Plant Circular RNA Database

Detail information of AT5G03560_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G03560_circ_g.2
					
						ID in PlantcircBase
						ath_circ_036194
					
						Alias
						At_ciR305, Ath_circ_FC3131, AT5G03560_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 900654-901168  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI, MapSplice, circRNA_finder, find_circ, CIRI2
					
						Parent gene
						
							AT5G03560						
					
						Parent gene annotation
						
							Tetratricopeptide repeat (TPR)-like superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G03560_circ_g.1 						
					
						Support reads
						37/8
					
						Tissues
						leaf/root, aerial, inflorescences, whole_plant
					
						Exon boundary  
						
							No-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
						AT5G03560.2:2
AT5G03560.4:1
AT5G03560.3:2
AT5G03560.1:2

General Information
CircRNA Name	AT5G03560_circ_g.2
ID in PlantcircBase	ath_circ_036194
Alias	At_ciR305, Ath_circ_FC3131, AT5G03560_C1
Organism	Arabidpsis thaliana
Position	chr5: 900654-901168 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRI, MapSplice, circRNA_finder, find_circ, CIRI2
Parent gene	AT5G03560
Parent gene annotation	Tetratricopeptide repeat (TPR)-like superfamily protein
Parent gene strand	-
Alternative splicing	AT5G03560_circ_g.1
Support reads	37/8
Tissues	leaf/root, aerial, inflorescences, whole_plant
Exon boundary	No-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	AT5G03560.2:2 AT5G03560.4:1 AT5G03560.3:2 AT5G03560.1:2

			
						 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  
						
							GTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATC
CTTTGCTCGACCACGTTGATTATATCAGTCTCTGACcttttggcttctgaagatgttattcttt
caagcgatcaatctctttctcccacttcagtccaaacatttgacggccgaaaggaacgatcaga
ttgtacct

									
								

					

						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: 126
Transcript exons: 900654-900702,901092-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCGTAAGTTCTCAAAGT
GGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 132
Transcript exons: 900654-900705,901089-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACGGGTAAGTTCT
CAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTC
TGAC
Transcript length: 142
Transcript exons: 900654-900698,901072-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTCAAGGGTTTGCCTTTACCG
GGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTA
TATCAGTCTCTGAC
Transcript length: 147
Transcript exons: 900654-900700,901069-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCGTTCAAGGGTTTGCCTT
TACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTT
GATTATATCAGTCTCTGAC
Transcript length: 156
Transcript exons: 900654-900704,901064-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCTGGAGGTTCAAGG
GTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTC
GACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 178
Transcript exons: 900654-900744,901082-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA
CATTTGACGGCCGAAAGGAACGATCAGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCA
TTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 180
Transcript exons: 900654-900704,901040-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCGCTGGGTCTGCGT
GAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTC
CATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 185
Transcript exons: 900654-900714,901045-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCGTC
TGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCT
TCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 192
Transcript exons: 900654-900718,901042-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA
CTGGGTCTGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAA
GTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 199
Transcript exons: 900654-900726,901043-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA
CATTTGACGGGGTCTGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGT
TCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGT
CTCTGAC
Transcript length: 211
Transcript exons: 900654-900746,901051-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA
CATTTGACGGCCGAAAGGAACGATCAGATGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTT
TACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTT
GATTATATCAGTCTCTGAC
Transcript length: 253
Transcript exons: 900654-900704,900961-901061,901068-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCGTTTCTTATCTCT
TTGTTGAGCTCCACCCATTCGGGAGCAAACCCGTTCTTGTTAAGAATCCGATACAATGTATCCT
CCGCTGGGTCTGCGTGAGGATTTGGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTG
GCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Transcript length: 300
Transcript exons: 900654-900754,900970-901168
CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA
CATTTGACGGCCGAAAGGAACGATCAGATTGTACCTGCTCTTTGTTGAGCTCCACCCATTCGGG
AGCAAACCCGTTCTTGTTAAGAATCCGATACAATGTATCCTCCGCTGGGTCTGCGTGAGGATTT
GTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAAT
GCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
						
					

						Genomic sequence
						
							CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA
CATTTGACGGCCGAAAGGAACGATCAGATTGTACCTGAATACCTGTCAACAAACAAGAGACCAC
ATAAGCAAACCATTATATATCGCAAACAGAATCTTGATTTGTAGTTGAATACTTGCCATGTTAT
TGATTTGTTTCAATTCGTTTTTCAGCAAATCTGATCTCTCTTCCCATCCCGATTGGTCTTCCTC
GAGTTTCATTGTCCATGCTTTCTTCAGTGAAACTCTCCATTCTTTTGCTTTGTTTCTTATCTCT
TTGTTGAGCTCCACCCATTCGGGAGCAAACCCGTTCTTGTTAAGAATCCGATACAATGTATCCT
CCGCTGGGTCTGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTC
AAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCT
GAC
						
					

			
		

Sequences
Splice junction sequence	GTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATC CTTTGCTCGACCACGTTGATTATATCAGTCTCTGACcttttggcttctgaagatgttattcttt caagcgatcaatctctttctcccacttcagtccaaacatttgacggccgaaaggaacgatcaga ttgtacct
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: 126 Transcript exons: 900654-900702,901092-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCGTAAGTTCTCAAAGT GGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC Transcript length: 132 Transcript exons: 900654-900705,901089-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACGGGTAAGTTCT CAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTC TGAC Transcript length: 142 Transcript exons: 900654-900698,901072-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTCAAGGGTTTGCCTTTACCG GGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTA TATCAGTCTCTGAC Transcript length: 147 Transcript exons: 900654-900700,901069-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCGTTCAAGGGTTTGCCTT TACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTT GATTATATCAGTCTCTGAC Transcript length: 156 Transcript exons: 900654-900704,901064-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCTGGAGGTTCAAGG GTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTC GACCACGTTGATTATATCAGTCTCTGAC Transcript length: 178 Transcript exons: 900654-900744,901082-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA CATTTGACGGCCGAAAGGAACGATCAGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCA TTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC Transcript length: 180 Transcript exons: 900654-900704,901040-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCGCTGGGTCTGCGT GAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTC CATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC Transcript length: 185 Transcript exons: 900654-900714,901045-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCGTC TGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCT TCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC Transcript length: 192 Transcript exons: 900654-900718,901042-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA CTGGGTCTGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAA GTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC Transcript length: 199 Transcript exons: 900654-900726,901043-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA CATTTGACGGGGTCTGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGT TCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGT CTCTGAC Transcript length: 211 Transcript exons: 900654-900746,901051-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA CATTTGACGGCCGAAAGGAACGATCAGATGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTT TACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTT GATTATATCAGTCTCTGAC Transcript length: 253 Transcript exons: 900654-900704,900961-901061,901068-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCGTTTCTTATCTCT TTGTTGAGCTCCACCCATTCGGGAGCAAACCCGTTCTTGTTAAGAATCCGATACAATGTATCCT CCGCTGGGTCTGCGTGAGGATTTGGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTG GCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC Transcript length: 300 Transcript exons: 900654-900754,900970-901168 CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA CATTTGACGGCCGAAAGGAACGATCAGATTGTACCTGCTCTTTGTTGAGCTCCACCCATTCGGG AGCAAACCCGTTCTTGTTAAGAATCCGATACAATGTATCCTCCGCTGGGTCTGCGTGAGGATTT GTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTCAAAGTGGCCTTCTTCCATTGAAT GCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCTGAC
Genomic sequence	CTTTTGGCTTCTGAAGATGTTATTCTTTCAAGCGATCAATCTCTTTCTCCCACTTCAGTCCAAA CATTTGACGGCCGAAAGGAACGATCAGATTGTACCTGAATACCTGTCAACAAACAAGAGACCAC ATAAGCAAACCATTATATATCGCAAACAGAATCTTGATTTGTAGTTGAATACTTGCCATGTTAT TGATTTGTTTCAATTCGTTTTTCAGCAAATCTGATCTCTCTTCCCATCCCGATTGGTCTTCCTC GAGTTTCATTGTCCATGCTTTCTTCAGTGAAACTCTCCATTCTTTTGCTTTGTTTCTTATCTCT TTGTTGAGCTCCACCCATTCGGGAGCAAACCCGTTCTTGTTAAGAATCCGATACAATGTATCCT CCGCTGGGTCTGCGTGAGGATTTGTATGGAGGTTCAAGGGTTTGCCTTTACCGGGTAAGTTCTC AAAGTGGCCTTCTTCCATTGAATGCCATATCCTTTGCTCGACCACGTTGATTATATCAGTCTCT GAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.796794366

Conservation Information
Conserved circRNAs	NA
PMCS	0.796794366

			
						 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
						Ye et al., 2015;Chu et al., 2017;Chen et al., 2017a;Liu et al., 2017;Zhang et al., 2019

circRNA

Detail information of AT5G03560_circ_g.2

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