Plant Circular RNA Database

Detail information of AT3G43610_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT3G43610_circ_g.3
					
						ID in PlantcircBase
						ath_circ_025937
					
						Alias
						3:15521254-15522344
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 15521254-15522344  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT3G43610						
					
						Parent gene annotation
						
							Spc97 / Spc98 family of spindle pole body (SBP) component
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						1/1
					
						Tissues
						seedling;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
						AT3G43610.2:3
AT3G43610.3:3
AT3G43610.1:3

General Information
CircRNA Name	AT3G43610_circ_g.3
ID in PlantcircBase	ath_circ_025937
Alias	3:15521254-15522344
Organism	Arabidpsis thaliana
Position	chr3: 15521254-15522344 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT3G43610
Parent gene annotation	Spc97 / Spc98 family of spindle pole body (SBP) component
Parent gene strand	-
Alternative splicing	NA
Support reads	1/1
Tissues	seedling;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	AT3G43610.2:3 AT3G43610.3:3 AT3G43610.1:3

			
						 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  
						
							GTTCGGCTTTAAACATCCAAGATCTTATAAACTCACAATATGGCTCACATGTTTTGAGGAACAA
AAACTTCAGCATAGCACTGTGAGTAGGATCAGCAACctggtcaagtctattgccattgttgaag
gaattagtaaactctcatccagtgtgaaataaatggaatttttgtctccgtcgccataggagat
tggtaaag

									
								

					

						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: 623
Transcript exons: 15521254-15521369,15521753-15522061,15522147-15522344
CTGGTCAAGTCTATTGCCATTGTTGAAGGAATTAGTAAACTCTCATCCAGTGTGAAATAAATGG
AATTTTTGTCTCCGTCGCCATAGGAGATTGGTAAAGATATTGCTCCAGGAACCTGCCCAGGGAA
CACTTCAAACTTTTCTGAAAAGTCACCAAGTTTTTCTTGCATCATTCTGTAGTAATCGTCTCTT
TTCTTTATCATCACTTCTATATGTAATTTGCTGAAAGTTATTGGAGATGGGTACCCTGGACTAG
TGGTAGAAAAATAGGTCCAACACGGAAGAAGATCTGTGTAATTTTTGTGTCCAGACGCAGGAAG
ATTACACAGTTCCAGAAGTTTTGTAATTACTTGAAGCTGTTGACCAGCCCTTACTATAGGTTCC
AAGAAGCCGTTTAAGAAACACGGAACAAGCCCTCCTCGCTCCCTTACGCTCTTCAATGGGGAGA
TGCCAGGCTTATTCCAAGAAAAAGATGTTGACTCACTGCGACATTCCACAATGAACTCCTTGTG
AGGATCGTTAAGTTCGGCTTTAAACATCCAAGATCTTATAAACTCACAATATGGCTCACATGTT
TTGAGGAACAAAAACTTCAGCATAGCACTGTGAGTAGGATCAGCAAC
						
					

						Genomic sequence
						
							CTGGTCAAGTCTATTGCCATTGTTGAAGGAATTAGTAAACTCTCATCCAGTGTGAAATAAATGG
AATTTTTGTCTCCGTCGCCATAGGAGATTGGTAAAGATATTGCTCCAGGAACCTAAGAATTAAA
ATGTCAACATAAGACAGAACTGAAAAGAAATAACTTCCTGTTAGCTCCAAGTACAACCAAAAAA
AGAATCACTTTTAAGGTCCCTATATTTTTCACTTGCACCATCAGCTCACAGTTAAGAAAACCAG
AGAATGAGACGCTTCTACAATGCTGAATGGTCTGATATGAATGAGACGCTTCTACAATGCTGAA
TGGTCTGATATGAATGAGTCCTTAATTTACCTAAGACAAACTTGATTTCACAACAGAGTAAAAC
CACCTATGGCCTATAAGACGAGTAAAGTAAGGACTAGCATAGCAACGAGAGAGTACATGCAGAC
ACGTATACCAAAAAGACTCCAGCTTCAGCAAAAAAATAATAAGCACAATACCTGCCCAGGGAAC
ACTTCAAACTTTTCTGAAAAGTCACCAAGTTTTTCTTGCATCATTCTGTAGTAATCGTCTCTTT
TCTTTATCATCACTTCTATATGTAATTTGCTGAAAGTTATTGGAGATGGGTACCCTGGACTAGT
GGTAGAAAAATAGGTCCAACACGGAAGAAGATCTGTGTAATTTTTGTGTCCAGACGCAGGAAGA
TTACACAGTTCCAGAAGTTTTGTAATTACTTGAAGCTGTTGACCAGCCCTTACTATAGGTTCCA
AGAAGCCGTTTAAGAAACACGGAACAAGCCCTCCTCGCTCCTAGGGGCAGAATATGAAGCAATT
TGATACCCATGGTTTAAAGATACCAAAGTCAAAGATGCAGTAAACGCAAATAAAATATTACCCT
TACGCTCTTCAATGGGGAGATGCCAGGCTTATTCCAAGAAAAAGATGTTGACTCACTGCGACAT
TCCACAATGAACTCCTTGTGAGGATCGTTAAGTTCGGCTTTAAACATCCAAGATCTTATAAACT
CACAATATGGCTCACATGTTTTGAGGAACAAAAACTTCAGCATAGCACTGTGAGTAGGATCAGC
AAC
						
					

			
		

Sequences
Splice junction sequence	GTTCGGCTTTAAACATCCAAGATCTTATAAACTCACAATATGGCTCACATGTTTTGAGGAACAA AAACTTCAGCATAGCACTGTGAGTAGGATCAGCAACctggtcaagtctattgccattgttgaag gaattagtaaactctcatccagtgtgaaataaatggaatttttgtctccgtcgccataggagat tggtaaag
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: 623 Transcript exons: 15521254-15521369,15521753-15522061,15522147-15522344 CTGGTCAAGTCTATTGCCATTGTTGAAGGAATTAGTAAACTCTCATCCAGTGTGAAATAAATGG AATTTTTGTCTCCGTCGCCATAGGAGATTGGTAAAGATATTGCTCCAGGAACCTGCCCAGGGAA CACTTCAAACTTTTCTGAAAAGTCACCAAGTTTTTCTTGCATCATTCTGTAGTAATCGTCTCTT TTCTTTATCATCACTTCTATATGTAATTTGCTGAAAGTTATTGGAGATGGGTACCCTGGACTAG TGGTAGAAAAATAGGTCCAACACGGAAGAAGATCTGTGTAATTTTTGTGTCCAGACGCAGGAAG ATTACACAGTTCCAGAAGTTTTGTAATTACTTGAAGCTGTTGACCAGCCCTTACTATAGGTTCC AAGAAGCCGTTTAAGAAACACGGAACAAGCCCTCCTCGCTCCCTTACGCTCTTCAATGGGGAGA TGCCAGGCTTATTCCAAGAAAAAGATGTTGACTCACTGCGACATTCCACAATGAACTCCTTGTG AGGATCGTTAAGTTCGGCTTTAAACATCCAAGATCTTATAAACTCACAATATGGCTCACATGTT TTGAGGAACAAAAACTTCAGCATAGCACTGTGAGTAGGATCAGCAAC
Genomic sequence	CTGGTCAAGTCTATTGCCATTGTTGAAGGAATTAGTAAACTCTCATCCAGTGTGAAATAAATGG AATTTTTGTCTCCGTCGCCATAGGAGATTGGTAAAGATATTGCTCCAGGAACCTAAGAATTAAA ATGTCAACATAAGACAGAACTGAAAAGAAATAACTTCCTGTTAGCTCCAAGTACAACCAAAAAA AGAATCACTTTTAAGGTCCCTATATTTTTCACTTGCACCATCAGCTCACAGTTAAGAAAACCAG AGAATGAGACGCTTCTACAATGCTGAATGGTCTGATATGAATGAGACGCTTCTACAATGCTGAA TGGTCTGATATGAATGAGTCCTTAATTTACCTAAGACAAACTTGATTTCACAACAGAGTAAAAC CACCTATGGCCTATAAGACGAGTAAAGTAAGGACTAGCATAGCAACGAGAGAGTACATGCAGAC ACGTATACCAAAAAGACTCCAGCTTCAGCAAAAAAATAATAAGCACAATACCTGCCCAGGGAAC ACTTCAAACTTTTCTGAAAAGTCACCAAGTTTTTCTTGCATCATTCTGTAGTAATCGTCTCTTT TCTTTATCATCACTTCTATATGTAATTTGCTGAAAGTTATTGGAGATGGGTACCCTGGACTAGT GGTAGAAAAATAGGTCCAACACGGAAGAAGATCTGTGTAATTTTTGTGTCCAGACGCAGGAAGA TTACACAGTTCCAGAAGTTTTGTAATTACTTGAAGCTGTTGACCAGCCCTTACTATAGGTTCCA AGAAGCCGTTTAAGAAACACGGAACAAGCCCTCCTCGCTCCTAGGGGCAGAATATGAAGCAATT TGATACCCATGGTTTAAAGATACCAAAGTCAAAGATGCAGTAAACGCAAATAAAATATTACCCT TACGCTCTTCAATGGGGAGATGCCAGGCTTATTCCAAGAAAAAGATGTTGACTCACTGCGACAT TCCACAATGAACTCCTTGTGAGGATCGTTAAGTTCGGCTTTAAACATCCAAGATCTTATAAACT CACAATATGGCTCACATGTTTTGAGGAACAAAAACTTCAGCATAGCACTGTGAGTAGGATCAGC AAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.199595731

Conservation Information
Conserved circRNAs	NA
PMCS	0.199595731

			
						 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 AT3G43610_circ_g.3

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