Plant Circular RNA Database

Detail information of AT4G16260_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT4G16260_circ_g.2
					
						ID in PlantcircBase
						ath_circ_031180
					
						Alias
						Ath_circ_FC2668
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 9200791-9201274  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, MapSplice
					
						Parent gene
						
							AT4G16260						
					
						Parent gene annotation
						
							Probable glucan endo-1,3-beta-glucosidase At4g16260
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT4G16260_circ_g.1 						
					
						Support reads
						2
					
						Tissues
						seed/leaf
					
						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
						AT4G16260.2:1
AT4G16260.1:1

General Information
CircRNA Name	AT4G16260_circ_g.2
ID in PlantcircBase	ath_circ_031180
Alias	Ath_circ_FC2668
Organism	Arabidpsis thaliana
Position	chr4: 9200791-9201274 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, MapSplice
Parent gene	AT4G16260
Parent gene annotation	Probable glucan endo-1,3-beta-glucosidase At4g16260
Parent gene strand	-
Alternative splicing	AT4G16260_circ_g.1
Support reads	2
Tissues	seed/leaf
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	AT4G16260.2:1 AT4G16260.1:1

			
						 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  
						
							ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC
CCATCATTCCATAGCATACACCTACTGATTCTCCACccgatgacgggatcgatataccatctaa
cgtcaccacgaaactctccggaggaaggagggaaagagtttccaatcaaagtcatatcaatggc
ggtagaaa

									
								

					

						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: 176
Transcript exons: 9200791-9200839,9201148-9201274
CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGGCGGCTTGGTTTGGA
TCGTAGAGTCTAACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAG
GAAGGTTGTTCCCCATCATTCCATAGCATACACCTACTGATTCTCCAC
Transcript length: 249
Transcript exons: 9200791-9200912,9201112-9201212,9201249-9201274
CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAAG
AGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTATGACT
TCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCTAACACGTC
GGATGTTGTTTTGTCTAAAGAGAGCGATTGTATAGCATACACCTACTGATTCTCCAC
Transcript length: 294
Transcript exons: 9200791-9200834,9200842-9200942,9201126-9201274
CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCGAAGGAGGGAAAGAGTTTCC
AATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCACCTCTTAGA
GCATCGTAAACGTTACGCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTC
TAACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTT
CCCCATCATTCCATAGCATACACCTACTGATTCTCCAC
Transcript length: 484
Transcript exons: 9200791-9201274
CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAAG
AGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCACC
TCTTAGAGCATCGTAAACGTTACGCATGGCAGGGAGCACAACATCACCGCCGTTCGACGGAGAT
ACTTCGTTACCTACGGCGATGTACTTGAAGCTAACGGCGGGGTAATAGTTGAGGACGTTGTTTT
GGAGCCATGATCTAGCGGAAGAAGGGTTAGTGAGTGAACGAAGATCGGTGTTTGGAACGCCGAT
GATGACTTCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCTA
ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC
CCATCATTCCATAGCATACACCTACTGATTCTCCAC
						
					

						Genomic sequence
						
							CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAAG
AGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCACC
TCTTAGAGCATCGTAAACGTTACGCATGGCAGGGAGCACAACATCACCGCCGTTCGACGGAGAT
ACTTCGTTACCTACGGCGATGTACTTGAAGCTAACGGCGGGGTAATAGTTGAGGACGTTGTTTT
GGAGCCATGATCTAGCGGAAGAAGGGTTAGTGAGTGAACGAAGATCGGTGTTTGGAACGCCGAT
GATGACTTCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCTA
ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC
CCATCATTCCATAGCATACACCTACTGATTCTCCAC
						
					

			
		

Sequences
Splice junction sequence	ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC CCATCATTCCATAGCATACACCTACTGATTCTCCACccgatgacgggatcgatataccatctaa cgtcaccacgaaactctccggaggaaggagggaaagagtttccaatcaaagtcatatcaatggc ggtagaaa
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: 176 Transcript exons: 9200791-9200839,9201148-9201274 CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGGCGGCTTGGTTTGGA TCGTAGAGTCTAACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAG GAAGGTTGTTCCCCATCATTCCATAGCATACACCTACTGATTCTCCAC Transcript length: 249 Transcript exons: 9200791-9200912,9201112-9201212,9201249-9201274 CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAAG AGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTATGACT TCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCTAACACGTC GGATGTTGTTTTGTCTAAAGAGAGCGATTGTATAGCATACACCTACTGATTCTCCAC Transcript length: 294 Transcript exons: 9200791-9200834,9200842-9200942,9201126-9201274 CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCGAAGGAGGGAAAGAGTTTCC AATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCACCTCTTAGA GCATCGTAAACGTTACGCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTC TAACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTT CCCCATCATTCCATAGCATACACCTACTGATTCTCCAC Transcript length: 484 Transcript exons: 9200791-9201274 CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAAG AGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCACC TCTTAGAGCATCGTAAACGTTACGCATGGCAGGGAGCACAACATCACCGCCGTTCGACGGAGAT ACTTCGTTACCTACGGCGATGTACTTGAAGCTAACGGCGGGGTAATAGTTGAGGACGTTGTTTT GGAGCCATGATCTAGCGGAAGAAGGGTTAGTGAGTGAACGAAGATCGGTGTTTGGAACGCCGAT GATGACTTCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCTA ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC CCATCATTCCATAGCATACACCTACTGATTCTCCAC
Genomic sequence	CCGATGACGGGATCGATATACCATCTAACGTCACCACGAAACTCTCCGGAGGAAGGAGGGAAAG AGTTTCCAATCAAAGTCATATCAATGGCGGTAGAAACTTTAATACGATCTTGAAGATTTGCACC TCTTAGAGCATCGTAAACGTTACGCATGGCAGGGAGCACAACATCACCGCCGTTCGACGGAGAT ACTTCGTTACCTACGGCGATGTACTTGAAGCTAACGGCGGGGTAATAGTTGAGGACGTTGTTTT GGAGCCATGATCTAGCGGAAGAAGGGTTAGTGAGTGAACGAAGATCGGTGTTTGGAACGCCGAT GATGACTTCGATACCCGTGTTTCTAAGAGCGTTTAAAGCGGCTTGGTTTGGATCGTAGAGTCTA ACACGTCGGATGTTGTTTTGTCTAAAGAGAGCGATTGTGTCTGATTGAGAAGGAAGGTTGTTCC CCATCATTCCATAGCATACACCTACTGATTCTCCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.319090905

Conservation Information
Conserved circRNAs	NA
PMCS	0.319090905

			
						 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
						responsive to methyl jasmonate; regulation of development and senescence of leaves

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	responsive to methyl jasmonate; regulation of development and senescence of leaves

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a;Liu et al., 2017

circRNA

Detail information of AT4G16260_circ_g.2

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