Plant Circular RNA Database

Detail information of AT3G63250_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT3G63250_circ_g.1
					
						ID in PlantcircBase
						ath_circ_028923
					
						Alias
						3:23369995-23371926
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 23369995-23371926  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G63250						
					
						Parent gene annotation
						
							Homocysteine S-methyltransferase 2
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G63250_circ_g.2 						
					
						Support reads
						2
					
						Tissues
						flower
					
						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
						AT3G63250.1:7
AT3G63250.3:6
AT3G63250.2:6

General Information
CircRNA Name	AT3G63250_circ_g.1
ID in PlantcircBase	ath_circ_028923
Alias	3:23369995-23371926
Organism	Arabidpsis thaliana
Position	chr3: 23369995-23371926 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G63250
Parent gene annotation	Homocysteine S-methyltransferase 2
Parent gene strand	-
Alternative splicing	AT3G63250_circ_g.2
Support reads	2
Tissues	flower
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	AT3G63250.1:7 AT3G63250.3:6 AT3G63250.2:6

			
						 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  
						
							AGATAGATAAACAAAGAAACATAGAATGATGGAGGTAAAGAACCTGATAAGAAGCGCTGGAGAT
GATATCAGCACCAGCTTCAAGGTAATCGAGATGCACctgtgtttgattcttcaagaaacagagc
cattagatgtatcatcggctcatccaatcatactcgttgtctccctgcacaccaaagcaacaac
ttgtgtaa

									
								

					

						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
						
							CTGTGTTTGATTCTTCAAGAAACAGAGCCATTAGATGTATCATCGGCTCATCCAATCATACTCG
TTGTCTCCCTGCACACCAAAGCAACAACTTGTGTAAAGATTTGAACCCAATGTTGGGGTTTTAA
GAGGATCAAAAGAGGTACTCAAAGGATTGTTAAACGTGCCTGACCATTGCTTCGAGGACTTTCT
ATACGCTGTCAGTATCTACATTTGAAAGCAAATTACACCATCTGAGACAAGCAAAGCTTTGACA
CAGGAGATACGAGATAGCCAAATAATGAAGGGTATTTTACAATCGCTCTCACCACATTTCCGCA
TATAGAATGCATTAAGAGCAGAGATCTCTCAAGCACATATAAATCAACAGCCTTGTATCCAGGC
GAGGTTGATGTAAAACATCCAAGATTTCTTCTCATGCAAGATGAAAACTTTCAAATTAACATCC
AAGCTTAAATGCAGTCACGCCTATCCTTGAAATTAGATTTGTAATTGGCAAAGGGAAGACAAAC
ATTCATGTTTTTGGTAGAAATCTATTGCCAAGGTTCTAGAGATTCATAGAAGAGAGTGAAGTTG
AATGCTAAAGAGATCTGCGGTTGACGAGTCTCTTGTGGATGGCTCTGATGGTGGTTGGTGTTGT
GCGGCAGCAACCTCCCAGGAGAGACACTCCTGCATCCATCCATTTCTCTACGTATGATACAAAG
TCTTCATCCCCAACTCCGGTGTTTTCCTGCAACAGTTTTTGAGCAACTCAGACAACTGTGCTCC
TTCCTCTCAAAGCAAATACTGTATATACGATGACTTACCACCCACTCCTTCCGATCAGCATCAT
AGCTTTCTCCGCTGTTTGGGTACACTAGTATGGGCTTGCTTGTCACCTACAAGTTATTCATATA
CCTTTTAGGGTCTCTACAAATACAAATACCTAATGAGTGTGGATCCAAGCCGCACCTTTTCTAT
CTCCAAAACTAGCCCCTCTATGAATCTTGGAGGGGTACAGTTGATTCCAACCGCCACTACTTTC
TCACAATTTTCAGCTATGGAGATACACTCCTTGATGGAATCCCCGCTAACCACGTTTACGCCAT
CCTTTGAGTTGAATGAAAACCACCCAGGAATCTTCACATCTCCCTCTTCTAATAGATCAGCAAA
TGCCTTGCATATCACAGAAAGAAACACCCACAGGAAGCTAACAACATCAAAATTGGGACGCTCG
ATATGAAAGGATAAATCTACTACAATATGTCAAATATCATCATCAGTACCTGAGCCTCTATCTT
GTTTGGAATGGTCTCAAATGCTATTAAATCAGCACCAGATTCCGCCAGAACTTGGAGTCGTCTG
CGGTGAAAATCCTTCAGCTTTTCCAGCGTGATCGAATCACCATAGATTCCACTGATATAATAAC
CACCAACAGTTAAAAGATAATTTTAAGGAGATAGTGCAAAAATACACGAAATCCACAAAAATCA
AAATCTGAATAGGGCAAGTGGTAAGAGCTTTAGAAACTTGTTCCAACCCAAACTCATATCATCT
ACATAGATAAGAGAAAAATGAAGCAATAACCTGTATTCAGACCCATCAGCCAAGTATGCACCGT
AGCTACCAACTGATGCTGCAACTAATATAGGGCGCTTTTTGAGAATCTTATCATCCATGGAAGA
GCTAGTTCCGCATTTGTCATAATACGAGTTCCGAGCTTCAGTCGCTATTTCTACGCTCTTTTTA
AGCAAAGATTCGCTCTCTTCTCTAGAAAATCCCTTTGCTTCAAACCCCTGAATCGTGGCCTGTT
CAGAATTATCATCAATCCAAGTTGTTAGTGTCCAAAAAAGAGATAGATAAACAAAGAAACATAG
AATGATGGAGGTAAAGAACCTGATAAGAAGCGCTGGAGATGATATCAGCACCAGCTTCAAGGTA
ATCGAGATGCAC
						
					

			
		

Sequences
Splice junction sequence	AGATAGATAAACAAAGAAACATAGAATGATGGAGGTAAAGAACCTGATAAGAAGCGCTGGAGAT GATATCAGCACCAGCTTCAAGGTAATCGAGATGCACctgtgtttgattcttcaagaaacagagc cattagatgtatcatcggctcatccaatcatactcgttgtctccctgcacaccaaagcaacaac ttgtgtaa
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	CTGTGTTTGATTCTTCAAGAAACAGAGCCATTAGATGTATCATCGGCTCATCCAATCATACTCG TTGTCTCCCTGCACACCAAAGCAACAACTTGTGTAAAGATTTGAACCCAATGTTGGGGTTTTAA GAGGATCAAAAGAGGTACTCAAAGGATTGTTAAACGTGCCTGACCATTGCTTCGAGGACTTTCT ATACGCTGTCAGTATCTACATTTGAAAGCAAATTACACCATCTGAGACAAGCAAAGCTTTGACA CAGGAGATACGAGATAGCCAAATAATGAAGGGTATTTTACAATCGCTCTCACCACATTTCCGCA TATAGAATGCATTAAGAGCAGAGATCTCTCAAGCACATATAAATCAACAGCCTTGTATCCAGGC GAGGTTGATGTAAAACATCCAAGATTTCTTCTCATGCAAGATGAAAACTTTCAAATTAACATCC AAGCTTAAATGCAGTCACGCCTATCCTTGAAATTAGATTTGTAATTGGCAAAGGGAAGACAAAC ATTCATGTTTTTGGTAGAAATCTATTGCCAAGGTTCTAGAGATTCATAGAAGAGAGTGAAGTTG AATGCTAAAGAGATCTGCGGTTGACGAGTCTCTTGTGGATGGCTCTGATGGTGGTTGGTGTTGT GCGGCAGCAACCTCCCAGGAGAGACACTCCTGCATCCATCCATTTCTCTACGTATGATACAAAG TCTTCATCCCCAACTCCGGTGTTTTCCTGCAACAGTTTTTGAGCAACTCAGACAACTGTGCTCC TTCCTCTCAAAGCAAATACTGTATATACGATGACTTACCACCCACTCCTTCCGATCAGCATCAT AGCTTTCTCCGCTGTTTGGGTACACTAGTATGGGCTTGCTTGTCACCTACAAGTTATTCATATA CCTTTTAGGGTCTCTACAAATACAAATACCTAATGAGTGTGGATCCAAGCCGCACCTTTTCTAT CTCCAAAACTAGCCCCTCTATGAATCTTGGAGGGGTACAGTTGATTCCAACCGCCACTACTTTC TCACAATTTTCAGCTATGGAGATACACTCCTTGATGGAATCCCCGCTAACCACGTTTACGCCAT CCTTTGAGTTGAATGAAAACCACCCAGGAATCTTCACATCTCCCTCTTCTAATAGATCAGCAAA TGCCTTGCATATCACAGAAAGAAACACCCACAGGAAGCTAACAACATCAAAATTGGGACGCTCG ATATGAAAGGATAAATCTACTACAATATGTCAAATATCATCATCAGTACCTGAGCCTCTATCTT GTTTGGAATGGTCTCAAATGCTATTAAATCAGCACCAGATTCCGCCAGAACTTGGAGTCGTCTG CGGTGAAAATCCTTCAGCTTTTCCAGCGTGATCGAATCACCATAGATTCCACTGATATAATAAC CACCAACAGTTAAAAGATAATTTTAAGGAGATAGTGCAAAAATACACGAAATCCACAAAAATCA AAATCTGAATAGGGCAAGTGGTAAGAGCTTTAGAAACTTGTTCCAACCCAAACTCATATCATCT ACATAGATAAGAGAAAAATGAAGCAATAACCTGTATTCAGACCCATCAGCCAAGTATGCACCGT AGCTACCAACTGATGCTGCAACTAATATAGGGCGCTTTTTGAGAATCTTATCATCCATGGAAGA GCTAGTTCCGCATTTGTCATAATACGAGTTCCGAGCTTCAGTCGCTATTTCTACGCTCTTTTTA AGCAAAGATTCGCTCTCTTCTCTAGAAAATCCCTTTGCTTCAAACCCCTGAATCGTGGCCTGTT CAGAATTATCATCAATCCAAGTTGTTAGTGTCCAAAAAAGAGATAGATAAACAAAGAAACATAG AATGATGGAGGTAAAGAACCTGATAAGAAGCGCTGGAGATGATATCAGCACCAGCTTCAAGGTA ATCGAGATGCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.119362401

Conservation Information
Conserved circRNAs	NA
PMCS	0.119362401

			
						 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 AT3G63250_circ_g.1

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