Plant Circular RNA Database

Detail information of AT3G49640_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G49640_circ_g.2
					
						ID in PlantcircBase
						ath_circ_026735
					
						Alias
						3:18400783-18401619
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 18400783-18401619  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G49640						
					
						Parent gene annotation
						
							Aldolase-type TIM barrel family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G49640_circ_g.1 						
					
						Support reads
						1/2
					
						Tissues
						seedling;root
					
						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
						AT3G49640.5:4
AT3G49640.2:4
AT3G49640.4:4
AT3G49640.1:4
AT3G49640.3:3

General Information
CircRNA Name	AT3G49640_circ_g.2
ID in PlantcircBase	ath_circ_026735
Alias	3:18400783-18401619
Organism	Arabidpsis thaliana
Position	chr3: 18400783-18401619 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G49640
Parent gene annotation	Aldolase-type TIM barrel family protein
Parent gene strand	-
Alternative splicing	AT3G49640_circ_g.1
Support reads	1/2
Tissues	seedling;root
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	AT3G49640.5:4 AT3G49640.2:4 AT3G49640.4:4 AT3G49640.1:4 AT3G49640.3:3

			
						 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  
						
							CGATTCTCCTAGCCAATTCAACAGTATCTGCTGGTGATTTTAATAGACGAATCTTGCAAGTAAC
CGGTACGTCTAAGTTCCTCTTAAGTGTTGCCAAAATgctaaatcttctaaagtgtctgctttgt
tgatagacttcccttccggtagttcaagacaagaatgatgcgctatcatctcctttatcgtgta
tttcgtgc

						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: 509
Transcript exons: 18400783-18400910,18400994-18401100,18401255-18401391,18
401483-18401619
GCTAAATCTTCTAAAGTGTCTGCTTTGTTGATAGACTTCCCTTCCGGTAGTTCAAGACAAGAAT
GATGCGCTATCATCTCCTTTATCGTGTATTTCGTGCTCTTAACATCGTTATTCCACAAGATGCT
CTTTCTAAGGTATTTCTTTTTCACATCTTCCCAGTGTGATTTTCCTTTTGGAGAGAAAATTGAA
GCATTCCACATAGCTCCTCTTGCAACCATAACTGATGCAGCGCCTGTTGCGGTTTTAATGCGAG
AAAAATCATCATATTCTAAAACATCGCCATTTGCAATGACGGGAATGGATAATGCTGCCACCAC
ATCTGCAATCTCATCCCATTTAGCAGGATCTCTTGGCCTGTCTGCAATTTTCCTCCCATGTACA
GCAAGAGCTGGTACACCAAGTTTCTCGATTCTCCTAGCCAATTCAACAGTATCTGCTGGTGATT
TTAATAGACGAATCTTGCAAGTAACCGGTACGTCTAAGTTCCTCTTAAGTGTTGCCAAAAT
						
						Genomic sequence
						
							GCTAAATCTTCTAAAGTGTCTGCTTTGTTGATAGACTTCCCTTCCGGTAGTTCAAGACAAGAAT
GATGCGCTATCATCTCCTTTATCGTGTATTTCGTGCTCTTAACATCGTTATTCCACAAGATGCT
CTGTTACACAATACCCCAAACCTGAAAATTAAATCTTATCCAGGGAAATTATCTTTTACTCTTG
AAAGGGTTTTCGTTTTTACCTTTCTAAGGTATTTCTTTTTCACATCTTCCCAGTGTGATTTTCC
TTTTGGAGAGAAAATTGAAGCATTCCACATAGCTCCTCTTGCAACCATAACTGATGCAGCGCCT
TTATGGGAACCAAAAAAAACAGCAAACAGTAAAGGGTTATATAAATCAGAGGTGAATCAAGTAT
AAACATTAGCACATGGCAGATAAAAAATGTTGTAGGGCTATATTTGCAAGTCTCATGAATCTGA
ATTCAATAAGTGTATCATGTGTACCTGTTGCGGTTTTAATGCGAGAAAAATCATCATATTCTAA
AACATCGCCATTTGCAATGACGGGAATGGATAATGCTGCCACCACATCTGCAATCTCATCCCAT
TTAGCAGGATCTCTTGGCCTGTCTGCAATTTTCCTGTATTTTAAGGAAGGAGGAATCAATTACC
AACTTTGATTAAAACAGCTTAAAGGAATGAGAACAAACTAACAACAGTGGTGTATATTACCTCC
CATGTACAGCAAGAGCTGGTACACCAAGTTTCTCGATTCTCCTAGCCAATTCAACAGTATCTGC
TGGTGATTTTAATAGACGAATCTTGCAAGTAACCGGTACGTCTAAGTTCCTCTTAAGTGTTGCC
AAAAT

Sequences
Splice junction sequence	CGATTCTCCTAGCCAATTCAACAGTATCTGCTGGTGATTTTAATAGACGAATCTTGCAAGTAAC CGGTACGTCTAAGTTCCTCTTAAGTGTTGCCAAAATgctaaatcttctaaagtgtctgctttgt tgatagacttcccttccggtagttcaagacaagaatgatgcgctatcatctcctttatcgtgta tttcgtgc
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: 509 Transcript exons: 18400783-18400910,18400994-18401100,18401255-18401391,18 401483-18401619 GCTAAATCTTCTAAAGTGTCTGCTTTGTTGATAGACTTCCCTTCCGGTAGTTCAAGACAAGAAT GATGCGCTATCATCTCCTTTATCGTGTATTTCGTGCTCTTAACATCGTTATTCCACAAGATGCT CTTTCTAAGGTATTTCTTTTTCACATCTTCCCAGTGTGATTTTCCTTTTGGAGAGAAAATTGAA GCATTCCACATAGCTCCTCTTGCAACCATAACTGATGCAGCGCCTGTTGCGGTTTTAATGCGAG AAAAATCATCATATTCTAAAACATCGCCATTTGCAATGACGGGAATGGATAATGCTGCCACCAC ATCTGCAATCTCATCCCATTTAGCAGGATCTCTTGGCCTGTCTGCAATTTTCCTCCCATGTACA GCAAGAGCTGGTACACCAAGTTTCTCGATTCTCCTAGCCAATTCAACAGTATCTGCTGGTGATT TTAATAGACGAATCTTGCAAGTAACCGGTACGTCTAAGTTCCTCTTAAGTGTTGCCAAAAT
Genomic sequence	GCTAAATCTTCTAAAGTGTCTGCTTTGTTGATAGACTTCCCTTCCGGTAGTTCAAGACAAGAAT GATGCGCTATCATCTCCTTTATCGTGTATTTCGTGCTCTTAACATCGTTATTCCACAAGATGCT CTGTTACACAATACCCCAAACCTGAAAATTAAATCTTATCCAGGGAAATTATCTTTTACTCTTG AAAGGGTTTTCGTTTTTACCTTTCTAAGGTATTTCTTTTTCACATCTTCCCAGTGTGATTTTCC TTTTGGAGAGAAAATTGAAGCATTCCACATAGCTCCTCTTGCAACCATAACTGATGCAGCGCCT TTATGGGAACCAAAAAAAACAGCAAACAGTAAAGGGTTATATAAATCAGAGGTGAATCAAGTAT AAACATTAGCACATGGCAGATAAAAAATGTTGTAGGGCTATATTTGCAAGTCTCATGAATCTGA ATTCAATAAGTGTATCATGTGTACCTGTTGCGGTTTTAATGCGAGAAAAATCATCATATTCTAA AACATCGCCATTTGCAATGACGGGAATGGATAATGCTGCCACCACATCTGCAATCTCATCCCAT TTAGCAGGATCTCTTGGCCTGTCTGCAATTTTCCTGTATTTTAAGGAAGGAGGAATCAATTACC AACTTTGATTAAAACAGCTTAAAGGAATGAGAACAAACTAACAACAGTGGTGTATATTACCTCC CATGTACAGCAAGAGCTGGTACACCAAGTTTCTCGATTCTCCTAGCCAATTCAACAGTATCTGC TGGTGATTTTAATAGACGAATCTTGCAAGTAACCGGTACGTCTAAGTTCCTCTTAAGTGTTGCC AAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.310108325

Conservation Information
Conserved circRNAs	NA
PMCS	0.310108325

			
						 Functional Information
					
						Coding potential
						NA
					
						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	NA
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT3G49640_circ_g.2

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