Plant Circular RNA Database

Detail information of AT3G01540_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G01540_circ_g.3
					
						ID in PlantcircBase
						ath_circ_019148
					
						Alias
						At_ciR3055, Ath_circ_FC1761, AT3G01540_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 213716-213993  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT3G01540						
					
						Parent gene annotation
						
							DEAD-box ATP-dependent RNA helicase 14
							
						Parent gene strand
						-
					
						Alternative splicing
						
							3_circ_ag.1 AT3G01540_circ_g.1 AT3G01540_circ_g.2 AT3G01540_circ_g.4 AT3G01540_circ_g.5 AT3G01540_circ_g.6 AT3G01540_circ_g.7 AT3G01560_circ_g.1 AT3G01560_circ_g.2 AT3G01560_circ_g.3 AT3G01560_circ_g.4 AT3G01560_circ_g.5 AT3G01560_circ_g.6 AT3G01590_circ_g.1 AT3G01590_circ_g.2 AT3G01590_circ_g.3 AT3G01590_circ_g.4 AT3G01600_circ_g.1 AT3G01610_circ_g.1 AT3G01640_circ_g.1 AT3G01650_circ_g.1 AT3G01650_circ_g.2 AT3G01650_circ_g.3 AT3G01650_circ_g.4 AT3G01650_circ_g.5 AT3G01650_circ_g.6 AT3G01670_circ_g.1 AT3G01670_circ_g.2 AT3G01670_circ_g.3 AT3G01680_circ_g.1 AT3G01690_circ_g.1 AT3G01690_circ_g.2 AT3G01710_circ_g.1 AT3G01720_circ_g.1 AT3G01720_circ_g.2 AT3G01770_circ_g.1 AT3G01770_circ_g.2 						
					
						Support reads
						2/57/6
					
						Tissues
						leaf/inflorescences, whole_plant/seedlings
					
						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
						AT3G01540.4:1
AT3G01540.2:1
AT3G01540.1:1
AT3G01540.3:1

General Information
CircRNA Name	AT3G01540_circ_g.3
ID in PlantcircBase	ath_circ_019148
Alias	At_ciR3055, Ath_circ_FC1761, AT3G01540_C1
Organism	Arabidpsis thaliana
Position	chr3: 213716-213993 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ, CIRI-full, CIRI2
Parent gene	AT3G01540
Parent gene annotation	DEAD-box ATP-dependent RNA helicase 14
Parent gene strand	-
Alternative splicing	3_circ_ag.1 AT3G01540_circ_g.1 AT3G01540_circ_g.2 AT3G01540_circ_g.4 AT3G01540_circ_g.5 AT3G01540_circ_g.6 AT3G01540_circ_g.7 AT3G01560_circ_g.1 AT3G01560_circ_g.2 AT3G01560_circ_g.3 AT3G01560_circ_g.4 AT3G01560_circ_g.5 AT3G01560_circ_g.6 AT3G01590_circ_g.1 AT3G01590_circ_g.2 AT3G01590_circ_g.3 AT3G01590_circ_g.4 AT3G01600_circ_g.1 AT3G01610_circ_g.1 AT3G01640_circ_g.1 AT3G01650_circ_g.1 AT3G01650_circ_g.2 AT3G01650_circ_g.3 AT3G01650_circ_g.4 AT3G01650_circ_g.5 AT3G01650_circ_g.6 AT3G01670_circ_g.1 AT3G01670_circ_g.2 AT3G01670_circ_g.3 AT3G01680_circ_g.1 AT3G01690_circ_g.1 AT3G01690_circ_g.2 AT3G01710_circ_g.1 AT3G01720_circ_g.1 AT3G01720_circ_g.2 AT3G01770_circ_g.1 AT3G01770_circ_g.2
Support reads	2/57/6
Tissues	leaf/inflorescences, whole_plant/seedlings
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	AT3G01540.4:1 AT3G01540.2:1 AT3G01540.1:1 AT3G01540.3:1

			
						 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  
						
							TGGTTGAGCAGAATATTATCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCT
CCTCTGTTTCTCCATTGGTGCTACCACTTCAATATGctgatgtccttaacgtccagaccacgag
cagcaacatcggttgctacaagaaccggagttctgccactgcggaattgattaagaacattgtc
tctctcag

						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: 277
Transcript exons: 213716-213910,213912-213993
CTGATGTCCTTAACGTCCAGACCACGAGCAGCAACATCGGTTGCTACAAGAACCGGAGTTCTGC
CACTGCGGAATTGATTAAGAACATTGTCTCTCTCAGGCTGGGACTTGTCTCCATGTATAGCAGC
AGCTCCAAATTGGCGGGTTAGATTGCGTGTTAGTTGATCACACATCCTTTTGGTTGAGCAGAAT
ATTTCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCTCCTCTGTTTCTCCAT
TGGTGCTACCACTTCAATATG
Transcript length: 278
Transcript exons: 213716-213993
CTGATGTCCTTAACGTCCAGACCACGAGCAGCAACATCGGTTGCTACAAGAACCGGAGTTCTGC
CACTGCGGAATTGATTAAGAACATTGTCTCTCTCAGGCTGGGACTTGTCTCCATGTATAGCAGC
AGCTCCAAATTGGCGGGTTAGATTGCGTGTTAGTTGATCACACATCCTTTTGGTTGAGCAGAAT
ATTATCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCTCCTCTGTTTCTCCA
TTGGTGCTACCACTTCAATATG
						
						Genomic sequence
						
							CTGATGTCCTTAACGTCCAGACCACGAGCAGCAACATCGGTTGCTACAAGAACCGGAGTTCTGC
CACTGCGGAATTGATTAAGAACATTGTCTCTCTCAGGCTGGGACTTGTCTCCATGTATAGCAGC
AGCTCCAAATTGGCGGGTTAGATTGCGTGTTAGTTGATCACACATCCTTTTGGTTGAGCAGAAT
ATTATCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCTCCTCTGTTTCTCCA
TTGGTGCTACCACTTCAATATG

Sequences
Splice junction sequence	TGGTTGAGCAGAATATTATCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCT CCTCTGTTTCTCCATTGGTGCTACCACTTCAATATGctgatgtccttaacgtccagaccacgag cagcaacatcggttgctacaagaaccggagttctgccactgcggaattgattaagaacattgtc tctctcag
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: 277 Transcript exons: 213716-213910,213912-213993 CTGATGTCCTTAACGTCCAGACCACGAGCAGCAACATCGGTTGCTACAAGAACCGGAGTTCTGC CACTGCGGAATTGATTAAGAACATTGTCTCTCTCAGGCTGGGACTTGTCTCCATGTATAGCAGC AGCTCCAAATTGGCGGGTTAGATTGCGTGTTAGTTGATCACACATCCTTTTGGTTGAGCAGAAT ATTTCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCTCCTCTGTTTCTCCAT TGGTGCTACCACTTCAATATG Transcript length: 278 Transcript exons: 213716-213993 CTGATGTCCTTAACGTCCAGACCACGAGCAGCAACATCGGTTGCTACAAGAACCGGAGTTCTGC CACTGCGGAATTGATTAAGAACATTGTCTCTCTCAGGCTGGGACTTGTCTCCATGTATAGCAGC AGCTCCAAATTGGCGGGTTAGATTGCGTGTTAGTTGATCACACATCCTTTTGGTTGAGCAGAAT ATTATCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCTCCTCTGTTTCTCCA TTGGTGCTACCACTTCAATATG
Genomic sequence	CTGATGTCCTTAACGTCCAGACCACGAGCAGCAACATCGGTTGCTACAAGAACCGGAGTTCTGC CACTGCGGAATTGATTAAGAACATTGTCTCTCTCAGGCTGGGACTTGTCTCCATGTATAGCAGC AGCTCCAAATTGGCGGGTTAGATTGCGTGTTAGTTGATCACACATCCTTTTGGTTGAGCAGAAT ATTATCACCTTTGAGCCTGGTTCCTGAGACCGCAAGATCTGCTCTAACCTCCTCTGTTTCTCCA TTGGTGCTACCACTTCAATATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.736550062

Conservation Information
Conserved circRNAs	NA
PMCS	0.736550062

			
						 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; responsive to heat 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; responsive to heat stress

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017;Pan et al., 2017;Chen et al., 2017a;Zhang et al., 2019

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Detail information of AT3G01540_circ_g.3

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