Plant Circular RNA Database

Detail information of AT5G23540_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT5G23540_circ_g.3
					
						ID in PlantcircBase
						ath_circ_040055
					
						Alias
						5:7938092-7939059
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 7938092-7939059  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G23540						
					
						Parent gene annotation
						
							26S proteasome non-ATPase regulatory subunit 14 homolog
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G23540_circ_g.1 AT5G23540_circ_g.2 						
					
						Support reads
						1/1/1
					
						Tissues
						root;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
						AT5G23540.2:4
AT5G23540.1:4

General Information
CircRNA Name	AT5G23540_circ_g.3
ID in PlantcircBase	ath_circ_040055
Alias	5:7938092-7939059
Organism	Arabidpsis thaliana
Position	chr5: 7938092-7939059 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G23540
Parent gene annotation	26S proteasome non-ATPase regulatory subunit 14 homolog
Parent gene strand	+
Alternative splicing	AT5G23540_circ_g.1 AT5G23540_circ_g.2
Support reads	1/1/1
Tissues	root;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	AT5G23540.2:4 AT5G23540.1:4

			
						 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  
						
							GGAGAAGATGTTACTCAACCTCCACAAGAAGAAATGGACAGATGGTCTGACGCTAAGACGCTTT
GACACCCACTCCAAGACCAACGAACAGACGGTCCAGgaagagctggtgttcctatggaagtcat
gggattgatgcttggagagtttgtggatgaatacactgttagggttgtggatgtttttgcgatg
cctcagag

									
								

					

						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: 605
Transcript exons: 7938092-7938269,7938361-7938442,7938624-7938800,7938892-
7939059
GAAGAGCTGGTGTTCCTATGGAAGTCATGGGATTGATGCTTGGAGAGTTTGTGGATGAATACAC
TGTTAGGGTTGTGGATGTTTTTGCGATGCCTCAGAGTGGTACTGGTGTTAGTGTTGAAGCTGTT
GATCATGTTTTCCAGACTAATATGCTCGACATGCTTAAACAGACCGGAAGACCTGAGATGGTGG
TTGGTTGGTATCATTCACATCCTGGATTCGGCTGCTGGCTTTCTGGGGTTGACATTAATACTCA
ACAGAGTTTTGAAGCTTTGAATCAGCGAGCTGTAGCAGTGGTGGTAGATCCGATTCAGAGTGTG
AAAGGAAAGGTGGTGATTGATGCGTTCCGCTCCATAAATCCACAGACCATTATGCTTGGGCAGG
AACCCCGTCAAACAACATCGAACCTTGGGCACTTGAACAAACCATCGATCCAGGCTTTGATTCA
CGGGTTGAACAGACACTATTACTCAATAGCAATCAACTATAGGAAGAACGAGCTTGAGGAGAAG
ATGTTACTCAACCTCCACAAGAAGAAATGGACAGATGGTCTGACGCTAAGACGCTTTGACACCC
ACTCCAAGACCAACGAACAGACGGTCCAG
						
					

						Genomic sequence
						
							GAAGAGCTGGTGTTCCTATGGAAGTCATGGGATTGATGCTTGGAGAGTTTGTGGATGAATACAC
TGTTAGGGTTGTGGATGTTTTTGCGATGCCTCAGAGTGGTACTGGTGTTAGTGTTGAAGCTGTT
GATCATGTTTTCCAGACTAATATGCTCGACATGCTTAAACAGACCGGAAGGTAACTAGTTCTTC
TCTAAACCTATTTACTACGCTTAAGTGAGGTTTCCTATTTAGGTTTTGGATCTGATTCTTCTTG
TATCTTGTTTCAGACCTGAGATGGTGGTTGGTTGGTATCATTCACATCCTGGATTCGGCTGCTG
GCTTTCTGGGGTTGACATTAATACTCAACAGGTAGAGTTTTGTTTGCTCTGTTTGCATACTTAT
CAATTTGTGAATTGCACTTGAGAATTTGTTGTTTGCTTTATTGATGGCTCAAAAAACTAAATAG
AATGTTACTCATTGTGTTCTATACCCTGTTGTGATTCACTTTGTATTATATATGTTCATTGTGA
ATATCTGTGTGCTTTTGTAGAGTTTTGAAGCTTTGAATCAGCGAGCTGTAGCAGTGGTGGTAGA
TCCGATTCAGAGTGTGAAAGGAAAGGTGGTGATTGATGCGTTCCGCTCCATAAATCCACAGACC
ATTATGCTTGGGCAGGAACCCCGTCAAACAACATCGAACCTTGGGCACTTGAACAAACCATCGA
TCCAGGTGATTATCACTAACTGAATGTGTCCTGTTTTTAAGTTGAAACGAAATCAAAGGTTTTC
TCTGATACTGACTTTTGGATACTACTATGCAGGCTTTGATTCACGGGTTGAACAGACACTATTA
CTCAATAGCAATCAACTATAGGAAGAACGAGCTTGAGGAGAAGATGTTACTCAACCTCCACAAG
AAGAAATGGACAGATGGTCTGACGCTAAGACGCTTTGACACCCACTCCAAGACCAACGAACAGA
CGGTCCAG
						
					

			
		

Sequences
Splice junction sequence	GGAGAAGATGTTACTCAACCTCCACAAGAAGAAATGGACAGATGGTCTGACGCTAAGACGCTTT GACACCCACTCCAAGACCAACGAACAGACGGTCCAGgaagagctggtgttcctatggaagtcat gggattgatgcttggagagtttgtggatgaatacactgttagggttgtggatgtttttgcgatg cctcagag
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: 605 Transcript exons: 7938092-7938269,7938361-7938442,7938624-7938800,7938892- 7939059 GAAGAGCTGGTGTTCCTATGGAAGTCATGGGATTGATGCTTGGAGAGTTTGTGGATGAATACAC TGTTAGGGTTGTGGATGTTTTTGCGATGCCTCAGAGTGGTACTGGTGTTAGTGTTGAAGCTGTT GATCATGTTTTCCAGACTAATATGCTCGACATGCTTAAACAGACCGGAAGACCTGAGATGGTGG TTGGTTGGTATCATTCACATCCTGGATTCGGCTGCTGGCTTTCTGGGGTTGACATTAATACTCA ACAGAGTTTTGAAGCTTTGAATCAGCGAGCTGTAGCAGTGGTGGTAGATCCGATTCAGAGTGTG AAAGGAAAGGTGGTGATTGATGCGTTCCGCTCCATAAATCCACAGACCATTATGCTTGGGCAGG AACCCCGTCAAACAACATCGAACCTTGGGCACTTGAACAAACCATCGATCCAGGCTTTGATTCA CGGGTTGAACAGACACTATTACTCAATAGCAATCAACTATAGGAAGAACGAGCTTGAGGAGAAG ATGTTACTCAACCTCCACAAGAAGAAATGGACAGATGGTCTGACGCTAAGACGCTTTGACACCC ACTCCAAGACCAACGAACAGACGGTCCAG
Genomic sequence	GAAGAGCTGGTGTTCCTATGGAAGTCATGGGATTGATGCTTGGAGAGTTTGTGGATGAATACAC TGTTAGGGTTGTGGATGTTTTTGCGATGCCTCAGAGTGGTACTGGTGTTAGTGTTGAAGCTGTT GATCATGTTTTCCAGACTAATATGCTCGACATGCTTAAACAGACCGGAAGGTAACTAGTTCTTC TCTAAACCTATTTACTACGCTTAAGTGAGGTTTCCTATTTAGGTTTTGGATCTGATTCTTCTTG TATCTTGTTTCAGACCTGAGATGGTGGTTGGTTGGTATCATTCACATCCTGGATTCGGCTGCTG GCTTTCTGGGGTTGACATTAATACTCAACAGGTAGAGTTTTGTTTGCTCTGTTTGCATACTTAT CAATTTGTGAATTGCACTTGAGAATTTGTTGTTTGCTTTATTGATGGCTCAAAAAACTAAATAG AATGTTACTCATTGTGTTCTATACCCTGTTGTGATTCACTTTGTATTATATATGTTCATTGTGA ATATCTGTGTGCTTTTGTAGAGTTTTGAAGCTTTGAATCAGCGAGCTGTAGCAGTGGTGGTAGA TCCGATTCAGAGTGTGAAAGGAAAGGTGGTGATTGATGCGTTCCGCTCCATAAATCCACAGACC ATTATGCTTGGGCAGGAACCCCGTCAAACAACATCGAACCTTGGGCACTTGAACAAACCATCGA TCCAGGTGATTATCACTAACTGAATGTGTCCTGTTTTTAAGTTGAAACGAAATCAAAGGTTTTC TCTGATACTGACTTTTGGATACTACTATGCAGGCTTTGATTCACGGGTTGAACAGACACTATTA CTCAATAGCAATCAACTATAGGAAGAACGAGCTTGAGGAGAAGATGTTACTCAACCTCCACAAG AAGAAATGGACAGATGGTCTGACGCTAAGACGCTTTGACACCCACTCCAAGACCAACGAACAGA CGGTCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.347787615

Conservation Information
Conserved circRNAs	NA
PMCS	0.347787615

			
						 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 AT5G23540_circ_g.3

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