Plant Circular RNA Database

Detail information of AT3G56040_circ_g.7

			
						 General Information
					
						CircRNA Name
						AT3G56040_circ_g.7
					
						ID in PlantcircBase
						ath_circ_027776
					
						Alias
						At_ciR2944, Ath_circ_FC2410, Ath_circ_FC5309
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20794982-20796096  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							AT3G56040						
					
						Parent gene annotation
						
							UTP--glucose-1-phosphate uridylyltransferase 3, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G56040_circ_g.5 AT3G56040_circ_g.6 AT3G56040_circ_g.8 						
					
						Support reads
						3/2
					
						Tissues
						leaf/seedlings
					
						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
						AT3G56040.1:4

General Information
CircRNA Name	AT3G56040_circ_g.7
ID in PlantcircBase	ath_circ_027776
Alias	At_ciR2944, Ath_circ_FC2410, Ath_circ_FC5309
Organism	Arabidpsis thaliana
Position	chr3: 20794982-20796096 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	AT3G56040
Parent gene annotation	UTP--glucose-1-phosphate uridylyltransferase 3, chloroplastic
Parent gene strand	-
Alternative splicing	AT3G56040_circ_g.5 AT3G56040_circ_g.6 AT3G56040_circ_g.8
Support reads	3/2
Tissues	leaf/seedlings
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	AT3G56040.1:4

			
						 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  
						
							AACTTACATGCTCATGGTTGTTCTTTGCAGCACTTGTCATAATGGCAACAGGTGTGACACATTG
CTTTCCATAAAGTTTGAAGTAAAGGAACTCTCTAGCccatttgaagaaggtgatctgttggaga
tatcgaatttatcaaattctgtgtactcaatgcacgatataccatattcccacttcccatcgaa
attcttct

									
								

					

						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: 569
Transcript exons: 20794982-20795148,20795506-20795572,20795657-20795829,20
795935-20796096
CCATTTGAAGAAGGTGATCTGTTGGAGATATCGAATTTATCAAATTCTGTGTACTCAATGCACG
ATATACCATATTCCCACTTCCCATCGAAATTCTTCTTCTCCATCAAAACATTAATCCCTTCGGT
TGCTCCAGCATTCCTTTTACAGGATGCAAACCCAAGTTTCTTATTATACCGTAAGCCAATCCCA
GCAAGGGCCAAGAGGGTAACATCTGTAGCAGCCACAACGTTACTAACTTGCCGAACGGTTGCTC
CTTTTCTTCCATGATCGTAAAACCAGTTAAAGACACCTTTGTCATAAGCCAATTTCCAAATTAC
ACCATGACCACCAGGTTTACTAACTGGAACAAAGGGCTTTGATACTATCCATTGACCATCTTCA
GCACTGACAGCTGGGACGAGAGGCTGTTCAAAGAGTCGGAAATTTGATTGACCTCTGCCAAACC
ATTTAAGCCTTTCACAAAGCGAACTTACATGCTCATGGTTGTTCTTTGCAGCACTTGTCATAAT
GGCAACAGGTGTGACACATTGCTTTCCATAAAGTTTGAAGTAAAGGAACTCTCTAGC
						
					

						Genomic sequence
						
							CCATTTGAAGAAGGTGATCTGTTGGAGATATCGAATTTATCAAATTCTGTGTACTCAATGCACG
ATATACCATATTCCCACTTCCCATCGAAATTCTTCTTCTCCATCAAAACATTAATCCCTTCGGT
TGCTCCAGCATTCCTTTTACAGGATGCAAACCCAAGTTTCTGTCAAATTAGGATTAATAAATCA
AGTTTAGTGGGAATCAATTGTTCGCAAGTCCAAAAAGGGTATTCCTATTTCTTGAAGTAGTTGA
GAGATGAATACATGGTTAATATATGTTCTCAACTAGTAAGCTAGTTTGGAAAGCATAGCCATAT
ATATCAGTAGATAGTTAACTGCCACACCTCATACTTCTAAAGGAACTTATCCATCATGATATAG
AACATGTTCTTCAAGCCCAACTAACATGAGACCATTTGCAATCAACACCAGATGCTCTCTTCTT
TATCTCTATAAGTGATACATTTAATGTTTTGAATCTATTTGCAGTGTGTCAGTTATAAACATAA
GATCAAGCATACCTTATTATACCGTAAGCCAATCCCAGCAAGGGCCAAGAGGGTAACATCTGTA
GCAGCCACAACGTTACTGTAATATCACAATTATATACACAAAATTCAGATAGTTCTGATTTATT
ATAATGAACAACTCACAAGGGTACAAGTGACTAACCTAACTTGCCGAACGGTTGCTCCTTTTCT
TCCATGATCGTAAAACCAGTTAAAGACACCTTTGTCATAAGCCAATTTCCAAATTACACCATGA
CCACCAGGTTTACTAACTGGAACAAAGGGCTTTGATACTATCCATTGACCATCTTCAGCACTGA
CAGCTGGGACGAGAGGCTAGCGAACAAAAACCATTCTATTAACTGTGAGTACAATACTCAAGAT
ACAGTTGTTCCAGAAAAAGGTAACAGAAATCAAAAGAAAATATATGTTCCCTGATACCTGTTCA
AAGAGTCGGAAATTTGATTGACCTCTGCCAAACCATTTAAGCCTTTCACAAAGCGAACTTACAT
GCTCATGGTTGTTCTTTGCAGCACTTGTCATAATGGCAACAGGTGTGACACATTGCTTTCCATA
AAGTTTGAAGTAAAGGAACTCTCTAGC
						
					

			
		

Sequences
Splice junction sequence	AACTTACATGCTCATGGTTGTTCTTTGCAGCACTTGTCATAATGGCAACAGGTGTGACACATTG CTTTCCATAAAGTTTGAAGTAAAGGAACTCTCTAGCccatttgaagaaggtgatctgttggaga tatcgaatttatcaaattctgtgtactcaatgcacgatataccatattcccacttcccatcgaa attcttct
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: 569 Transcript exons: 20794982-20795148,20795506-20795572,20795657-20795829,20 795935-20796096 CCATTTGAAGAAGGTGATCTGTTGGAGATATCGAATTTATCAAATTCTGTGTACTCAATGCACG ATATACCATATTCCCACTTCCCATCGAAATTCTTCTTCTCCATCAAAACATTAATCCCTTCGGT TGCTCCAGCATTCCTTTTACAGGATGCAAACCCAAGTTTCTTATTATACCGTAAGCCAATCCCA GCAAGGGCCAAGAGGGTAACATCTGTAGCAGCCACAACGTTACTAACTTGCCGAACGGTTGCTC CTTTTCTTCCATGATCGTAAAACCAGTTAAAGACACCTTTGTCATAAGCCAATTTCCAAATTAC ACCATGACCACCAGGTTTACTAACTGGAACAAAGGGCTTTGATACTATCCATTGACCATCTTCA GCACTGACAGCTGGGACGAGAGGCTGTTCAAAGAGTCGGAAATTTGATTGACCTCTGCCAAACC ATTTAAGCCTTTCACAAAGCGAACTTACATGCTCATGGTTGTTCTTTGCAGCACTTGTCATAAT GGCAACAGGTGTGACACATTGCTTTCCATAAAGTTTGAAGTAAAGGAACTCTCTAGC
Genomic sequence	CCATTTGAAGAAGGTGATCTGTTGGAGATATCGAATTTATCAAATTCTGTGTACTCAATGCACG ATATACCATATTCCCACTTCCCATCGAAATTCTTCTTCTCCATCAAAACATTAATCCCTTCGGT TGCTCCAGCATTCCTTTTACAGGATGCAAACCCAAGTTTCTGTCAAATTAGGATTAATAAATCA AGTTTAGTGGGAATCAATTGTTCGCAAGTCCAAAAAGGGTATTCCTATTTCTTGAAGTAGTTGA GAGATGAATACATGGTTAATATATGTTCTCAACTAGTAAGCTAGTTTGGAAAGCATAGCCATAT ATATCAGTAGATAGTTAACTGCCACACCTCATACTTCTAAAGGAACTTATCCATCATGATATAG AACATGTTCTTCAAGCCCAACTAACATGAGACCATTTGCAATCAACACCAGATGCTCTCTTCTT TATCTCTATAAGTGATACATTTAATGTTTTGAATCTATTTGCAGTGTGTCAGTTATAAACATAA GATCAAGCATACCTTATTATACCGTAAGCCAATCCCAGCAAGGGCCAAGAGGGTAACATCTGTA GCAGCCACAACGTTACTGTAATATCACAATTATATACACAAAATTCAGATAGTTCTGATTTATT ATAATGAACAACTCACAAGGGTACAAGTGACTAACCTAACTTGCCGAACGGTTGCTCCTTTTCT TCCATGATCGTAAAACCAGTTAAAGACACCTTTGTCATAAGCCAATTTCCAAATTACACCATGA CCACCAGGTTTACTAACTGGAACAAAGGGCTTTGATACTATCCATTGACCATCTTCAGCACTGA CAGCTGGGACGAGAGGCTAGCGAACAAAAACCATTCTATTAACTGTGAGTACAATACTCAAGAT ACAGTTGTTCCAGAAAAAGGTAACAGAAATCAAAAGAAAATATATGTTCCCTGATACCTGTTCA AAGAGTCGGAAATTTGATTGACCTCTGCCAAACCATTTAAGCCTTTCACAAAGCGAACTTACAT GCTCATGGTTGTTCTTTGCAGCACTTGTCATAATGGCAACAGGTGTGACACATTGCTTTCCATA AAGTTTGAAGTAAAGGAACTCTCTAGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.404368662

Conservation Information
Conserved circRNAs	NA
PMCS	0.404368662

			
						 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
						NA

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	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Pan et al., 2017;Chen et al., 2017a

circRNA

Detail information of AT3G56040_circ_g.7

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