Plant Circular RNA Database

Detail information of AT5G46280_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G46280_circ_g.1
					
						ID in PlantcircBase
						ath_circ_042664
					
						Alias
						At_ciR1359, Ath_circ_FC0079, AT5G46280_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 18770049-18770268  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
					
						Parent gene
						
							AT5G46280						
					
						Parent gene annotation
						
							DNA replication licensing factor MCM3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3/6
					
						Tissues
						leaf/root, aerial, seed, 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
						AT5G46280.3:1
AT5G46280.2:1
AT5G46280.4:1
AT5G46280.1:1

General Information
CircRNA Name	AT5G46280_circ_g.1
ID in PlantcircBase	ath_circ_042664
Alias	At_ciR1359, Ath_circ_FC0079, AT5G46280_C1
Organism	Arabidpsis thaliana
Position	chr5: 18770049-18770268 JBrowse»
Reference genome	TAIR10.38
Type	u-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI-full, CIRI2
Parent gene	AT5G46280
Parent gene annotation	DNA replication licensing factor MCM3
Parent gene strand	-
Alternative splicing	NA
Support reads	3/6
Tissues	leaf/root, aerial, seed, 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	AT5G46280.3:1 AT5G46280.2:1 AT5G46280.4:1 AT5G46280.1:1

			
						 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  
						
							CCCAAACACTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACA
GAAGGTTCATCTACTTCCATTGGATCTGCTGTTTCActctaagagagccataatctcatctgca
gagtaacgagatgctccaaccccattgttgttgacaacagtctctatatctgcaatagagatgt
catcgagc

									
								

					

						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: 163
Transcript exons: 18770049-18770084,18770142-18770268
CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGATCGAGCCTGTGTGTCCTCATGTGCTGC
CCAAACACTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAG
AAGGTTCATCTACTTCCATTGGATCTGCTGTTTCA
Transcript length: 201
Transcript exons: 18770049-18770125,18770145-18770268
CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA
ACAGTCTCTATATGAGCCTGTGTGTCCTCATGTGCTGCCCAAACACTCGCTCAAAGGTTTCAAT
CCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTCATCTACTTCCATTGGATCT
GCTGTTTCA
Transcript length: 220
Transcript exons: 18770049-18770268
CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA
ACAGTCTCTATATCTGCAATAGAGATGTCATCGAGCCTGTGTGTCCTCATGTGCTGCCCAAACA
CTCGCTCAAAGGTTTCAATCCTTACTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTC
ATCTACTTCCATTGGATCTGCTGTTTCA
Transcript length: 220
Transcript exons: 18770049-18770268
CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA
ACAGTCTCTATATCTGCAATAGAGATGTCATCGAGCCTGTGTGTCCTCATGTGCTGCCCAAACA
CTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTC
ATCTACTTCCATTGGATCTGCTGTTTCA
						
					

						Genomic sequence
						
							CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA
ACAGTCTCTATATCTGCAATAGAGATGTCATCGAGCCTGTGTGTCCTCATGTGCTGCCCAAACA
CTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTC
ATCTACTTCCATTGGATCTGCTGTTTCA
						
					

			
		

Sequences
Splice junction sequence	CCCAAACACTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACA GAAGGTTCATCTACTTCCATTGGATCTGCTGTTTCActctaagagagccataatctcatctgca gagtaacgagatgctccaaccccattgttgttgacaacagtctctatatctgcaatagagatgt catcgagc
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: 163 Transcript exons: 18770049-18770084,18770142-18770268 CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGATCGAGCCTGTGTGTCCTCATGTGCTGC CCAAACACTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAG AAGGTTCATCTACTTCCATTGGATCTGCTGTTTCA Transcript length: 201 Transcript exons: 18770049-18770125,18770145-18770268 CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA ACAGTCTCTATATGAGCCTGTGTGTCCTCATGTGCTGCCCAAACACTCGCTCAAAGGTTTCAAT CCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTCATCTACTTCCATTGGATCT GCTGTTTCA Transcript length: 220 Transcript exons: 18770049-18770268 CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA ACAGTCTCTATATCTGCAATAGAGATGTCATCGAGCCTGTGTGTCCTCATGTGCTGCCCAAACA CTCGCTCAAAGGTTTCAATCCTTACTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTC ATCTACTTCCATTGGATCTGCTGTTTCA Transcript length: 220 Transcript exons: 18770049-18770268 CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA ACAGTCTCTATATCTGCAATAGAGATGTCATCGAGCCTGTGTGTCCTCATGTGCTGCCCAAACA CTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTC ATCTACTTCCATTGGATCTGCTGTTTCA
Genomic sequence	CTCTAAGAGAGCCATAATCTCATCTGCAGAGTAACGAGATGCTCCAACCCCATTGTTGTTGACA ACAGTCTCTATATCTGCAATAGAGATGTCATCGAGCCTGTGTGTCCTCATGTGCTGCCCAAACA CTCGCTCAAAGGTTTCAATCCTTGCTGCAGAGACCGTGCCGCTGAATTGCTCTACAGAAGGTTC ATCTACTTCCATTGGATCTGCTGTTTCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.661739394

Conservation Information
Conserved circRNAs	NA
PMCS	0.661739394

			
						 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;Zhang et al., 2019

circRNA

Detail information of AT5G46280_circ_g.1

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