Plant Circular RNA Database

Detail information of AT5G39510_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G39510_circ_g.3
					
						ID in PlantcircBase
						ath_circ_041593
					
						Alias
						5:15822008-15823587
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 15822008-15823587  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G39510						
					
						Parent gene annotation
						
							Vesicle transport v-SNARE 11
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G39510_circ_g.4 AT5G39510_circ_g.5 						
					
						Support reads
						1/1
					
						Tissues
						seedling;root
					
						Exon boundary  
						
							Yes-No							"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
						AT5G39510.1:5

General Information
CircRNA Name	AT5G39510_circ_g.3
ID in PlantcircBase	ath_circ_041593
Alias	5:15822008-15823587
Organism	Arabidpsis thaliana
Position	chr5: 15822008-15823587 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G39510
Parent gene annotation	Vesicle transport v-SNARE 11
Parent gene strand	+
Alternative splicing	AT5G39510_circ_g.4 AT5G39510_circ_g.5
Support reads	1/1
Tissues	seedling;root
Exon boundary	Yes-No "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	AT5G39510.1:5

			
						 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  
						
							ACATGACGAGGAGGATGAACAAGAACAAATGGACCATTGGAGCCATCATCATCGCATTGATTGC
CGCCATTTTCATCATCTTGTACTTCAAACTCACCAAagtttttagtagtcttcctttggaacaa
tgagtgacgtgtttgatggatatgagcgacaatactgtgagctctcggcgagtctttcaaagaa
gtgttcct

									
								

					

						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
						
							AGTTTTTAGTAGTCTTCCTTTGGAACAATGAGTGACGTGTTTGATGGATATGAGCGACAATACT
GTGAGCTCTCGGCGAGTCTTTCAAAGAAGTGTTCCTCTGCTATTTCGCTTGATGGAGGTAAAAT
TGTTACTCTAATCTTTTCTAAGATGTGATACTTTTCCTACTCAGGCATTGCCTTACCTTCCTTA
AGATTTGAAATAACTAATTCTGGTTTAGCTTATGAATGTAACAATGTACGAATTAGAGATATCT
TGGTTTGTGTTTTTGATGCAGAGTATTGTGCGATTTAGATCCTTTAATTACTACTTCGTTGTAA
GGACATAGTATTGGTTTCTGATTACGAAGAGAGCTTGTGATTAGTATTGGTCGCTGATCATCGC
CATTTTTTTACACTGGGGATACTTCGGTTTTTGTTTGTTACTGAGAACGATTCTATAGATAGTT
TGGTTTGTGTTTGATGACTATAAACTTCTTGTCTCCTTCATGTGTTGCTAGGACATAGTAGTGT
GCCTTTCTTTTGCTTTCTTTGGAGATTGTGATTAGTAGTGTTCGCTGATCATCGGGATTGTTTT
TTTTCCCCTAGATGAGTATGCTCTGTTGATTGCATAGATAAAAATGCATTGATGATACCTTATT
AATTTGCAGAACAAAAGAAGCAGAAGTTGTCTGAAATAAAATCCGGGCTGGAAAATGCAGAAGT
ATTGGTATGTGATATGCGTAACGTGAAGTTATAGAAGCTTCTCTATTGTCCATTATTCATTTTG
ATGCTTCTCTGTCCTTTTCTTCACCAGATTAGGAAAATGGATCTCGAGGCAAGGACCCTTCCAC
CTAATCTTAAGTCCAGCCTCCTTGTCAAATTAAGAGAATTCAAGTCTGATCTGAACAATTTCAA
AACTGAAGTGAAGAGAATCACATCTGGACAGTTGAACGCTGCTGCTCGTGATGAGTTGCTAGAA
GCTGGTATGGCTGACACAAAGACGGTATGTAAAGGACTCGGTAGTATTGTTTCAATTTTATCTC
ATCTCATATCTTTGCTATTAAAACGACCTATGATTTTCTTTTTTTATTGAAACGCTGAGATCAG
GCTTCAGCTGATCAGAGAGCAAGATTGATGATGTCAACTGAGCGTCTGGGCCGAACCACTGACA
GAGTCAAGGACAGTCGTAGAACAATGATGGAGACTGAAGAAATCGGTGTTTCAATCCTCCAAGA
CTTGCACGGTCAGAGACAGTCTCTCTTACGTGCCCACGAAACGGTATTGTCTCTCTGCAACACA
TTTACTCCATATTCTCAACGATATTCTGAACAAAGTGACAAAATAAGATGAGAATTAAGGGCTA
TATCATAAAGAAGACTATGTTTTCTTGTTTTCTTTATCAACGCTGGATTGATATCGCGCTAACC
AAAATTTAGAACTCTGTTGACAGCTTCATGGAGTAGACGATAACATTGGAAAGAGCAAGAAGAT
CTTGACAGACATGACGAGGAGGATGAACAAGAACAAATGGACCATTGGAGCCATCATCATCGCA
TTGATTGCCGCCATTTTCATCATCTTGTACTTCAAACTCACCAA
						
					

			
		

Sequences
Splice junction sequence	ACATGACGAGGAGGATGAACAAGAACAAATGGACCATTGGAGCCATCATCATCGCATTGATTGC CGCCATTTTCATCATCTTGTACTTCAAACTCACCAAagtttttagtagtcttcctttggaacaa tgagtgacgtgtttgatggatatgagcgacaatactgtgagctctcggcgagtctttcaaagaa gtgttcct
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	AGTTTTTAGTAGTCTTCCTTTGGAACAATGAGTGACGTGTTTGATGGATATGAGCGACAATACT GTGAGCTCTCGGCGAGTCTTTCAAAGAAGTGTTCCTCTGCTATTTCGCTTGATGGAGGTAAAAT TGTTACTCTAATCTTTTCTAAGATGTGATACTTTTCCTACTCAGGCATTGCCTTACCTTCCTTA AGATTTGAAATAACTAATTCTGGTTTAGCTTATGAATGTAACAATGTACGAATTAGAGATATCT TGGTTTGTGTTTTTGATGCAGAGTATTGTGCGATTTAGATCCTTTAATTACTACTTCGTTGTAA GGACATAGTATTGGTTTCTGATTACGAAGAGAGCTTGTGATTAGTATTGGTCGCTGATCATCGC CATTTTTTTACACTGGGGATACTTCGGTTTTTGTTTGTTACTGAGAACGATTCTATAGATAGTT TGGTTTGTGTTTGATGACTATAAACTTCTTGTCTCCTTCATGTGTTGCTAGGACATAGTAGTGT GCCTTTCTTTTGCTTTCTTTGGAGATTGTGATTAGTAGTGTTCGCTGATCATCGGGATTGTTTT TTTTCCCCTAGATGAGTATGCTCTGTTGATTGCATAGATAAAAATGCATTGATGATACCTTATT AATTTGCAGAACAAAAGAAGCAGAAGTTGTCTGAAATAAAATCCGGGCTGGAAAATGCAGAAGT ATTGGTATGTGATATGCGTAACGTGAAGTTATAGAAGCTTCTCTATTGTCCATTATTCATTTTG ATGCTTCTCTGTCCTTTTCTTCACCAGATTAGGAAAATGGATCTCGAGGCAAGGACCCTTCCAC CTAATCTTAAGTCCAGCCTCCTTGTCAAATTAAGAGAATTCAAGTCTGATCTGAACAATTTCAA AACTGAAGTGAAGAGAATCACATCTGGACAGTTGAACGCTGCTGCTCGTGATGAGTTGCTAGAA GCTGGTATGGCTGACACAAAGACGGTATGTAAAGGACTCGGTAGTATTGTTTCAATTTTATCTC ATCTCATATCTTTGCTATTAAAACGACCTATGATTTTCTTTTTTTATTGAAACGCTGAGATCAG GCTTCAGCTGATCAGAGAGCAAGATTGATGATGTCAACTGAGCGTCTGGGCCGAACCACTGACA GAGTCAAGGACAGTCGTAGAACAATGATGGAGACTGAAGAAATCGGTGTTTCAATCCTCCAAGA CTTGCACGGTCAGAGACAGTCTCTCTTACGTGCCCACGAAACGGTATTGTCTCTCTGCAACACA TTTACTCCATATTCTCAACGATATTCTGAACAAAGTGACAAAATAAGATGAGAATTAAGGGCTA TATCATAAAGAAGACTATGTTTTCTTGTTTTCTTTATCAACGCTGGATTGATATCGCGCTAACC AAAATTTAGAACTCTGTTGACAGCTTCATGGAGTAGACGATAACATTGGAAAGAGCAAGAAGAT CTTGACAGACATGACGAGGAGGATGAACAAGAACAAATGGACCATTGGAGCCATCATCATCGCA TTGATTGCCGCCATTTTCATCATCTTGTACTTCAAACTCACCAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.183572227

Conservation Information
Conserved circRNAs	NA
PMCS	0.183572227

			
						 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 AT5G39510_circ_g.3

Address

Any questions?

Supported by