Plant Circular RNA Database

Detail information of AT3G01370_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT3G01370_circ_g.4
					
						ID in PlantcircBase
						ath_circ_019090
					
						Alias
						3:140717-141724
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 140717-141724  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G01370						
					
						Parent gene annotation
						
							CRM-domain containing factor CFM2, chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT3G01370_circ_g.3 AT3G01370_circ_g.5 						
					
						Support reads
						1/4
					
						Tissues
						leaf;flower
					
						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  
						
							GT-AG							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
						AT3G01370.1:3

General Information
CircRNA Name	AT3G01370_circ_g.4
ID in PlantcircBase	ath_circ_019090
Alias	3:140717-141724
Organism	Arabidpsis thaliana
Position	chr3: 140717-141724 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G01370
Parent gene annotation	CRM-domain containing factor CFM2, chloroplastic
Parent gene strand	+
Alternative splicing	AT3G01370_circ_g.3 AT3G01370_circ_g.5
Support reads	1/4
Tissues	leaf;flower
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	GT-AG 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	AT3G01370.1:3

			
						 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  
						
							TCGTGGAAAGAATTATGAGCGGCCTCAATGTCTACGACCTCAAACACTTCTCAGTAAGAGAGAG
GCGCTGAAGCGGTCTGTGGAGGCACAACGTCGAAAGtggttgactggagggactctgatatctc
gggataaagatttcattgtcctgtacagaggaaaggatttcctcccatctgcagtttcttctgc
aatagaag

									
								

					

						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: 765
Transcript exons: 140717-141031,141117-141273,141432-141724
TGGTTGACTGGAGGGACTCTGATATCTCGGGATAAAGATTTCATTGTCCTGTACAGAGGAAAGG
ATTTCCTCCCATCTGCAGTTTCTTCTGCAATAGAAGAGAGGAGAAGGCAAACAATGATAATGGA
GAATTCTAGTGTGCATGGTAATAAGCTGACTGAAAACGAAGAGGAAATAAAACCTCGGGCTGTT
AAAGAGGATATTGAACTAGAAGCTAAGGATCAGAAGGATCATATACAAACCCATCAGATGAAAT
CAAGACAGCGAAATTCTCCTGAGGCAATCCTTGAAAAAACTAGTATGAAGTTGTCCATGGCGTT
GGAAAAGAAAGCAAATGCAGAAAAAGTCCTGGCGGATCTGGAGAATAGAGAGAGTCCTCAACTT
TCTGATATTGACAAGGAGGGTATTACTAATGATGAAAAGTACATGCTCCGGAAAATTGGCTTGA
AAATGAAGCCTTTCCTTTTACTAGGTAGAAGAGGCGTCTTTGATGGAACAATAGAGAACATGCA
TCTTCACTGGAAGTATAGGGAACTTGTGAAGATCATTTGTAATGAATATAGCATTGAAGCTGCT
CACAAAGTAGCAGAAATCTTGGAAGCAGAAAGTGGTGGCATACTAGTTGCTGTGGAGATGGTTA
GTAAGGGCTATGCAATCATTGTGTATCGTGGAAAGAATTATGAGCGGCCTCAATGTCTACGACC
TCAAACACTTCTCAGTAAGAGAGAGGCGCTGAAGCGGTCTGTGGAGGCACAACGTCGAAAG
						
					

						Genomic sequence
						
							TGGTTGACTGGAGGGACTCTGATATCTCGGGATAAAGATTTCATTGTCCTGTACAGAGGAAAGG
ATTTCCTCCCATCTGCAGTTTCTTCTGCAATAGAAGAGAGGAGAAGGCAAACAATGATAATGGA
GAATTCTAGTGTGCATGGTAATAAGCTGACTGAAAACGAAGAGGAAATAAAACCTCGGGCTGTT
AAAGAGGATATTGAACTAGAAGCTAAGGATCAGAAGGATCATATACAAACCCATCAGATGAAAT
CAAGACAGCGAAATTCTCCTGAGGCAATCCTTGAAAAAACTAGTATGAAGTTGTCCATGGTATG
CCCTAACAGACAATTTATACTTGAATCCATTGGGTTTGCGAGACCTTTTTTAGTTCTGAACGGT
TAGTTTTTGTCTTTAGGCGTTGGAAAAGAAAGCAAATGCAGAAAAAGTCCTGGCGGATCTGGAG
AATAGAGAGAGTCCTCAACTTTCTGATATTGACAAGGAGGGTATTACTAATGATGAAAAGTACA
TGCTCCGGAAAATTGGCTTGAAAATGAAGCCTTTCCTTTTACTAGGTAGGTCATTGTTTTTCCT
CTTTTTCCAATTGAAAGCAGTCTGTTCCCGTCTTTCATGTAAATACTCGTGGTAAATGAGTAGT
AACTGTCATGGACTCATCTCTTTGACATGGTTTATGTAAACTTCCTGTTCTGACGTATCTTGTT
GTGTTCTCAAGGTAGAAGAGGCGTCTTTGATGGAACAATAGAGAACATGCATCTTCACTGGAAG
TATAGGGAACTTGTGAAGATCATTTGTAATGAATATAGCATTGAAGCTGCTCACAAAGTAGCAG
AAATCTTGGAAGCAGAAAGTGGTGGCATACTAGTTGCTGTGGAGATGGTTAGTAAGGGCTATGC
AATCATTGTGTATCGTGGAAAGAATTATGAGCGGCCTCAATGTCTACGACCTCAAACACTTCTC
AGTAAGAGAGAGGCGCTGAAGCGGTCTGTGGAGGCACAACGTCGAAAG
						
					

			
		

Sequences
Splice junction sequence	TCGTGGAAAGAATTATGAGCGGCCTCAATGTCTACGACCTCAAACACTTCTCAGTAAGAGAGAG GCGCTGAAGCGGTCTGTGGAGGCACAACGTCGAAAGtggttgactggagggactctgatatctc gggataaagatttcattgtcctgtacagaggaaaggatttcctcccatctgcagtttcttctgc aatagaag
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: 765 Transcript exons: 140717-141031,141117-141273,141432-141724 TGGTTGACTGGAGGGACTCTGATATCTCGGGATAAAGATTTCATTGTCCTGTACAGAGGAAAGG ATTTCCTCCCATCTGCAGTTTCTTCTGCAATAGAAGAGAGGAGAAGGCAAACAATGATAATGGA GAATTCTAGTGTGCATGGTAATAAGCTGACTGAAAACGAAGAGGAAATAAAACCTCGGGCTGTT AAAGAGGATATTGAACTAGAAGCTAAGGATCAGAAGGATCATATACAAACCCATCAGATGAAAT CAAGACAGCGAAATTCTCCTGAGGCAATCCTTGAAAAAACTAGTATGAAGTTGTCCATGGCGTT GGAAAAGAAAGCAAATGCAGAAAAAGTCCTGGCGGATCTGGAGAATAGAGAGAGTCCTCAACTT TCTGATATTGACAAGGAGGGTATTACTAATGATGAAAAGTACATGCTCCGGAAAATTGGCTTGA AAATGAAGCCTTTCCTTTTACTAGGTAGAAGAGGCGTCTTTGATGGAACAATAGAGAACATGCA TCTTCACTGGAAGTATAGGGAACTTGTGAAGATCATTTGTAATGAATATAGCATTGAAGCTGCT CACAAAGTAGCAGAAATCTTGGAAGCAGAAAGTGGTGGCATACTAGTTGCTGTGGAGATGGTTA GTAAGGGCTATGCAATCATTGTGTATCGTGGAAAGAATTATGAGCGGCCTCAATGTCTACGACC TCAAACACTTCTCAGTAAGAGAGAGGCGCTGAAGCGGTCTGTGGAGGCACAACGTCGAAAG
Genomic sequence	TGGTTGACTGGAGGGACTCTGATATCTCGGGATAAAGATTTCATTGTCCTGTACAGAGGAAAGG ATTTCCTCCCATCTGCAGTTTCTTCTGCAATAGAAGAGAGGAGAAGGCAAACAATGATAATGGA GAATTCTAGTGTGCATGGTAATAAGCTGACTGAAAACGAAGAGGAAATAAAACCTCGGGCTGTT AAAGAGGATATTGAACTAGAAGCTAAGGATCAGAAGGATCATATACAAACCCATCAGATGAAAT CAAGACAGCGAAATTCTCCTGAGGCAATCCTTGAAAAAACTAGTATGAAGTTGTCCATGGTATG CCCTAACAGACAATTTATACTTGAATCCATTGGGTTTGCGAGACCTTTTTTAGTTCTGAACGGT TAGTTTTTGTCTTTAGGCGTTGGAAAAGAAAGCAAATGCAGAAAAAGTCCTGGCGGATCTGGAG AATAGAGAGAGTCCTCAACTTTCTGATATTGACAAGGAGGGTATTACTAATGATGAAAAGTACA TGCTCCGGAAAATTGGCTTGAAAATGAAGCCTTTCCTTTTACTAGGTAGGTCATTGTTTTTCCT CTTTTTCCAATTGAAAGCAGTCTGTTCCCGTCTTTCATGTAAATACTCGTGGTAAATGAGTAGT AACTGTCATGGACTCATCTCTTTGACATGGTTTATGTAAACTTCCTGTTCTGACGTATCTTGTT GTGTTCTCAAGGTAGAAGAGGCGTCTTTGATGGAACAATAGAGAACATGCATCTTCACTGGAAG TATAGGGAACTTGTGAAGATCATTTGTAATGAATATAGCATTGAAGCTGCTCACAAAGTAGCAG AAATCTTGGAAGCAGAAAGTGGTGGCATACTAGTTGCTGTGGAGATGGTTAGTAAGGGCTATGC AATCATTGTGTATCGTGGAAAGAATTATGAGCGGCCTCAATGTCTACGACCTCAAACACTTCTC AGTAAGAGAGAGGCGCTGAAGCGGTCTGTGGAGGCACAACGTCGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.29640057

Conservation Information
Conserved circRNAs	NA
PMCS	0.29640057

			
						 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 AT3G01370_circ_g.4

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