Plant Circular RNA Database

Detail information of AT3G43790_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G43790_circ_g.1
					
						ID in PlantcircBase
						ath_circ_025947
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 15657086-15658851  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						PcircRNA_finder
					
						Parent gene
						
							AT3G43790						
					
						Parent gene annotation
						
							Probable peptide/nitrate transporter At3g43790
							
						Parent gene strand
						+
					
						Alternative splicing
						
							3_circ_ag.2 						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						AT3G43790.3:8
AT3G43790.2:8
AT3G43790.1:8
AT3G43790.5:7
AT3G43790.4:8

General Information
CircRNA Name	AT3G43790_circ_g.1
ID in PlantcircBase	ath_circ_025947
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 15657086-15658851 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	PcircRNA_finder
Parent gene	AT3G43790
Parent gene annotation	Probable peptide/nitrate transporter At3g43790
Parent gene strand	+
Alternative splicing	3_circ_ag.2
Support reads	1
Tissues	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	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	AT3G43790.3:8 AT3G43790.2:8 AT3G43790.1:8 AT3G43790.5:7 AT3G43790.4:8

			
						 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  
						
							ACATACAGGTGATGAGATGGTGTTCTTGGTGTTGAATTTGGTACAGCTCGTAGGATTGATACTA
ACGTTCATACCTTACATTTCCCAAATCCAGTAAAAGgaaactcttcatacacgttgtagaattg
cacaagggagacttaatccaacagagctaaacgatgatgaaagtagaggaggaggacttgatga
acagaaaa

									
								

					

						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: 747
Transcript exons: 15657086-15657280,15657402-15657489,15657769-15657854,15
658066-15658173,15658247-15658291,15658387-15658475,1565
8589-15658632,15658760-15658851
GAAACTCTTCATACACGTTGTAGAATTGCACAAGGGAGACTTAATCCAACAGAGCTAAACGATG
ATGAAAGTAGAGGAGGAGGACTTGATGAACAGAAAATAATTAATAAGCCAAGTCTCTTGAGGAA
TCGTCCATTGATGGCTATCATCATTGTTTATTGTGTTTTTTCCCTCCAAGAGATAGCATACAAT
GAGATATTCTCACTCTGGGCTGTTAGTGACCGAAGCTATGGAGGATTGAGCTTCTCATCTCAAG
ATGTTGGTGAAGTTTTAGCTATATCAGGACTTGGGCTTCTGGTGTTTCAACTTTTGGTATACCC
GCCATTGGAGAAATCCGTGGGACTCCTTGCGGTTATACGTCTTTCTGCGGTATTGCTGATACCG
CTGCTTTCGTGTTACCCCTATATAGCTTTGCTTTCTGGGGTGACTCTCCATTTGGTGATAAATT
GTGCATCCATCATAAAAAACGCTTTGTCTATCTCACTTGTCACAGGACTGTTTATCATGTTGAA
CAAAGCTGTGCCTCAGAATCAGAGAGGTGCTGCTAATGGCATTTCTATGACCGCGATGTCTGTT
TTCAAATCATTTGGCCCTGCCGGTGGAGGGGTCTTATTCTCATGGGCGCAAAAGAGACAAGACG
CTACATTCCTTCCAGGTGATGAGATGGTGTTCTTGGTGTTGAATTTGGTACAGCTCGTAGGATT
GATACTAACGTTCATACCTTACATTTCCCAAATCCAGTAAAAG
						
					

						Genomic sequence
						
							GAAACTCTTCATACACGTTGTAGAATTGCACAAGGGAGACTTAATCCAACAGAGCTAAACGATG
ATGAAAGTAGAGGAGGAGGACTTGATGAACAGAAAATAATTAATAAGCCAAGTCTCTTGAGGAA
TCGTCCATTGATGGCTATCATCATTGTTTATTGTGTTTTTTCCCTCCAAGAGATAGCATACAAT
GAGGTAAGAGTGTTACAATTCACTTGCATACAATCATATGGGGGTATCTTTAACTGTAGCTTTT
CGATTGATTCTTCGATAGAGGATATGATATTTTGGGTGCCCTTTTCTGTAACTTTGCAAGATAT
TCTCACTCTGGGCTGTTAGTGACCGAAGCTATGGAGGATTGAGCTTCTCATCTCAAGATGTTGG
TGAAGTTTTAGCTATATCAGGTGGCTGTTCTATTTACCTTACATTGTTTGGTGGATCGGTCCAG
AAAACTATGTCTACTTATTTGCAATTTCTCTGTGAAGGAGCTCATTGCTTAACCAGTCGTTGTA
AAATCTATCTATTTAAAATCTTTAGGCTTCACATCTTTGTGGTTCATACTGATTTGGTTATTGT
TTTGTATACAGTCGTTGTTTTCAACTCTGTTTCTTTAGTTTCTTGATGTATTGTCTATCCATCT
CCCCCTTGGATGTTTATCATGATTTGAGTTACAATTCTTTCAGGACTTGGGCTTCTGGTGTTTC
AACTTTTGGTATACCCGCCATTGGAGAAATCCGTGGGACTCCTTGCGGTTATACGTCTTTCTGC
GGTAAATCTTCTTTATTTTGAATGATGTTATGTGCTTTGATATATTAGGAATGGTGTAACACCC
CGGTTTGAAGAATATGGTAATTCAGACGGAGAGGTTTAAAAGAATTGATTTGACCACCTATGTC
ACCAAAGTGCTCTTATTTTTTCGGAGTAGGAATGGGTTGTCCAATAATCCCATCCTGTTCATTT
CTTTACATTTTGTTGTTCAGGTATTGCTGATACCGCTGCTTTCGTGTTACCCCTATATAGCTTT
GCTTTCTGGGGTGACTCTCCATTTGGTGATAAATTGTGCATCCATCATAAAAAACGCTTTGTCT
GTGAGTTCTTGTTATAACCCTGATGCTTTTCATAATAAGCAAGATTCTAAATATGTTTCCGTGT
AATGTGCAGATCTCACTTGTCACAGGACTGTTTATCATGTTGAACAAAGCTGTGGTATAGTTCT
TTGGCTAGTGTATCTCTATCTTTTACATCGGTAACTTCCTCTGCCATGGCTCATACTCTCACTT
TTCTTTAATATAACATTGTAGCCTCAGAATCAGAGAGGTGCTGCTAATGGCATTTCTATGACCG
CGATGTCTGTTTTCAAATCATTTGGCCCTGCCGGTGGAGGGGTCTTGTAAGTATTGTCAAATGC
ACTCACATTCTTGCAAAAACTATTAGCAAGTACAAGATGTAGACAAGCTTCACATTGCTAATTC
ACCTTTTATCCATGTTTTGTTAACTCTACAGATTCTCATGGGCGCAAAAGAGACAAGACGCTAC
ATTCCTTCCAGGTCAAATTTTTGCACCATGTACATGTTAAACTAATTTTTTAGCCGTGGTTTAA
AAACTGCGAATCATCATCAAAAATTTTATGTGAAAGACAGTGTTTTAATTACTTTATGAAAACT
ACACATACAGGTGATGAGATGGTGTTCTTGGTGTTGAATTTGGTACAGCTCGTAGGATTGATAC
TAACGTTCATACCTTACATTTCCCAAATCCAGTAAAAG
						
					

			
		

Sequences
Splice junction sequence	ACATACAGGTGATGAGATGGTGTTCTTGGTGTTGAATTTGGTACAGCTCGTAGGATTGATACTA ACGTTCATACCTTACATTTCCCAAATCCAGTAAAAGgaaactcttcatacacgttgtagaattg cacaagggagacttaatccaacagagctaaacgatgatgaaagtagaggaggaggacttgatga acagaaaa
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: 747 Transcript exons: 15657086-15657280,15657402-15657489,15657769-15657854,15 658066-15658173,15658247-15658291,15658387-15658475,1565 8589-15658632,15658760-15658851 GAAACTCTTCATACACGTTGTAGAATTGCACAAGGGAGACTTAATCCAACAGAGCTAAACGATG ATGAAAGTAGAGGAGGAGGACTTGATGAACAGAAAATAATTAATAAGCCAAGTCTCTTGAGGAA TCGTCCATTGATGGCTATCATCATTGTTTATTGTGTTTTTTCCCTCCAAGAGATAGCATACAAT GAGATATTCTCACTCTGGGCTGTTAGTGACCGAAGCTATGGAGGATTGAGCTTCTCATCTCAAG ATGTTGGTGAAGTTTTAGCTATATCAGGACTTGGGCTTCTGGTGTTTCAACTTTTGGTATACCC GCCATTGGAGAAATCCGTGGGACTCCTTGCGGTTATACGTCTTTCTGCGGTATTGCTGATACCG CTGCTTTCGTGTTACCCCTATATAGCTTTGCTTTCTGGGGTGACTCTCCATTTGGTGATAAATT GTGCATCCATCATAAAAAACGCTTTGTCTATCTCACTTGTCACAGGACTGTTTATCATGTTGAA CAAAGCTGTGCCTCAGAATCAGAGAGGTGCTGCTAATGGCATTTCTATGACCGCGATGTCTGTT TTCAAATCATTTGGCCCTGCCGGTGGAGGGGTCTTATTCTCATGGGCGCAAAAGAGACAAGACG CTACATTCCTTCCAGGTGATGAGATGGTGTTCTTGGTGTTGAATTTGGTACAGCTCGTAGGATT GATACTAACGTTCATACCTTACATTTCCCAAATCCAGTAAAAG
Genomic sequence	GAAACTCTTCATACACGTTGTAGAATTGCACAAGGGAGACTTAATCCAACAGAGCTAAACGATG ATGAAAGTAGAGGAGGAGGACTTGATGAACAGAAAATAATTAATAAGCCAAGTCTCTTGAGGAA TCGTCCATTGATGGCTATCATCATTGTTTATTGTGTTTTTTCCCTCCAAGAGATAGCATACAAT GAGGTAAGAGTGTTACAATTCACTTGCATACAATCATATGGGGGTATCTTTAACTGTAGCTTTT CGATTGATTCTTCGATAGAGGATATGATATTTTGGGTGCCCTTTTCTGTAACTTTGCAAGATAT TCTCACTCTGGGCTGTTAGTGACCGAAGCTATGGAGGATTGAGCTTCTCATCTCAAGATGTTGG TGAAGTTTTAGCTATATCAGGTGGCTGTTCTATTTACCTTACATTGTTTGGTGGATCGGTCCAG AAAACTATGTCTACTTATTTGCAATTTCTCTGTGAAGGAGCTCATTGCTTAACCAGTCGTTGTA AAATCTATCTATTTAAAATCTTTAGGCTTCACATCTTTGTGGTTCATACTGATTTGGTTATTGT TTTGTATACAGTCGTTGTTTTCAACTCTGTTTCTTTAGTTTCTTGATGTATTGTCTATCCATCT CCCCCTTGGATGTTTATCATGATTTGAGTTACAATTCTTTCAGGACTTGGGCTTCTGGTGTTTC AACTTTTGGTATACCCGCCATTGGAGAAATCCGTGGGACTCCTTGCGGTTATACGTCTTTCTGC GGTAAATCTTCTTTATTTTGAATGATGTTATGTGCTTTGATATATTAGGAATGGTGTAACACCC CGGTTTGAAGAATATGGTAATTCAGACGGAGAGGTTTAAAAGAATTGATTTGACCACCTATGTC ACCAAAGTGCTCTTATTTTTTCGGAGTAGGAATGGGTTGTCCAATAATCCCATCCTGTTCATTT CTTTACATTTTGTTGTTCAGGTATTGCTGATACCGCTGCTTTCGTGTTACCCCTATATAGCTTT GCTTTCTGGGGTGACTCTCCATTTGGTGATAAATTGTGCATCCATCATAAAAAACGCTTTGTCT GTGAGTTCTTGTTATAACCCTGATGCTTTTCATAATAAGCAAGATTCTAAATATGTTTCCGTGT AATGTGCAGATCTCACTTGTCACAGGACTGTTTATCATGTTGAACAAAGCTGTGGTATAGTTCT TTGGCTAGTGTATCTCTATCTTTTACATCGGTAACTTCCTCTGCCATGGCTCATACTCTCACTT TTCTTTAATATAACATTGTAGCCTCAGAATCAGAGAGGTGCTGCTAATGGCATTTCTATGACCG CGATGTCTGTTTTCAAATCATTTGGCCCTGCCGGTGGAGGGGTCTTGTAAGTATTGTCAAATGC ACTCACATTCTTGCAAAAACTATTAGCAAGTACAAGATGTAGACAAGCTTCACATTGCTAATTC ACCTTTTATCCATGTTTTGTTAACTCTACAGATTCTCATGGGCGCAAAAGAGACAAGACGCTAC ATTCCTTCCAGGTCAAATTTTTGCACCATGTACATGTTAAACTAATTTTTTAGCCGTGGTTTAA AAACTGCGAATCATCATCAAAAATTTTATGTGAAAGACAGTGTTTTAATTACTTTATGAAAACT ACACATACAGGTGATGAGATGGTGTTCTTGGTGTTGAATTTGGTACAGCTCGTAGGATTGATAC TAACGTTCATACCTTACATTTCCCAAATCCAGTAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171475313

Conservation Information
Conserved circRNAs	NA
PMCS	0.171475313

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G43790_circ_g.1

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