Plant Circular RNA Database

Detail information of AT4G12840_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT4G12840_circ_g.1
					
						ID in PlantcircBase
						ath_circ_030614
					
						Alias
						4:7533548-7535802
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr4: 7533548-7535802  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT4G12840						
					
						Parent gene annotation
						
							At4g12840
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						3
					
						Tissues
						root
					
						Exon boundary  
						
							No-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
						AT4G12840.2:13
AT4G12840.1:13
AT4G12840.3:11

General Information
CircRNA Name	AT4G12840_circ_g.1
ID in PlantcircBase	ath_circ_030614
Alias	4:7533548-7535802
Organism	Arabidpsis thaliana
Position	chr4: 7533548-7535802 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT4G12840
Parent gene annotation	At4g12840
Parent gene strand	-
Alternative splicing	NA
Support reads	3
Tissues	root
Exon boundary	No-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	AT4G12840.2:13 AT4G12840.1:13 AT4G12840.3:11

			
						 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  
						
							AAGCATTCCCTATAAGGAAGATCATTGCAAGAAAAAACACTAAAGAGAACAAGCGACGAAGAGA
CAAGCCCTTTCGTTTTTGATTCATACTTAATGATCCcttctcttttgcttccttgaggtatgca
tgtgctttctatatatgtataattgtgtccacaacaagcaatctttcatgtttggaatcggtct
atccagca

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							CTTCTCTTTTGCTTCCTTGAGGTATGCATGTGCTTTCTATATATGTATAATTGTGTCCACAACA
AGCAATCTTTCATGTTTGGAATCGGTCTATCCAGCACTCATCGTTCTTCACAGCATTTTTCCAT
CTATGTTTAAAAGTCTCTAACTCGACATAAGTTTGCTTCCGAACCTAGGTAATGATCATTGTTT
TGAATAGAGATTTTAGCTAAAACAAAGCACTCTATCATCTTTTTAAATACCAAACTGGTTAGAA
ACTTACCTCAGTTCTACCAGTTGACACTGATGATGATTTGTCTGCAGCATGCGGAGTCTTGGTC
TTATCGAGCTTCCCTGAATCCGTCTGCTTATACACAGTAACTATAATTACTTCCTAAATAAAAC
TCATGTAGACTAGTATGAAGAAATGACAAGAGAACCAGTTTCAAACCTTGTTTTCAGCTGAACC
TCCTCCTAATGTAGGAAGACCCATATGAAGTATATACTCGGAATCAACAATACCGATATTTTTG
GTTCGATCACCCTATGCCAAGCAACAACAACAATACTAAGAAAAAAACAAAACCAACAAATAAA
AGAATGTACATATTAGCTTGGCTCAGTCACAATTTACCTGTGCACAATATCCAAGCTGAAAATC
TATACCCCATCCATGGTTTAAGTCATTCTATAAAAGAAAAAACACAAAGTCAAGTATCCAGATG
TTGATGGTCTTCATGAGTCTGTAACATAATTAGTTCAAACATATGAAATACCTGAATCATATGC
CATGTACACCTCCAAGCTGCTCTGGAAAACACAGGAGCCATCATTTCAACAAATCTGTAGGAGA
GAGTTTTTTTTAATGAGTTTAAGAACAAGTTATGCTTTCCACTGAAGAAGGAAATGAAGATTCA
GTTCTTTTACCCTGTGCAAGGAGGTCCAGTGCTATTCTCGTTGCACCTCGCCCGACCAATGACT
TTGTATGTTCTCCTTTTAAACATCAAAACGTTGTAAAAAGATTCATTCTTACAATCTCTTTTCT
TCTCTTTGCTAAAATTTTTTCTATTGGAGCTTGAGAGAAGTACCTATGTACTCTTGATTTCTTG
TCTCGTGAGGTAAGTTGATGATGCACTTCAGAGAAATTGGGATCAAGAGCAGGTTGTGATATTT
CAAGCTTTTCTTCTTTAATAATTGAAACATACCTGAAAATTTTCATCTCATTAGATACCACATC
TTTACCAAGTGACAAACAATATATTCTTTGTATAACATTGTACCTTCTAGCATCAAAATGGTCA
ACACCGAGATCTTCATCCCATAGAAAAATGTAAGAATAAGCTGAGACAATATCCGGGTGTAGAA
AACGCTTTGCAAACCACCTAAAAGAGTCACAAACATATTCAAACTGTACAGCCAAATGTAAAAA
ATCCTCGTCGGGTTTTACGATTATAACAGAACAGTTACCATTTGGTTTGGTTTACTACAGAAAT
ATGAATGGCAGTGTCACTCCACTCAAACTCCTTCCATTCATCCACAGCACCATCGTAGTGAAAC
AGCATCACAACAAACTCACTTGATGGAAACTGCCATATAAGAAAGTGGAAAAACAGAGATATCA
CATCAAAACTGTTTCATTACCGAGAAGGTAATGTCCGAGGTTTTACCTTCTTGACAATCTTGTT
GACACTTTCCTTTTGTCTTATTCCAACTGCCATAGCTAATAAGCTTGGTTTCGGTTTCTAAGCA
AACAAAAACAGAAAATATAGCGTTAAAGGAATGACAACAGAGAAACTTGTGAACGTTTGGCAAC
AGGTAAAGATACCTTATCGCGCTTTGCTCCCCATAACGGTCGCATTTCCAAGTCAGATGTACTT
GCAACAATACCTCGCGGTAACGTCTCGCTACCAGGAGGCCTAAGTTGTGTCTAATTAAGCAAAG
CAACATGAAAAAATGTTAAGATTCATATAGAAAGGGAACTTTGTTTTGAGCAGCTTATTCAACA
GACCTTGCACATCTTTAGTTTAGCAAGATTTAGTCTAATTATCGAACTCCATCCCGCGATACCC
TGTCAATTAGTACACTCAAAACTGTTCTATAACATTATTCAGATTCAAGATAATGCTTAAAAGT
TGCAGTCTAAGAACTCATACCTCTTTATAGTCTACTGTAATAAAAGCATTCCCTATAAGGAAGA
TCATTGCAAGAAAAAACACTAAAGAGAACAAGCGACGAAGAGACAAGCCCTTTCGTTTTTGATT
CATACTTAATGATCC
						
					

			
		

Sequences
Splice junction sequence	AAGCATTCCCTATAAGGAAGATCATTGCAAGAAAAAACACTAAAGAGAACAAGCGACGAAGAGA CAAGCCCTTTCGTTTTTGATTCATACTTAATGATCCcttctcttttgcttccttgaggtatgca tgtgctttctatatatgtataattgtgtccacaacaagcaatctttcatgtttggaatcggtct atccagca
Assembled circRNA sequence	NA 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	NA
Genomic sequence	CTTCTCTTTTGCTTCCTTGAGGTATGCATGTGCTTTCTATATATGTATAATTGTGTCCACAACA AGCAATCTTTCATGTTTGGAATCGGTCTATCCAGCACTCATCGTTCTTCACAGCATTTTTCCAT CTATGTTTAAAAGTCTCTAACTCGACATAAGTTTGCTTCCGAACCTAGGTAATGATCATTGTTT TGAATAGAGATTTTAGCTAAAACAAAGCACTCTATCATCTTTTTAAATACCAAACTGGTTAGAA ACTTACCTCAGTTCTACCAGTTGACACTGATGATGATTTGTCTGCAGCATGCGGAGTCTTGGTC TTATCGAGCTTCCCTGAATCCGTCTGCTTATACACAGTAACTATAATTACTTCCTAAATAAAAC TCATGTAGACTAGTATGAAGAAATGACAAGAGAACCAGTTTCAAACCTTGTTTTCAGCTGAACC TCCTCCTAATGTAGGAAGACCCATATGAAGTATATACTCGGAATCAACAATACCGATATTTTTG GTTCGATCACCCTATGCCAAGCAACAACAACAATACTAAGAAAAAAACAAAACCAACAAATAAA AGAATGTACATATTAGCTTGGCTCAGTCACAATTTACCTGTGCACAATATCCAAGCTGAAAATC TATACCCCATCCATGGTTTAAGTCATTCTATAAAAGAAAAAACACAAAGTCAAGTATCCAGATG TTGATGGTCTTCATGAGTCTGTAACATAATTAGTTCAAACATATGAAATACCTGAATCATATGC CATGTACACCTCCAAGCTGCTCTGGAAAACACAGGAGCCATCATTTCAACAAATCTGTAGGAGA GAGTTTTTTTTAATGAGTTTAAGAACAAGTTATGCTTTCCACTGAAGAAGGAAATGAAGATTCA GTTCTTTTACCCTGTGCAAGGAGGTCCAGTGCTATTCTCGTTGCACCTCGCCCGACCAATGACT TTGTATGTTCTCCTTTTAAACATCAAAACGTTGTAAAAAGATTCATTCTTACAATCTCTTTTCT TCTCTTTGCTAAAATTTTTTCTATTGGAGCTTGAGAGAAGTACCTATGTACTCTTGATTTCTTG TCTCGTGAGGTAAGTTGATGATGCACTTCAGAGAAATTGGGATCAAGAGCAGGTTGTGATATTT CAAGCTTTTCTTCTTTAATAATTGAAACATACCTGAAAATTTTCATCTCATTAGATACCACATC TTTACCAAGTGACAAACAATATATTCTTTGTATAACATTGTACCTTCTAGCATCAAAATGGTCA ACACCGAGATCTTCATCCCATAGAAAAATGTAAGAATAAGCTGAGACAATATCCGGGTGTAGAA AACGCTTTGCAAACCACCTAAAAGAGTCACAAACATATTCAAACTGTACAGCCAAATGTAAAAA ATCCTCGTCGGGTTTTACGATTATAACAGAACAGTTACCATTTGGTTTGGTTTACTACAGAAAT ATGAATGGCAGTGTCACTCCACTCAAACTCCTTCCATTCATCCACAGCACCATCGTAGTGAAAC AGCATCACAACAAACTCACTTGATGGAAACTGCCATATAAGAAAGTGGAAAAACAGAGATATCA CATCAAAACTGTTTCATTACCGAGAAGGTAATGTCCGAGGTTTTACCTTCTTGACAATCTTGTT GACACTTTCCTTTTGTCTTATTCCAACTGCCATAGCTAATAAGCTTGGTTTCGGTTTCTAAGCA AACAAAAACAGAAAATATAGCGTTAAAGGAATGACAACAGAGAAACTTGTGAACGTTTGGCAAC AGGTAAAGATACCTTATCGCGCTTTGCTCCCCATAACGGTCGCATTTCCAAGTCAGATGTACTT GCAACAATACCTCGCGGTAACGTCTCGCTACCAGGAGGCCTAAGTTGTGTCTAATTAAGCAAAG CAACATGAAAAAATGTTAAGATTCATATAGAAAGGGAACTTTGTTTTGAGCAGCTTATTCAACA GACCTTGCACATCTTTAGTTTAGCAAGATTTAGTCTAATTATCGAACTCCATCCCGCGATACCC TGTCAATTAGTACACTCAAAACTGTTCTATAACATTATTCAGATTCAAGATAATGCTTAAAAGT TGCAGTCTAAGAACTCATACCTCTTTATAGTCTACTGTAATAAAAGCATTCCCTATAAGGAAGA TCATTGCAAGAAAAAACACTAAAGAGAACAAGCGACGAAGAGACAAGCCCTTTCGTTTTTGATT CATACTTAATGATCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.296055576

Conservation Information
Conserved circRNAs	NA
PMCS	0.296055576

			
						 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 AT4G12840_circ_g.1

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