Plant Circular RNA Database

Detail information of AT5G02840_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT5G02840_circ_g.2
					
						ID in PlantcircBase
						ath_circ_036073
					
						Alias
						5:649604-650920
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 649604-650920  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G02840						
					
						Parent gene annotation
						
							LCL1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G02840_circ_g.3 						
					
						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  
						
							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
						AT5G02840.5:6
AT5G02840.4:6
AT5G02840.1:6
AT5G02840.2:6
AT5G02840.3:6

General Information
CircRNA Name	AT5G02840_circ_g.2
ID in PlantcircBase	ath_circ_036073
Alias	5:649604-650920
Organism	Arabidpsis thaliana
Position	chr5: 649604-650920 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G02840
Parent gene annotation	LCL1
Parent gene strand	+
Alternative splicing	AT5G02840_circ_g.3
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	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	AT5G02840.5:6 AT5G02840.4:6 AT5G02840.1:6 AT5G02840.2:6 AT5G02840.3:6

			
						 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  
						
							TTTTCCTAGTATCCGTCACTAATCACAGTTTTTCTTGCAGGTTTTGCTGTTGATGAGAAACCTC
ACAGTGAACTTGTCAAACCCTGACTTTGAACCTACTgtttgatcgtgactggaaaaagatagaa
gattttgttggttcaaagacagttattcaggtttgagatcagcttctttggatttttggtttaa
tatacaac

						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
						
							GTTTGATCGTGACTGGAAAAAGATAGAAGATTTTGTTGGTTCAAAGACAGTTATTCAGGTTTGA
GATCAGCTTCTTTGGATTTTTGGTTTAATATACAACCTTGGCACATTTCCCCACTCAATCATCC
TGTGCCTGTTTGATTTACTGCAGATCAGGAGCCATGCCCAAAAATACTTTCTAAAGGTCCAAAA
AAATGGGACTTTAGCACATGTTCCACCCCCTAGGCCTAAGCGCAAAGCTGCTCATCCATATCCT
CAAAAGGCATCGAAAAATGGTTAGTTCTATTGTAATAGATATTACTTTGGGTTGACAGATGGAG
TAACATGTAATCAATCTGATTTCAACTCAAATCTGCAGCTCAAATGTCGCTTCACGTTTCCATG
TCCTTTCCTACTCAAATAAATAACCTGCCTGGATATACTCCATGGGATGATGATACATCTGCAT
TGTTAAACATTGCTGTAAGTGGGGTTATTCCACCAGAAGATGAACTTGATACTCTTTGTGGAGC
AGAAGGCATGCGTTCTCATCTGTACTCAGTTTTTATATTTTGCTTTGGTAGTCTAGTCACTCTA
TCTTCTGAAGTTTTCATATGCTAAATGCGGCTTACATATCATTGTTTCAGTTGATGTTGGATCA
AATGACATGATAAGTGAAACTAGTCCTTCAGCATCTGGTATCGGAAGCTCAAGCAGAACACTAT
CAGATTCTAAGGGTTTGAGACTGGCGAAACAAGCTCCCTCAATGCATGGTAATTATCTGAACAA
TTGAGGGACTATTTCTTAGTTTTCATTTTGTGGTGGACGCTGTTGTAATGGTTGCTTTGCAGGT
CTTCCTGATTTTGCTGAGGTTTATAACTTCATTGGGAGTGTGTTCGATCCTGACAGCAAAGGCC
GCATGAAAAAGCTCAAGGAAATGGATCCTATAAATTTCGAAACTGTGAGTTGGAGCTTTACTTG
CCTTTAGATTAACTGATATGTGTGTTGCAGCATATCAATCATTTAGTCTTCTTCTTTGAGTTCC
CGAATAAATTCAGCTGTGTGAGAAGATAAATATAAAGATCAGTACTTGCAATATATAGATTCAC
GAGTTGGAAACACCAAAAAGCCAAAGTACCATGATTCTATGGAGATGTTGGTCAAATAATGGGA
TTGTTACAACCATGAGTCAGTTTTAGGTGTCATGGTACCTATTTGTAGCTGTCAGTGATTGTTC
TTTTTCCTAGTATCCGTCACTAATCACAGTTTTTCTTGCAGGTTTTGCTGTTGATGAGAAACCT
CACAGTGAACTTGTCAAACCCTGACTTTGAACCTACT

Sequences
Splice junction sequence	TTTTCCTAGTATCCGTCACTAATCACAGTTTTTCTTGCAGGTTTTGCTGTTGATGAGAAACCTC ACAGTGAACTTGTCAAACCCTGACTTTGAACCTACTgtttgatcgtgactggaaaaagatagaa gattttgttggttcaaagacagttattcaggtttgagatcagcttctttggatttttggtttaa tatacaac
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	GTTTGATCGTGACTGGAAAAAGATAGAAGATTTTGTTGGTTCAAAGACAGTTATTCAGGTTTGA GATCAGCTTCTTTGGATTTTTGGTTTAATATACAACCTTGGCACATTTCCCCACTCAATCATCC TGTGCCTGTTTGATTTACTGCAGATCAGGAGCCATGCCCAAAAATACTTTCTAAAGGTCCAAAA AAATGGGACTTTAGCACATGTTCCACCCCCTAGGCCTAAGCGCAAAGCTGCTCATCCATATCCT CAAAAGGCATCGAAAAATGGTTAGTTCTATTGTAATAGATATTACTTTGGGTTGACAGATGGAG TAACATGTAATCAATCTGATTTCAACTCAAATCTGCAGCTCAAATGTCGCTTCACGTTTCCATG TCCTTTCCTACTCAAATAAATAACCTGCCTGGATATACTCCATGGGATGATGATACATCTGCAT TGTTAAACATTGCTGTAAGTGGGGTTATTCCACCAGAAGATGAACTTGATACTCTTTGTGGAGC AGAAGGCATGCGTTCTCATCTGTACTCAGTTTTTATATTTTGCTTTGGTAGTCTAGTCACTCTA TCTTCTGAAGTTTTCATATGCTAAATGCGGCTTACATATCATTGTTTCAGTTGATGTTGGATCA AATGACATGATAAGTGAAACTAGTCCTTCAGCATCTGGTATCGGAAGCTCAAGCAGAACACTAT CAGATTCTAAGGGTTTGAGACTGGCGAAACAAGCTCCCTCAATGCATGGTAATTATCTGAACAA TTGAGGGACTATTTCTTAGTTTTCATTTTGTGGTGGACGCTGTTGTAATGGTTGCTTTGCAGGT CTTCCTGATTTTGCTGAGGTTTATAACTTCATTGGGAGTGTGTTCGATCCTGACAGCAAAGGCC GCATGAAAAAGCTCAAGGAAATGGATCCTATAAATTTCGAAACTGTGAGTTGGAGCTTTACTTG CCTTTAGATTAACTGATATGTGTGTTGCAGCATATCAATCATTTAGTCTTCTTCTTTGAGTTCC CGAATAAATTCAGCTGTGTGAGAAGATAAATATAAAGATCAGTACTTGCAATATATAGATTCAC GAGTTGGAAACACCAAAAAGCCAAAGTACCATGATTCTATGGAGATGTTGGTCAAATAATGGGA TTGTTACAACCATGAGTCAGTTTTAGGTGTCATGGTACCTATTTGTAGCTGTCAGTGATTGTTC TTTTTCCTAGTATCCGTCACTAATCACAGTTTTTCTTGCAGGTTTTGCTGTTGATGAGAAACCT CACAGTGAACTTGTCAAACCCTGACTTTGAACCTACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.157970217

Conservation Information
Conserved circRNAs	NA
PMCS	0.157970217

			
						 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 AT5G02840_circ_g.2

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