Plant Circular RNA Database

Detail information of AT5G13840_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G13840_circ_g.1
					
						ID in PlantcircBase
						ath_circ_038126
					
						Alias
						5:4468625-4470402
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 4468625-4470402  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G13840						
					
						Parent gene annotation
						
							Protein FIZZY-RELATED 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G13840_circ_g.2 AT5G13840_circ_g.3 AT5G13840_circ_g.4 						
					
						Support reads
						2/1
					
						Tissues
						seedling;root
					
						Exon boundary  
						
							No-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  
						
							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
						AT5G13840.1:7
AT5G13840.2:7

General Information
CircRNA Name	AT5G13840_circ_g.1
ID in PlantcircBase	ath_circ_038126
Alias	5:4468625-4470402
Organism	Arabidpsis thaliana
Position	chr5: 4468625-4470402 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G13840
Parent gene annotation	Protein FIZZY-RELATED 3
Parent gene strand	-
Alternative splicing	AT5G13840_circ_g.2 AT5G13840_circ_g.3 AT5G13840_circ_g.4
Support reads	2/1
Tissues	seedling;root
Exon boundary	No-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	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	AT5G13840.1:7 AT5G13840.2:7

			
						 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  
						
							GGAGAAAACGGCGAACTAGGACTTGAATTGGAACGATCCGTCTTGAATCTCAACATGTTAGTAC
ATGGACTCATCGGAGAAGAAGCAGATCCTTGACCACattccagcttctctgtctgtatctctgt
gcagttgtgtatgtctccctgttattatcggatctgtgtcctccccaatgaccagagacctgtg
tctttcac

									
								

					

						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
						
							ATTCCAGCTTCTCTGTCTGTATCTCTGTGCAGTTGTGTATGTCTCCCTGTTATTATCGGATCTG
TGTCCTCCCCAATGACCAGAGACCTGTGTCTTTCACTGGTGTCTGTAAACAGAAAAATTGTCAT
TAATCAACTGAGCATAAAGAGCCAGAAGATCTGATTCTGGTCTGAAGGAATTTATAAACTCGAA
AAAAGAATACAAACCTGCATTTTTACTGAAGGAAAGACGTTCCAAAACCGCAGGGTCTCATCTC
CTGCTCCGGTCACTATAGTCTGGCCATCAGGTGACGTAGCCAAGTAAAGTACTCTCATACTGTG
GCCCGTAAGTGTTGCAACCTACATCAGTTGATGCGTCAGTTATACATATTGAAGATGAGAGAAA
GATCAAGAAAATGAGCTTTCAAGTGTGAACAAAACTATGTACCTTTGACATGGATGGGTACTTC
CAGAGCATGATTTGGTTTTGAGAGTATCCATGAGTACTCACTATCTCGTTAACATTCTTGCTCC
ACGCCAGATTGCAGACCTGGCTCCCAGTGTCGATGCTGTTTAACTGATTTCCGTTTGTCGTGTT
CCAGAATCTAATGCATCTGTCTGCGGTTCCACCTCCCGAAGCAAGGAGGCTGCTCTGATGAGGA
GACCATGTAATTGCCTTAACCGCTGCTGTATGCTCAGTCAGCTTCAGAATAGGTTGCTGTGAAT
GATTGTTCCATACCAATAACTGTTTCCAAAAAAAGTACTCACCAGTGTTAATATGATAAGCTTC
AAAGAAGTTCAACTTTTGCTCTTAACATATGGAACACAGAGATTGCAGAGCACTGAGTAGCTTA
TGCTCAAGATCACCTGATTATCATTGCCTCCAGACGCAAGCTCTCTATCATCATGAGACCATTT
CAGACCGCAGACTTCAGATTTGTGGCCCACGAGTTTGCTGACAAAATCGCTCTGGACTCGGATA
TCATGCTGAAGGATGTTTCTGTCTCTGCTCCCTGATGATAAGATCCTTGAGTTCCATGCCAAGA
CACCAGTTCTTGTTTGATGACCTCCCATGGTTCGGACTCTCTTGCACTGTGTTCCGTCCCAAAC
CTGCCAAAAAGTAAACCGTTAGTAACTTCATTGCATCATAACAAAACTTTCCACAACCACAGAT
TGGAAGGTAACAAACAACACACCTGAACCTGACCATGACTTGTACCAATAGATATATATGAACC
TTCCCGTGTCCACTGAACCGAGCACACACTGTCATTAGGCCCTAGGTCACATAACTTAGTCACC
TAACCAACAAATTCACTGTTAAATGAATACACCACAACTAAAAACATTGTGCAAATCTTAAGAA
CTAGTCAAGTATATCAAAACACTCACTTTGCTATTGGAAGCCGTCCAAAGATAAACACAAGTAC
CAAGCCCAACGGCAAGAACATTCTGTGAACTCCAGTCCACAACATTCAAGTAGAAGTCATCTTG
TAAAGAAGGAGCATCCAAGACCTGAGACCACATCAAAAACAAAACAATCTATCATTTCTACTTC
TCATGAATCTGTAATAACATCACATAAACAGGTTGGATCTAAACGATATAATACCTTATGAGGT
GTTTTAGGAACCTTGCGAGGGGGCTTCGGAGGCGGAGACGAGTCACTGGAGTGACCATTATCAT
TTCCGAGAATGGAAGGAGAAAACGGCGAACTAGGACTTGAATTGGAACGATCCGTCTTGAATCT
CAACATGTTAGTACATGGACTCATCGGAGAAGAAGCAGATCCTTGACCAC
						
					

			
		

Sequences
Splice junction sequence	GGAGAAAACGGCGAACTAGGACTTGAATTGGAACGATCCGTCTTGAATCTCAACATGTTAGTAC ATGGACTCATCGGAGAAGAAGCAGATCCTTGACCACattccagcttctctgtctgtatctctgt gcagttgtgtatgtctccctgttattatcggatctgtgtcctccccaatgaccagagacctgtg tctttcac
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	ATTCCAGCTTCTCTGTCTGTATCTCTGTGCAGTTGTGTATGTCTCCCTGTTATTATCGGATCTG TGTCCTCCCCAATGACCAGAGACCTGTGTCTTTCACTGGTGTCTGTAAACAGAAAAATTGTCAT TAATCAACTGAGCATAAAGAGCCAGAAGATCTGATTCTGGTCTGAAGGAATTTATAAACTCGAA AAAAGAATACAAACCTGCATTTTTACTGAAGGAAAGACGTTCCAAAACCGCAGGGTCTCATCTC CTGCTCCGGTCACTATAGTCTGGCCATCAGGTGACGTAGCCAAGTAAAGTACTCTCATACTGTG GCCCGTAAGTGTTGCAACCTACATCAGTTGATGCGTCAGTTATACATATTGAAGATGAGAGAAA GATCAAGAAAATGAGCTTTCAAGTGTGAACAAAACTATGTACCTTTGACATGGATGGGTACTTC CAGAGCATGATTTGGTTTTGAGAGTATCCATGAGTACTCACTATCTCGTTAACATTCTTGCTCC ACGCCAGATTGCAGACCTGGCTCCCAGTGTCGATGCTGTTTAACTGATTTCCGTTTGTCGTGTT CCAGAATCTAATGCATCTGTCTGCGGTTCCACCTCCCGAAGCAAGGAGGCTGCTCTGATGAGGA GACCATGTAATTGCCTTAACCGCTGCTGTATGCTCAGTCAGCTTCAGAATAGGTTGCTGTGAAT GATTGTTCCATACCAATAACTGTTTCCAAAAAAAGTACTCACCAGTGTTAATATGATAAGCTTC AAAGAAGTTCAACTTTTGCTCTTAACATATGGAACACAGAGATTGCAGAGCACTGAGTAGCTTA TGCTCAAGATCACCTGATTATCATTGCCTCCAGACGCAAGCTCTCTATCATCATGAGACCATTT CAGACCGCAGACTTCAGATTTGTGGCCCACGAGTTTGCTGACAAAATCGCTCTGGACTCGGATA TCATGCTGAAGGATGTTTCTGTCTCTGCTCCCTGATGATAAGATCCTTGAGTTCCATGCCAAGA CACCAGTTCTTGTTTGATGACCTCCCATGGTTCGGACTCTCTTGCACTGTGTTCCGTCCCAAAC CTGCCAAAAAGTAAACCGTTAGTAACTTCATTGCATCATAACAAAACTTTCCACAACCACAGAT TGGAAGGTAACAAACAACACACCTGAACCTGACCATGACTTGTACCAATAGATATATATGAACC TTCCCGTGTCCACTGAACCGAGCACACACTGTCATTAGGCCCTAGGTCACATAACTTAGTCACC TAACCAACAAATTCACTGTTAAATGAATACACCACAACTAAAAACATTGTGCAAATCTTAAGAA CTAGTCAAGTATATCAAAACACTCACTTTGCTATTGGAAGCCGTCCAAAGATAAACACAAGTAC CAAGCCCAACGGCAAGAACATTCTGTGAACTCCAGTCCACAACATTCAAGTAGAAGTCATCTTG TAAAGAAGGAGCATCCAAGACCTGAGACCACATCAAAAACAAAACAATCTATCATTTCTACTTC TCATGAATCTGTAATAACATCACATAAACAGGTTGGATCTAAACGATATAATACCTTATGAGGT GTTTTAGGAACCTTGCGAGGGGGCTTCGGAGGCGGAGACGAGTCACTGGAGTGACCATTATCAT TTCCGAGAATGGAAGGAGAAAACGGCGAACTAGGACTTGAATTGGAACGATCCGTCTTGAATCT CAACATGTTAGTACATGGACTCATCGGAGAAGAAGCAGATCCTTGACCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.313759969

Conservation Information
Conserved circRNAs	NA
PMCS	0.313759969

			
						 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 AT5G13840_circ_g.1

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