Plant Circular RNA Database

Detail information of AT2G45140_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT2G45140_circ_g.3
					
						ID in PlantcircBase
						ath_circ_018454
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr2: 18612010-18612506  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							i-circRNA							
									
						Identification method
						CIRCexplorer, CIRI
					
						Parent gene
						
							AT2G45140						
					
						Parent gene annotation
						
							Vesicle-associated protein 1-2
							
						Parent gene strand
						+
					
						Alternative splicing
						
							2_circ_igg.3 2_circ_igg.4 2_circ_ag.5 2_circ_ag.6 AT2G44860_circ_g.1 AT2G44860_circ_g.2 AT2G44860_circ_g.3 AT2G44870_circ_g.1 AT2G44900_circ_g.1 AT2G44900_circ_g.2 AT2G44910_circ_g.1 AT2G44910_circ_g.2 AT2G44920_circ_g.1 AT2G44920_circ_g.2 AT2G44920_circ_g.3 AT2G44950_circ_g.1 AT2G44950_circ_g.2 AT2G44950_circ_g.3 AT2G44950_circ_g.4 AT2G44950_circ_g.5 AT2G44950_circ_g.6 AT2G44950_circ_g.7 AT2G44970_circ_g.1 AT2G44970_circ_g.2 AT2G44970_circ_g.3 AT2G44970_circ_g.4 AT2G44970_circ_g.5 AT2G44980_circ_g.1 AT2G45000_circ_g.1 AT2G45000_circ_g.2 AT2G45000_circ_g.3 AT2G45023_circ_g.1 AT2G45030_circ_g.1 AT2G45030_circ_g.2 AT2G45030_circ_g.3 AT2G45060_circ_g.1 AT2G45060_circ_g.2 AT2G45060_circ_g.3 AT2G45060_circ_g.4 AT2G45060_circ_g.5 AT2G45100_circ_g.1 AT2G45135_circ_g.1 AT2G45140_circ_g.1 AT2G45140_circ_g.2 AT2G45160_circ_g.1 AT2G45170_circ_g.1 AT2G45170_circ_g.2 AT2G45170_circ_g.3 AT2G45170_circ_g.4 AT2G45180_circ_g.1 AT2G45180_circ_g.2 AT2G45180_circ_g.3 AT2G45180_circ_g.4 AT2G45180_circ_g.5 AT2G45180_circ_g.6 AT2G45180_circ_g.7 AT2G45180_circ_g.8 AT2G45180_circ_g.9 AT2G45180_circ_g.10 AT2G45180_circ_g.11 AT2G45180_circ_g.12 AT2G45180_circ_g.13 AT2G45180_circ_g.14 AT2G45180_circ_g.15 AT2G45180_circ_g.16 AT2G45190_circ_g.1 AT2G45190_circ_g.2 AT2G45190_circ_g.3 AT2G45200_circ_g.1 AT2G45200_circ_g.2 AT2G45200_circ_g.3 AT2G45200_circ_g.4 AT2G45200_circ_g.5 AT2G45200_circ_g.6 AT2G45240_circ_g.1 AT2G45240_circ_g.2 AT2G45240_circ_g.3 AT2G45240_circ_g.4 AT2G45240_circ_g.5 AT2G45240_circ_g.6 AT2G45240_circ_g.7 AT2G45240_circ_g.8 AT2G45240_circ_g.9 2_circ_ag.10 AT2G45250_circ_g.1 AT2G45250_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						root
					
						Exon boundary  
						
							No-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
						0

General Information
CircRNA Name	AT2G45140_circ_g.3
ID in PlantcircBase	ath_circ_018454
Alias	NA
Organism	Arabidpsis thaliana
Position	chr2: 18612010-18612506 JBrowse»
Reference genome	TAIR10.38
Type	i-circRNA
Identification method	CIRCexplorer, CIRI
Parent gene	AT2G45140
Parent gene annotation	Vesicle-associated protein 1-2
Parent gene strand	+
Alternative splicing	2_circ_igg.3 2_circ_igg.4 2_circ_ag.5 2_circ_ag.6 AT2G44860_circ_g.1 AT2G44860_circ_g.2 AT2G44860_circ_g.3 AT2G44870_circ_g.1 AT2G44900_circ_g.1 AT2G44900_circ_g.2 AT2G44910_circ_g.1 AT2G44910_circ_g.2 AT2G44920_circ_g.1 AT2G44920_circ_g.2 AT2G44920_circ_g.3 AT2G44950_circ_g.1 AT2G44950_circ_g.2 AT2G44950_circ_g.3 AT2G44950_circ_g.4 AT2G44950_circ_g.5 AT2G44950_circ_g.6 AT2G44950_circ_g.7 AT2G44970_circ_g.1 AT2G44970_circ_g.2 AT2G44970_circ_g.3 AT2G44970_circ_g.4 AT2G44970_circ_g.5 AT2G44980_circ_g.1 AT2G45000_circ_g.1 AT2G45000_circ_g.2 AT2G45000_circ_g.3 AT2G45023_circ_g.1 AT2G45030_circ_g.1 AT2G45030_circ_g.2 AT2G45030_circ_g.3 AT2G45060_circ_g.1 AT2G45060_circ_g.2 AT2G45060_circ_g.3 AT2G45060_circ_g.4 AT2G45060_circ_g.5 AT2G45100_circ_g.1 AT2G45135_circ_g.1 AT2G45140_circ_g.1 AT2G45140_circ_g.2 AT2G45160_circ_g.1 AT2G45170_circ_g.1 AT2G45170_circ_g.2 AT2G45170_circ_g.3 AT2G45170_circ_g.4 AT2G45180_circ_g.1 AT2G45180_circ_g.2 AT2G45180_circ_g.3 AT2G45180_circ_g.4 AT2G45180_circ_g.5 AT2G45180_circ_g.6 AT2G45180_circ_g.7 AT2G45180_circ_g.8 AT2G45180_circ_g.9 AT2G45180_circ_g.10 AT2G45180_circ_g.11 AT2G45180_circ_g.12 AT2G45180_circ_g.13 AT2G45180_circ_g.14 AT2G45180_circ_g.15 AT2G45180_circ_g.16 AT2G45190_circ_g.1 AT2G45190_circ_g.2 AT2G45190_circ_g.3 AT2G45200_circ_g.1 AT2G45200_circ_g.2 AT2G45200_circ_g.3 AT2G45200_circ_g.4 AT2G45200_circ_g.5 AT2G45200_circ_g.6 AT2G45240_circ_g.1 AT2G45240_circ_g.2 AT2G45240_circ_g.3 AT2G45240_circ_g.4 AT2G45240_circ_g.5 AT2G45240_circ_g.6 AT2G45240_circ_g.7 AT2G45240_circ_g.8 AT2G45240_circ_g.9 2_circ_ag.10 AT2G45250_circ_g.1 AT2G45250_circ_g.2
Support reads	2
Tissues	root
Exon boundary	No-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	0

			
						 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  
						
							ATGCAATTGAATTGGTCTAAGCTGCAACATATCTACTAGCTATTAATTGGCACATTTTAGCATT
GAAGTTACGAGACCTGAGTGATCATTCTATTACAATgtaatttaataacccatctgacgcttca
tgtaactgagctaacttggcatgataaagagtggatgagttttacactattacgctacctacat
tagtttac

						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: 497
Transcript exons: 18612010-18612506
GTAATTTAATAACCCATCTGACGCTTCATGTAACTGAGCTAACTTGGCATGATAAAGAGTGGAT
GAGTTTTACACTATTACGCTACCTACATTAGTTTACCATTCAACCCTATGGAATTCTCTTTCTT
GTCAGGTTGTTTAGAGCAGTTTAGTCTTTTTTTTGTTGAAGTTCAGATCATTCCAGTTATTAGC
AACTTAATGGCTCTTTTATTGTACACTGCTTGATGTGAAATTCTCAAACCTATTAGGCCAATAA
TCTTAACTTTTTGTTTATTACTGAAGAATTCTGAATAATCTTAACCTTGTTTGAATGAAGCTTT
AACTAATTTCTGAAAATACTGTCGTCCAGAAGAATATTGTTTCCTCTGCTGTAGTTTTAGCTTT
TTACTGATTATGCATGCAATTGAATTGGTCTAAGCTGCAACATATCTACTAGCTATTAATTGGC
ACATTTTAGCATTGAAGTTACGAGACCTGAGTGATCATTCTATTACAAT
						
						Genomic sequence
						
							GTAATTTAATAACCCATCTGACGCTTCATGTAACTGAGCTAACTTGGCATGATAAAGAGTGGAT
GAGTTTTACACTATTACGCTACCTACATTAGTTTACCATTCAACCCTATGGAATTCTCTTTCTT
GTCAGGTTGTTTAGAGCAGTTTAGTCTTTTTTTTGTTGAAGTTCAGATCATTCCAGTTATTAGC
AACTTAATGGCTCTTTTATTGTACACTGCTTGATGTGAAATTCTCAAACCTATTAGGCCAATAA
TCTTAACTTTTTGTTTATTACTGAAGAATTCTGAATAATCTTAACCTTGTTTGAATGAAGCTTT
AACTAATTTCTGAAAATACTGTCGTCCAGAAGAATATTGTTTCCTCTGCTGTAGTTTTAGCTTT
TTACTGATTATGCATGCAATTGAATTGGTCTAAGCTGCAACATATCTACTAGCTATTAATTGGC
ACATTTTAGCATTGAAGTTACGAGACCTGAGTGATCATTCTATTACAAT

Sequences
Splice junction sequence	ATGCAATTGAATTGGTCTAAGCTGCAACATATCTACTAGCTATTAATTGGCACATTTTAGCATT GAAGTTACGAGACCTGAGTGATCATTCTATTACAATgtaatttaataacccatctgacgcttca tgtaactgagctaacttggcatgataaagagtggatgagttttacactattacgctacctacat tagtttac
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: 497 Transcript exons: 18612010-18612506 GTAATTTAATAACCCATCTGACGCTTCATGTAACTGAGCTAACTTGGCATGATAAAGAGTGGAT GAGTTTTACACTATTACGCTACCTACATTAGTTTACCATTCAACCCTATGGAATTCTCTTTCTT GTCAGGTTGTTTAGAGCAGTTTAGTCTTTTTTTTGTTGAAGTTCAGATCATTCCAGTTATTAGC AACTTAATGGCTCTTTTATTGTACACTGCTTGATGTGAAATTCTCAAACCTATTAGGCCAATAA TCTTAACTTTTTGTTTATTACTGAAGAATTCTGAATAATCTTAACCTTGTTTGAATGAAGCTTT AACTAATTTCTGAAAATACTGTCGTCCAGAAGAATATTGTTTCCTCTGCTGTAGTTTTAGCTTT TTACTGATTATGCATGCAATTGAATTGGTCTAAGCTGCAACATATCTACTAGCTATTAATTGGC ACATTTTAGCATTGAAGTTACGAGACCTGAGTGATCATTCTATTACAAT
Genomic sequence	GTAATTTAATAACCCATCTGACGCTTCATGTAACTGAGCTAACTTGGCATGATAAAGAGTGGAT GAGTTTTACACTATTACGCTACCTACATTAGTTTACCATTCAACCCTATGGAATTCTCTTTCTT GTCAGGTTGTTTAGAGCAGTTTAGTCTTTTTTTTGTTGAAGTTCAGATCATTCCAGTTATTAGC AACTTAATGGCTCTTTTATTGTACACTGCTTGATGTGAAATTCTCAAACCTATTAGGCCAATAA TCTTAACTTTTTGTTTATTACTGAAGAATTCTGAATAATCTTAACCTTGTTTGAATGAAGCTTT AACTAATTTCTGAAAATACTGTCGTCCAGAAGAATATTGTTTCCTCTGCTGTAGTTTTAGCTTT TTACTGATTATGCATGCAATTGAATTGGTCTAAGCTGCAACATATCTACTAGCTATTAATTGGC ACATTTTAGCATTGAAGTTACGAGACCTGAGTGATCATTCTATTACAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.515537419

Conservation Information
Conserved circRNAs	NA
PMCS	0.515537419

			
						 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 AT2G45140_circ_g.3

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