Plant Circular RNA Database

Detail information of 3_circ_igg.12

			
						 General Information
					
						CircRNA Name
						3_circ_igg.12
					
						ID in PlantcircBase
						ath_circ_028943
					
						Alias
						Ath_circ_FC2488, Ath_circ_FC2489, AtciR94
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 23405523-23406369  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							igg-circRNA							
									
						Identification method
						circRNA_finder, circseq_cup, find_circ, CIRI2
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							3_circ_ag.13 						
					
						Support reads
						4
					
						Tissues
						leaf, inflorescences, whole_plant
					
						Exon boundary  
						
							Yes-No							"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  
						
							GT-AG							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
						NA

General Information
CircRNA Name	3_circ_igg.12
ID in PlantcircBase	ath_circ_028943
Alias	Ath_circ_FC2488, Ath_circ_FC2489, AtciR94
Organism	Arabidpsis thaliana
Position	chr3: 23405523-23406369 JBrowse»
Reference genome	TAIR10.38
Type	igg-circRNA
Identification method	circRNA_finder, circseq_cup, find_circ, CIRI2
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	3_circ_ag.13
Support reads	4
Tissues	leaf, inflorescences, whole_plant
Exon boundary	Yes-No "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	GT-AG 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	NA

			
						 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  
						
							CCTTCCTGGTTTAGGACCATTCATTGATGAAGCATTCCACATGCCGATTGAAAGAAAAATAAGA
GTCCCGAACGCACACAGTTGACTACACGAAACCGGTgaggaaacatatgaggggtgattaaggc
aaaaaccttaagatgtggtcatttagatacatggagtcaaactaagaatggaccttggcgaaag
cttcttca

									
								

					

						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: 218
Transcript exons: 23405523-23405641,23406271-23406369
GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG
TCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGGTCAAGATTTAAAATCACTTCCTGGT
TTAGGACCATTCATTGATGAAGCATTCCACATGCCGATTGAAAGAAAAATAAGAGTCCCGAACG
CACACAGTTGACTACACGAAACCGGT
Transcript length: 243
Transcript exons: 23405523-23405609,23406169-23406269,23406315-23406369
GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG
TCAAACTAAGAATGGACCTTGGCGGAACAAGTGAAGCTGCCAGCATGATCTATCTTTGGTTAAG
AGATGAATGTGGAAACATATTGCTTAAACCCAAGCTAGGTCATGCTCTGACAGCCTCACTGATT
GAAAGAAAAATAAGAGTCCCGAACGCACACAGTTGACTACACGAAACCGGT
Transcript length: 690
Transcript exons: 23405523-23406369
GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG
TCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGGTCAAGATTTAAAATCAGGTATTTTG
AAGACAAGTCCACAAGGGAACAAGTGAAGCTGCCAGCATGATCTATCTTTGGTTAAGAGATGAA
TGTGGAAACATATTGCTTAAACCCAAGCTAGGTCATGCTCTGACAGCCTCACTCCTTCCTGGTT
TAGGACCATTCATTGATGAAGCATTCCACATCCCGATTGAAAGAAAAATAAGAGTCCCGAACGC
ACACAGTTGACTACACGAAACCGGTGAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAA
GATGTGGTCATTTAGATACATGGAGTCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGG
TCAAGATTTAAAATCAGGTATTTTGAAGACAAGTCCACAAGGGAACAAGTGAAGCTGCCAGCAT
GATCTATCTTTGGTTAAGAGATGAATGTGGAAACATATTGCTTAAACCCAAGCTAGGTCATGCT
CTGACAGCCTCACTCCTTCCTGGTTTAGGACCATTCATTGATGAAGCATTCCACATGCCGATTG
AAAGAAAAATAAGAGTCCCGAACGCACACAGTTGACTACACGAAACCGGT
						
					

						Genomic sequence
						
							GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG
TCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGGTCAAGATTTAAAATCAGGTACGACA
CTGTGTACGTGAGAGAGAGAGAGAGAGAGAGAAAGAGATTATAGAAAGAAAGAGATGTATCACA
ATAAAGGAGTATATTTAGGGTCACAGGTGGTGGAGATATAGGTATGCAGGGCCAAGGCTCTAAT
CTCTTCATAGCCCTATTGATTTTGTCCCTCTCTCTCTCTCTTTCTTCCTCTCTTAGCTGTATGC
ATTATGATGCGTCTTTTAATTCACTGTTTCAGGCTTCTTTAATTCGTGGTGTCTCTCTCCTTTT
TACCCAACCATCTCTTAAAATTTTTAACATCTGTTCCTCAAATCCTCTCTCATCTCTTTCTATA
AGTATCTATAGCGCCTCTTAAACCACAAAGCATCACCTCTGTCTTCTCTCATCTCCTTTCTGTA
TTCTCTTTCATTGCCTTCACGTCTGTTGCAATTTCTCCACTTCTTGAGCTTCCGTTTTTTACAA
TTATTGATCCGTCAAATATGTGAGATTTGCACAACTTGTTGCTCAGGTATTTTGAAGACAAGTC
CACAAGGGAACAAGTGAAGCTGCCAGCATGATCTATCTTTGGTTAAGAGATGAATGTGGAAACA
TATTGCTTAAACCCAAGCTAGGTCATGCTCTGACAGCCTCACTCCTTCCTGGTTTAGGACCATT
CATTGATGAAGCATTCCACATGCCGATTGAAAGAAAAATAAGAGTCCCGAACGCACACAGTTGA
CTACACGAAACCGGT
						
					

			
		

Sequences
Splice junction sequence	CCTTCCTGGTTTAGGACCATTCATTGATGAAGCATTCCACATGCCGATTGAAAGAAAAATAAGA GTCCCGAACGCACACAGTTGACTACACGAAACCGGTgaggaaacatatgaggggtgattaaggc aaaaaccttaagatgtggtcatttagatacatggagtcaaactaagaatggaccttggcgaaag cttcttca
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: 218 Transcript exons: 23405523-23405641,23406271-23406369 GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG TCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGGTCAAGATTTAAAATCACTTCCTGGT TTAGGACCATTCATTGATGAAGCATTCCACATGCCGATTGAAAGAAAAATAAGAGTCCCGAACG CACACAGTTGACTACACGAAACCGGT Transcript length: 243 Transcript exons: 23405523-23405609,23406169-23406269,23406315-23406369 GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG TCAAACTAAGAATGGACCTTGGCGGAACAAGTGAAGCTGCCAGCATGATCTATCTTTGGTTAAG AGATGAATGTGGAAACATATTGCTTAAACCCAAGCTAGGTCATGCTCTGACAGCCTCACTGATT GAAAGAAAAATAAGAGTCCCGAACGCACACAGTTGACTACACGAAACCGGT Transcript length: 690 Transcript exons: 23405523-23406369 GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG TCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGGTCAAGATTTAAAATCAGGTATTTTG AAGACAAGTCCACAAGGGAACAAGTGAAGCTGCCAGCATGATCTATCTTTGGTTAAGAGATGAA TGTGGAAACATATTGCTTAAACCCAAGCTAGGTCATGCTCTGACAGCCTCACTCCTTCCTGGTT TAGGACCATTCATTGATGAAGCATTCCACATCCCGATTGAAAGAAAAATAAGAGTCCCGAACGC ACACAGTTGACTACACGAAACCGGTGAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAA GATGTGGTCATTTAGATACATGGAGTCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGG TCAAGATTTAAAATCAGGTATTTTGAAGACAAGTCCACAAGGGAACAAGTGAAGCTGCCAGCAT GATCTATCTTTGGTTAAGAGATGAATGTGGAAACATATTGCTTAAACCCAAGCTAGGTCATGCT CTGACAGCCTCACTCCTTCCTGGTTTAGGACCATTCATTGATGAAGCATTCCACATGCCGATTG AAAGAAAAATAAGAGTCCCGAACGCACACAGTTGACTACACGAAACCGGT
Genomic sequence	GAGGAAACATATGAGGGGTGATTAAGGCAAAAACCTTAAGATGTGGTCATTTAGATACATGGAG TCAAACTAAGAATGGACCTTGGCGAAAGCTTCTTCACGGTCAAGATTTAAAATCAGGTACGACA CTGTGTACGTGAGAGAGAGAGAGAGAGAGAGAAAGAGATTATAGAAAGAAAGAGATGTATCACA ATAAAGGAGTATATTTAGGGTCACAGGTGGTGGAGATATAGGTATGCAGGGCCAAGGCTCTAAT CTCTTCATAGCCCTATTGATTTTGTCCCTCTCTCTCTCTCTTTCTTCCTCTCTTAGCTGTATGC ATTATGATGCGTCTTTTAATTCACTGTTTCAGGCTTCTTTAATTCGTGGTGTCTCTCTCCTTTT TACCCAACCATCTCTTAAAATTTTTAACATCTGTTCCTCAAATCCTCTCTCATCTCTTTCTATA AGTATCTATAGCGCCTCTTAAACCACAAAGCATCACCTCTGTCTTCTCTCATCTCCTTTCTGTA TTCTCTTTCATTGCCTTCACGTCTGTTGCAATTTCTCCACTTCTTGAGCTTCCGTTTTTTACAA TTATTGATCCGTCAAATATGTGAGATTTGCACAACTTGTTGCTCAGGTATTTTGAAGACAAGTC CACAAGGGAACAAGTGAAGCTGCCAGCATGATCTATCTTTGGTTAAGAGATGAATGTGGAAACA TATTGCTTAAACCCAAGCTAGGTCATGCTCTGACAGCCTCACTCCTTCCTGGTTTAGGACCATT CATTGATGAAGCATTCCACATGCCGATTGAAAGAAAAATAAGAGTCCCGAACGCACACAGTTGA CTACACGAAACCGGT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.514254173

Conservation Information
Conserved circRNAs	NA
PMCS	0.514254173

			
						 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;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of 3_circ_igg.12

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