAACAGTTTGCAGG
TCAAAATTATTAAGTTCAAGTAAATATAACCCATTCCACTAACATAGATAATTCAAAGCAGAAG
TTCTGGCTATCTACAATAGGAAGAGCACATAACCCGTAACATGTTGCACATCTAAAGGGCATGC
AATAGGATATGTTTCGTGTGAGGAATGTATACAGCTAAAGGGCATGTTTTCTGTCAGTCAAACA
AAAGAGAAAGTAAATGGATAAAGCATTACCATGAATGCCAAAGCCTGCATTCCTGCTGACCGTA
ATTGGAGTGATCTTTCATCATCACCCATTTCTTGAGCAAGTTGACAAAGTTTAGGGATTAGACC
TTCTAAGTTGAACATGTGCGAATTCACAGTCTGTATGTAAACAGATGTGTTACCATATGTAGTG
GTAGCAGGAAAAGTAGCTTGCAAAACCATGTCTCAAAAAAATGCTAAAATGTACCTGTAAACTT
ATAAAGTCGACAAGAGTATTGCAACCCAAGATCTGAACTTCTTCCTCTTTTGTTTGCTCCAAAA
GAGTTCTGACAATGCTTAGCAAACTACACGAAAAAAGAGGCCTACAAGAAAAATAGACAGTCTC
AGTAAAACGTAAATAAGGAACCTGGAAAGAAACCTATAAAACATACAGGAATTCGAAAGTAAAT
GATCGAGCAACAAGAAAGAAAAAAGTAAGCATTATTTCTGAAGATCTAATTTAACAAAAGCGAA
ATATGATATACTGATTCTAAGTAACCAGTTGACTTACATCTGCTCCTTACATGATGAAAGCAGT
TTCTTATAAATGCATAAGACGACTTTCACTGAACCAATATTTCCATTTCGCAATTCTTTGTAAC
ATTTTTGCTCAAGGTACTCTGTAATCTGTCATAATGGAAAACTGAAACACATGAGAATAAAATT
GAGAGAAGTATGCTAAGAAAATTGAAAAGGGAATAACAGAAAAAAAAATGCAACAACCTTTGGA
ATTCGTAAAGGATTCCTAGACGCATACTCACACAGCTTGCCGATTTTTCTATCATTAGGCTCAG
CTTCCTGCCAAATCACAACATAGAAAAATGTTGAAACTTGTATCATTCCGTGTAGCAAACCTCA
TTTTAGTTTCATTGGGAATCCATTCCACTTACATTTCCCCACTTACAATTAGAGAGATCTTAAC
TAGTACACACAAAAAAAAATTGAAAATAAAGAAGTTCTCCAATCAAAGAGTGGGTAAGGAAAAA
AGACCTGATTACGAGGGAAGATTTCAGCGAGCATTTTCTTGTAGCGTTTAACGGGATGCCTAGA
CCTTGCCCTCAAAGAAGGACAGAAGAAACAGAGGTTACCACAGGCGGGCAAAACCCGTCTGGAC
ATAACCCCCATTTTCTTCTCCGCCTAATATCCCCCC
						
					

			
		

Sequences
Splice junction sequence	CCTTGCCCTCAAAGAAGGACAGAAGAAACAGAGGTTACCACAGGCGGGCAAAACCCGTCTGGAC ATAACCCCCATTTTCTTCTCCGCCTAATATCCCCCCcatatccaagtccattgatagttgggaa tgctcaccaatgaaagatacctggtattaactattgattagtagcaaaagttccaagcagaaac agttgtgg
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: 643 Transcript exons: 1813386-1813433,1813927-1814055,1814144-1814258,1814447- 1814562,1814659-1814733,1814926-1815085 CATATCCAAGTCCATTGATAGTTGGGAATGCTCACCAATGAAAGATACCATGAATGCCAAAGCC TGCATTCCTGCTGACCGTAATTGGAGTGATCTTTCATCATCACCCATTTCTTGAGCAAGTTGAC AAAGTTTAGGGATTAGACCTTCTAAGTTGAACATGTGCGAATTCACAGTCTGTAAACTTATAAA GTCGACAAGAGTATTGCAACCCAAGATCTGAACTTCTTCCTCTTTTGTTTGCTCCAAAAGAGTT CTGACAATGCTTAGCAAACTACACGAAAAAAGAGGCATCTGCTCCTTACATGATGAAAGCAGTT TCTTATAAATGCATAAGACGACTTTCACTGAACCAATATTTCCATTTCGCAATTCTTTGTAACA TTTTTGCTCAAGGTACTCTGTAATCTTTGGAATTCGTAAAGGATTCCTAGACGCATACTCACAC AGCTTGCCGATTTTTCTATCATTAGGCTCAGCTTCCTGATTACGAGGGAAGATTTCAGCGAGCA TTTTCTTGTAGCGTTTAACGGGATGCCTAGACCTTGCCCTCAAAGAAGGACAGAAGAAACAGAG GTTACCACAGGCGGGCAAAACCCGTCTGGACATAACCCCCATTTTCTTCTCCGCCTAATATCCC CCC Transcript length: 706 Transcript exons: 1813386-1813433,1813927-1814055,1814144-1814258,1814328- 1814390,1814447-1814562,1814659-1814733,1814926-1815085 CATATCCAAGTCCATTGATAGTTGGGAATGCTCACCAATGAAAGATACCATGAATGCCAAAGCC TGCATTCCTGCTGACCGTAATTGGAGTGATCTTTCATCATCACCCATTTCTTGAGCAAGTTGAC AAAGTTTAGGGATTAGACCTTCTAAGTTGAACATGTGCGAATTCACAGTCTGTAAACTTATAAA GTCGACAAGAGTATTGCAACCCAAGATCTGAACTTCTTCCTCTTTTGTTTGCTCCAAAAGAGTT CTGACAATGCTTAGCAAACTACACGAAAAAAGAGGCAGGAATTCGAAAGTAAATGATCGAGCAA CAAGAAAGAAAAAAGTAAGCATTATTTCTGAAGATATCTGCTCCTTACATGATGAAAGCAGTTT CTTATAAATGCATAAGACGACTTTCACTGAACCAATATTTCCATTTCGCAATTCTTTGTAACAT TTTTGCTCAAGGTACTCTGTAATCTTTGGAATTCGTAAAGGATTCCTAGACGCATACTCACACA GCTTGCCGATTTTTCTATCATTAGGCTCAGCTTCCTGATTACGAGGGAAGATTTCAGCGAGCAT TTTCTTGTAGCGTTTAACGGGATGCCTAGACCTTGCCCTCAAAGAAGGACAGAAGAAACAGAGG TTACCACAGGCGGGCAAAACCCGTCTGGACATAACCCCCATTTTCTTCTCCGCCTAATATCCCC CC
Genomic sequence	CATATCCAAGTCCATTGATAGTTGGGAATGCTCACCAATGAAAGATACCTGGTATTAACTATTG ATTAGTAGCAAAAGTTCCAAGCAGAAACAGTTGTGGACTTTGCACCACATAAGACGAAGGTCGA AATAAAATAGGATTTCAACTAAAGAGAAACTAACAACAGAATTCCCTTTGAACTGAAATGGAAC TAACTAGTAAAACTAAACAGGTTGACCATAAATTCTATACTAGCTGAATAAGGACTACCATGCT TAAAATGTTTTCTTGAACAAGAAAAAAAACTCATTAATAAAAGTGTCCGTTAACAGTTTGCAGG TCAAAATTATTAAGTTCAAGTAAATATAACCCATTCCACTAACATAGATAATTCAAAGCAGAAG TTCTGGCTATCTACAATAGGAAGAGCACATAACCCGTAACATGTTGCACATCTAAAGGGCATGC AATAGGATATGTTTCGTGTGAGGAATGTATACAGCTAAAGGGCATGTTTTCTGTCAGTCAAACA AAAGAGAAAGTAAATGGATAAAGCATTACCATGAATGCCAAAGCCTGCATTCCTGCTGACCGTA ATTGGAGTGATCTTTCATCATCACCCATTTCTTGAGCAAGTTGACAAAGTTTAGGGATTAGACC TTCTAAGTTGAACATGTGCGAATTCACAGTCTGTATGTAAACAGATGTGTTACCATATGTAGTG GTAGCAGGAAAAGTAGCTTGCAAAACCATGTCTCAAAAAAATGCTAAAATGTACCTGTAAACTT ATAAAGTCGACAAGAGTATTGCAACCCAAGATCTGAACTTCTTCCTCTTTTGTTTGCTCCAAAA GAGTTCTGACAATGCTTAGCAAACTACACGAAAAAAGAGGCCTACAAGAAAAATAGACAGTCTC AGTAAAACGTAAATAAGGAACCTGGAAAGAAACCTATAAAACATACAGGAATTCGAAAGTAAAT GATCGAGCAACAAGAAAGAAAAAAGTAAGCATTATTTCTGAAGATCTAATTTAACAAAAGCGAA ATATGATATACTGATTCTAAGTAACCAGTTGACTTACATCTGCTCCTTACATGATGAAAGCAGT TTCTTATAAATGCATAAGACGACTTTCACTGAACCAATATTTCCATTTCGCAATTCTTTGTAAC ATTTTTGCTCAAGGTACTCTGTAATCTGTCATAATGGAAAACTGAAACACATGAGAATAAAATT GAGAGAAGTATGCTAAGAAAATTGAAAAGGGAATAACAGAAAAAAAAATGCAACAACCTTTGGA ATTCGTAAAGGATTCCTAGACGCATACTCACACAGCTTGCCGATTTTTCTATCATTAGGCTCAG CTTCCTGCCAAATCACAACATAGAAAAATGTTGAAACTTGTATCATTCCGTGTAGCAAACCTCA TTTTAGTTTCATTGGGAATCCATTCCACTTACATTTCCCCACTTACAATTAGAGAGATCTTAAC TAGTACACACAAAAAAAAATTGAAAATAAAGAAGTTCTCCAATCAAAGAGTGGGTAAGGAAAAA AGACCTGATTACGAGGGAAGATTTCAGCGAGCATTTTCTTGTAGCGTTTAACGGGATGCCTAGA CCTTGCCCTCAAAGAAGGACAGAAGAAACAGAGGTTACCACAGGCGGGCAAAACCCGTCTGGAC ATAACCCCCATTTTCTTCTCCGCCTAATATCCCCCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.313514142

Conservation Information
Conserved circRNAs	NA
PMCS	0.313514142

			
						 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
						response to drought stress

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	response to drought stress

			
						 Other Information
					
						References
						Chu et al., 2017;Pan et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT1G05960_circ_g.7

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