Plant Circular RNA Database

Detail information of AT3G54970_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G54970_circ_g.2
					
						ID in PlantcircBase
						ath_circ_027572
					
						Alias
						3:20368500-20369048
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20368500-20369048  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G54970						
					
						Parent gene annotation
						
							D-aminoacid aminotransferase-like PLP-dependent enzymes superfam
ily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G54970_circ_g.1 						
					
						Support reads
						1/1/1
					
						Tissues
						seedling
					
						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
						AT3G54970.4:3
AT3G54970.6:2
AT3G54970.1:3
AT3G54970.5:1
AT3G54970.2:3
AT3G54970.3:2

General Information
CircRNA Name	AT3G54970_circ_g.2
ID in PlantcircBase	ath_circ_027572
Alias	3:20368500-20369048
Organism	Arabidpsis thaliana
Position	chr3: 20368500-20369048 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G54970
Parent gene annotation	D-aminoacid aminotransferase-like PLP-dependent enzymes superfam ily protein
Parent gene strand	-
Alternative splicing	AT3G54970_circ_g.1
Support reads	1/1/1
Tissues	seedling
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	AT3G54970.4:3 AT3G54970.6:2 AT3G54970.1:3 AT3G54970.5:1 AT3G54970.2:3 AT3G54970.3:2

			
						 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  
						
							GGTCTCTTATAACTCCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGCT
CAAACTCCCGCCGTAGAGATTCTCTGATGACTTCACcttgattaattcagtgatcatcccaggt
ctttccttaaaccttttctccttccattgaatctcctcaggtttgttacaagccaatccctcca
ttgaacca

									
								

					

						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: 322
Transcript exons: 20368500-20368625,20368768-20368853,20368939-20369048
CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC
TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGTT
GTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCTCTCGCGGTATGGAA
TCCCCTCGCTTAAACACACTTCGATGACAAGGTCTCTTATAACTCCTGCTAGCACACCATCAGT
TATAGGCGCGGTCTGCACCTCAAACTCGCTCAAACTCCCGCCGTAGAGATTCTCTGATGACTTC
AC
Transcript length: 342
Transcript exons: 20368500-20368645,20368768-20368853,20368939-20369048
CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC
TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT
GCAAAATCCTCAGACTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGG
TGCTCTCTCGCGGTATGGAATCCCCTCGCTTAAACACACTTCGATGACAAGGTCTCTTATAACT
CCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGCTCAAACTCCCGCCGT
AGAGATTCTCTGATGACTTCAC
Transcript length: 464
Transcript exons: 20368500-20368853,20368939-20369048
CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC
TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT
GCAAAATCCTCAGACTACCTGAACCCAGTGAGTTCTTGGGATGTTAAAATATACAAACATCACA
CAACACATTGAAAGTGTTCAGGCCAATATATATGCGAGAAGATGAAAAAACAGATTATGGATAT
GGAAAGATCTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCT
CTCGCGGTATGGAATCCCCTCGCTTAAACACACTTCGATGACAAGGTCTCTTATAACTCCTGCT
AGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGCTCAAACTCCCGCCGTAGAGAT
TCTCTGATGACTTCAC
Transcript length: 549
Transcript exons: 20368500-20369048
CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC
TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT
GCAAAATCCTCAGACTACCTGAACCCAGTGAGTTCTTGGGATGTTAAAATATACAAACATCACA
CAACACATTGAAAGTGTTCAGGCCAATATATATGCGAGAAGATGAAAAAACAGATTATGGATAT
GGAAAGATCTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCT
CTCGCGGTATGGAATCCCCTCGCTTAAACACACTCTGACAGAAAAGCAAATCTTATTGGTTGAT
CAGGCCATAAACACAGACGAATATAATCAACATTCTTAATGGTCTAACATATTACTCGATGACA
AGGTCTCTTATAACTCCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGC
TCAAACTCCCGCCGTAGAGATTCTCTGATGACTTCAC
						
					

						Genomic sequence
						
							CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC
TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT
GCAAAATCCTCAGACTACCTGAACCCAGTGAGTTCTTGGGATGTTAAAATATACAAACATCACA
CAACACATTGAAAGTGTTCAGGCCAATATATATGCGAGAAGATGAAAAAACAGATTATGGATAT
GGAAAGATCTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCT
CTCGCGGTATGGAATCCCCTCGCTTAAACACACTCTGACAGAAAAGCAAATCTTATTGGTTGAT
CAGGCCATAAACACAGACGAATATAATCAACATTCTTAATGGTCTAACATATTACTCGATGACA
AGGTCTCTTATAACTCCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGC
TCAAACTCCCGCCGTAGAGATTCTCTGATGACTTCAC
						
					

			
		

Sequences
Splice junction sequence	GGTCTCTTATAACTCCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGCT CAAACTCCCGCCGTAGAGATTCTCTGATGACTTCACcttgattaattcagtgatcatcccaggt ctttccttaaaccttttctccttccattgaatctcctcaggtttgttacaagccaatccctcca ttgaacca
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: 322 Transcript exons: 20368500-20368625,20368768-20368853,20368939-20369048 CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGTT GTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCTCTCGCGGTATGGAA TCCCCTCGCTTAAACACACTTCGATGACAAGGTCTCTTATAACTCCTGCTAGCACACCATCAGT TATAGGCGCGGTCTGCACCTCAAACTCGCTCAAACTCCCGCCGTAGAGATTCTCTGATGACTTC AC Transcript length: 342 Transcript exons: 20368500-20368645,20368768-20368853,20368939-20369048 CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT GCAAAATCCTCAGACTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGG TGCTCTCTCGCGGTATGGAATCCCCTCGCTTAAACACACTTCGATGACAAGGTCTCTTATAACT CCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGCTCAAACTCCCGCCGT AGAGATTCTCTGATGACTTCAC Transcript length: 464 Transcript exons: 20368500-20368853,20368939-20369048 CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT GCAAAATCCTCAGACTACCTGAACCCAGTGAGTTCTTGGGATGTTAAAATATACAAACATCACA CAACACATTGAAAGTGTTCAGGCCAATATATATGCGAGAAGATGAAAAAACAGATTATGGATAT GGAAAGATCTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCT CTCGCGGTATGGAATCCCCTCGCTTAAACACACTTCGATGACAAGGTCTCTTATAACTCCTGCT AGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGCTCAAACTCCCGCCGTAGAGAT TCTCTGATGACTTCAC Transcript length: 549 Transcript exons: 20368500-20369048 CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT GCAAAATCCTCAGACTACCTGAACCCAGTGAGTTCTTGGGATGTTAAAATATACAAACATCACA CAACACATTGAAAGTGTTCAGGCCAATATATATGCGAGAAGATGAAAAAACAGATTATGGATAT GGAAAGATCTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCT CTCGCGGTATGGAATCCCCTCGCTTAAACACACTCTGACAGAAAAGCAAATCTTATTGGTTGAT CAGGCCATAAACACAGACGAATATAATCAACATTCTTAATGGTCTAACATATTACTCGATGACA AGGTCTCTTATAACTCCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGC TCAAACTCCCGCCGTAGAGATTCTCTGATGACTTCAC
Genomic sequence	CTTGATTAATTCAGTGATCATCCCAGGTCTTTCCTTAAACCTTTTCTCCTTCCATTGAATCTCC TCAGGTTTGTTACAAGCCAATCCCTCCATTGAACCAACGGGTACTTTGATCGTCCCTACATGCT GCAAAATCCTCAGACTACCTGAACCCAGTGAGTTCTTGGGATGTTAAAATATACAAACATCACA CAACACATTGAAAGTGTTCAGGCCAATATATATGCGAGAAGATGAAAAAACAGATTATGGATAT GGAAAGATCTACTTGTAATGAAGGCTTCTTCCCAAAGCTCACGCTCAGACCACGAAGGTGCTCT CTCGCGGTATGGAATCCCCTCGCTTAAACACACTCTGACAGAAAAGCAAATCTTATTGGTTGAT CAGGCCATAAACACAGACGAATATAATCAACATTCTTAATGGTCTAACATATTACTCGATGACA AGGTCTCTTATAACTCCTGCTAGCACACCATCAGTTATAGGCGCGGTCTGCACCTCAAACTCGC TCAAACTCCCGCCGTAGAGATTCTCTGATGACTTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.330011931

Conservation Information
Conserved circRNAs	NA
PMCS	0.330011931

			
						 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 AT3G54970_circ_g.2

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