Plant Circular RNA Database

Detail information of AT3G54750_circ_g.8

			
						 General Information
					
						CircRNA Name
						AT3G54750_circ_g.8
					
						ID in PlantcircBase
						ath_circ_027521
					
						Alias
						3:20267304-20268471
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20267304-20268471  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G54750						
					
						Parent gene annotation
						
							Downstream neighbor of Son
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G54750_circ_g.5 AT3G54750_circ_g.6 AT3G54750_circ_g.7 AT3G54750_circ_g.9 AT3G54750_circ_g.10 AT3G54750_circ_g.11 						
					
						Support reads
						2
					
						Tissues
						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
						AT3G54750.4:6
AT3G54750.1:6
AT3G54750.3:6
AT3G54750.2:6
AT3G54750.5:6

General Information
CircRNA Name	AT3G54750_circ_g.8
ID in PlantcircBase	ath_circ_027521
Alias	3:20267304-20268471
Organism	Arabidpsis thaliana
Position	chr3: 20267304-20268471 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G54750
Parent gene annotation	Downstream neighbor of Son
Parent gene strand	-
Alternative splicing	AT3G54750_circ_g.5 AT3G54750_circ_g.6 AT3G54750_circ_g.7 AT3G54750_circ_g.9 AT3G54750_circ_g.10 AT3G54750_circ_g.11
Support reads	2
Tissues	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	AT3G54750.4:6 AT3G54750.1:6 AT3G54750.3:6 AT3G54750.2:6 AT3G54750.5:6

			
						 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  
						
							TCTCAGTTCAGAAGGCGTCTTCCTCTTAGCAACTACTTTCGTCATTTCCAAATGATACTGTTCG
CTTGATCCCCAAATTTACCTAACCCCAATACCAAATcaacttaatggagaagaggaaacaagtc
gagcataagtcttcaaggaaaggtccagaggaatcttctgcccagaaacttgaaactcggacat
gaaacttc

									
								

					

						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: 735
Transcript exons: 20267304-20267494,20267576-20267726,20267810-20267892,20
267994-20268129,20268196-20268269,20268372-20268471
CAACTTAATGGAGAAGAGGAAACAAGTCGAGCATAAGTCTTCAAGGAAAGGTCCAGAGGAATCT
TCTGCCCAGAAACTTGAAACTCGGACATGAAACTTCCACTTAATGAAGCAGTATCATCTTCCCC
AGTTATGTCGCCAGGATGAACCAGCAAAGGTTCACAAGTAGCAAGTCCTTTCAATGCTTTGTTC
ATATCAATATCTGGCAAGCAGGATAATTCTTCACCCCTGGTTGAAAGTTGTGTGACACTGCGAA
ATATGCTCTGGCTACATCTCTCATTTGTTTGACGAGCTTCAGCCTTAGTGTCATCAGGAACTTC
AGTAGAAGCATTATTCTCCTCACGAATAAGTTGTCTTTTGGTGGCAGCAAGATTCGAGAGTAAA
GAAACATTGATTAGGCTGCTGGATTGCTTCGCACCATTTTCCTTAGAGTTTTCTTTGCCAGAGA
GCATCCAAGGCCTAGCCTTTTTGACAGGATACAGTTCATCCATACGCATCTCAATGTATTTTGG
ATTCTTCGAAAGCTCTGATTTCTTGAACCCATTTTCTCTCTCAGCACTACTTTTGCAAGGACGC
AATGCATCAAAAGCTTCTTTAGCTTGGTCCACAAAAGCAGTCCGTTTCAATTGTTCTCCTCTCA
GTTCAGAAGGCGTCTTCCTCTTAGCAACTACTTTCGTCATTTCCAAATGATACTGTTCGCTTGA
TCCCCAAATTTACCTAACCCCAATACCAAAT
						
					

						Genomic sequence
						
							CAACTTAATGGAGAAGAGGAAACAAGTCGAGCATAAGTCTTCAAGGAAAGGTCCAGAGGAATCT
TCTGCCCAGAAACTTGAAACTCGGACATGAAACTTCCACTTAATGAAGCAGTATCATCTTCCCC
AGTTATGTCGCCAGGATGAACCAGCAAAGGTTCACAAGTAGCAAGTCCTTTCAATGCTTTGTTC
TGTTGAAAGATGACATCAGTTTCACCAGGACCAGATACATAACCATCTGACAGTATCAAAGACT
ACCTAGTGAAACATACCATATCAATATCTGGCAAGCAGGATAATTCTTCACCCCTGGTTGAAAG
TTGTGTGACACTGCGAAATATGCTCTGGCTACATCTCTCATTTGTTTGACGAGCTTCAGCCTTA
GTGTCATCAGGAACTTCAGTAGAAGCATTATTCTCCTCACTGCTAATACATTAAAGCATTAACA
TAAGTTGCAGCACATAAAGTCAGCTTACTCCAGATAGAAATTGCCTGAGGGGTTTTACCGAATA
AGTTGTCTTTTGGTGGCAGCAAGATTCGAGAGTAAAGAAACATTGATTAGGCTGCTGGATTGCT
TCGCACCATTTTCCTGTGGTAAAGACAAAAAAACTAATAAAAACGATGTTTACTAAACTATATT
ACTTTCACGAAATCAAAAGAATCAACAATAGAGTCAGAGAGGTCATGAACCTTAGAGTTTTCTT
TGCCAGAGAGCATCCAAGGCCTAGCCTTTTTGACAGGATACAGTTCATCCATACGCATCTCAAT
GTATTTTGGATTCTTCGAAAGCTCTGATTTCTTGAACCCATTTTCTCTCTCAGCACTACTGCCA
AGACAAATCTAGTAAGAAAACATAAAAGTTGAAAAACTTGACAGACATGATGCTTTATACCTTT
TGCAAGGACGCAATGCATCAAAAGCTTCTTTAGCTTGGTCCACAAAAGCAGTCCGTTTCAATTG
TTCTCCCTGTTGAGTGAGAAGGGTATTCAAATAAACAATCTTCAGAGATAACTTCCAATAACTC
AACGAGGAAAACATTGCACAATAAAGAGAAAGAATCAAACTTACTCTCAGTTCAGAAGGCGTCT
TCCTCTTAGCAACTACTTTCGTCATTTCCAAATGATACTGTTCGCTTGATCCCCAAATTTACCT
AACCCCAATACCAAAT
						
					

			
		

Sequences
Splice junction sequence	TCTCAGTTCAGAAGGCGTCTTCCTCTTAGCAACTACTTTCGTCATTTCCAAATGATACTGTTCG CTTGATCCCCAAATTTACCTAACCCCAATACCAAATcaacttaatggagaagaggaaacaagtc gagcataagtcttcaaggaaaggtccagaggaatcttctgcccagaaacttgaaactcggacat gaaacttc
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: 735 Transcript exons: 20267304-20267494,20267576-20267726,20267810-20267892,20 267994-20268129,20268196-20268269,20268372-20268471 CAACTTAATGGAGAAGAGGAAACAAGTCGAGCATAAGTCTTCAAGGAAAGGTCCAGAGGAATCT TCTGCCCAGAAACTTGAAACTCGGACATGAAACTTCCACTTAATGAAGCAGTATCATCTTCCCC AGTTATGTCGCCAGGATGAACCAGCAAAGGTTCACAAGTAGCAAGTCCTTTCAATGCTTTGTTC ATATCAATATCTGGCAAGCAGGATAATTCTTCACCCCTGGTTGAAAGTTGTGTGACACTGCGAA ATATGCTCTGGCTACATCTCTCATTTGTTTGACGAGCTTCAGCCTTAGTGTCATCAGGAACTTC AGTAGAAGCATTATTCTCCTCACGAATAAGTTGTCTTTTGGTGGCAGCAAGATTCGAGAGTAAA GAAACATTGATTAGGCTGCTGGATTGCTTCGCACCATTTTCCTTAGAGTTTTCTTTGCCAGAGA GCATCCAAGGCCTAGCCTTTTTGACAGGATACAGTTCATCCATACGCATCTCAATGTATTTTGG ATTCTTCGAAAGCTCTGATTTCTTGAACCCATTTTCTCTCTCAGCACTACTTTTGCAAGGACGC AATGCATCAAAAGCTTCTTTAGCTTGGTCCACAAAAGCAGTCCGTTTCAATTGTTCTCCTCTCA GTTCAGAAGGCGTCTTCCTCTTAGCAACTACTTTCGTCATTTCCAAATGATACTGTTCGCTTGA TCCCCAAATTTACCTAACCCCAATACCAAAT
Genomic sequence	CAACTTAATGGAGAAGAGGAAACAAGTCGAGCATAAGTCTTCAAGGAAAGGTCCAGAGGAATCT TCTGCCCAGAAACTTGAAACTCGGACATGAAACTTCCACTTAATGAAGCAGTATCATCTTCCCC AGTTATGTCGCCAGGATGAACCAGCAAAGGTTCACAAGTAGCAAGTCCTTTCAATGCTTTGTTC TGTTGAAAGATGACATCAGTTTCACCAGGACCAGATACATAACCATCTGACAGTATCAAAGACT ACCTAGTGAAACATACCATATCAATATCTGGCAAGCAGGATAATTCTTCACCCCTGGTTGAAAG TTGTGTGACACTGCGAAATATGCTCTGGCTACATCTCTCATTTGTTTGACGAGCTTCAGCCTTA GTGTCATCAGGAACTTCAGTAGAAGCATTATTCTCCTCACTGCTAATACATTAAAGCATTAACA TAAGTTGCAGCACATAAAGTCAGCTTACTCCAGATAGAAATTGCCTGAGGGGTTTTACCGAATA AGTTGTCTTTTGGTGGCAGCAAGATTCGAGAGTAAAGAAACATTGATTAGGCTGCTGGATTGCT TCGCACCATTTTCCTGTGGTAAAGACAAAAAAACTAATAAAAACGATGTTTACTAAACTATATT ACTTTCACGAAATCAAAAGAATCAACAATAGAGTCAGAGAGGTCATGAACCTTAGAGTTTTCTT TGCCAGAGAGCATCCAAGGCCTAGCCTTTTTGACAGGATACAGTTCATCCATACGCATCTCAAT GTATTTTGGATTCTTCGAAAGCTCTGATTTCTTGAACCCATTTTCTCTCTCAGCACTACTGCCA AGACAAATCTAGTAAGAAAACATAAAAGTTGAAAAACTTGACAGACATGATGCTTTATACCTTT TGCAAGGACGCAATGCATCAAAAGCTTCTTTAGCTTGGTCCACAAAAGCAGTCCGTTTCAATTG TTCTCCCTGTTGAGTGAGAAGGGTATTCAAATAAACAATCTTCAGAGATAACTTCCAATAACTC AACGAGGAAAACATTGCACAATAAAGAGAAAGAATCAAACTTACTCTCAGTTCAGAAGGCGTCT TCCTCTTAGCAACTACTTTCGTCATTTCCAAATGATACTGTTCGCTTGATCCCCAAATTTACCT AACCCCAATACCAAAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.213703312

Conservation Information
Conserved circRNAs	NA
PMCS	0.213703312

			
						 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 AT3G54750_circ_g.8

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