Plant Circular RNA Database

Detail information of AT5G60040_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT5G60040_circ_g.1
					
						ID in PlantcircBase
						ath_circ_044913
					
						Alias
						5:24174068-24174939
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 24174068-24174939  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G60040						
					
						Parent gene annotation
						
							DNA-directed RNA polymerase subunit
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT5G60040_circ_g.2 AT5G60040_circ_g.3 AT5G60040_circ_g.4 						
					
						Support reads
						1/1
					
						Tissues
						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
						AT5G60040.2:3
AT5G60040.1:3

General Information
CircRNA Name	AT5G60040_circ_g.1
ID in PlantcircBase	ath_circ_044913
Alias	5:24174068-24174939
Organism	Arabidpsis thaliana
Position	chr5: 24174068-24174939 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G60040
Parent gene annotation	DNA-directed RNA polymerase subunit
Parent gene strand	+
Alternative splicing	AT5G60040_circ_g.2 AT5G60040_circ_g.3 AT5G60040_circ_g.4
Support reads	1/1
Tissues	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	AT5G60040.2:3 AT5G60040.1:3

			
						 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  
						
							CCATTGAAGAAGACAGAATTGGCAAAAGCCGTTGTCAAGAAGTGCAGTACGATGGCGAGCCAGA
GAATTATAACGTGCAAAAAATGTGGCTACCTGAATGaaaaagcataaacttctctgtgctttct
gatcttgaggtcatgaaagccgctgaagttcaagtctggaacatcggtttatacgaccacagtt
ttaaaccc

									
								

					

						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: 455
Transcript exons: 24174068-24174197,24174402-24174551,24174765-24174939
AAAAAGCATAAACTTCTCTGTGCTTTCTGATCTTGAGGTCATGAAAGCCGCTGAAGTTCAAGTC
TGGAACATCGGTTTATACGACCACAGTTTTAAACCCTATGAAAACGGCTTGTTGGATCCTCGAA
TGGGTCCTCCAAACAAAAAGTCTATATGCACAACCTGTGAAGGAAACTTCCAAAATTGTCCGGG
ACACTATGGATATCTGAAGCTTGACCTCCCAGTTTACAACGTTGGATACTTTAATTTTATCCTT
GATATTTTGAAGTGCATTTGTAAGCGCTGTTCCAACATGCTTTTAGATGAGAAATTGTATGAAG
ATCACTTGAGGAAGATGCGGAATCCCAGAATGGAGCCATTGAAGAAGACAGAATTGGCAAAAGC
CGTTGTCAAGAAGTGCAGTACGATGGCGAGCCAGAGAATTATAACGTGCAAAAAATGTGGCTAC
CTGAATG
Transcript length: 485
Transcript exons: 24174068-24174197,24174402-24174581,24174765-24174939
AAAAAGCATAAACTTCTCTGTGCTTTCTGATCTTGAGGTCATGAAAGCCGCTGAAGTTCAAGTC
TGGAACATCGGTTTATACGACCACAGTTTTAAACCCTATGAAAACGGCTTGTTGGATCCTCGAA
TGGGTCCTCCAAACAAAAAGTCTATATGCACAACCTGTGAAGGAAACTTCCAAAATTGTCCGGG
ACACTATGGATATCTGAAGCTTGACCTCCCAGTTTACAACGTTGGATACTTTAATTTTATCCTT
GATATTTTGAAGTGCATTTGTAAGGTAACAGAGTTAGCAGATTATGTCTCTCTACGCTGTTCCA
ACATGCTTTTAGATGAGAAATTGTATGAAGATCACTTGAGGAAGATGCGGAATCCCAGAATGGA
GCCATTGAAGAAGACAGAATTGGCAAAAGCCGTTGTCAAGAAGTGCAGTACGATGGCGAGCCAG
AGAATTATAACGTGCAAAAAATGTGGCTACCTGAATG
						
					

						Genomic sequence
						
							AAAAAGCATAAACTTCTCTGTGCTTTCTGATCTTGAGGTCATGAAAGCCGCTGAAGTTCAAGTC
TGGAACATCGGTTTATACGACCACAGTTTTAAACCCTATGAAAACGGCTTGTTGGATCCTCGAA
TGGTATCCGATTTTCTTATATACACCTACTATCTTTTGGTTTAACTTCTCTTATGCCAATAACC
ATGGCAAGTATTGTATGTCATGTTTTTGCCTCCTGCAGTTATTTGCATCAGTATATGTGATTCT
AAACATTCTATACTCCAAGATATTTTTTTCATTGTAAGAAGATAAGTACTAAATGGTTTGTTCA
TTATGATTTTGCAGGGTCCTCCAAACAAAAAGTCTATATGCACAACCTGTGAAGGAAACTTCCA
AAATTGTCCGGGACACTATGGATATCTGAAGCTTGACCTCCCAGTTTACAACGTTGGATACTTT
AATTTTATCCTTGATATTTTGAAGTGCATTTGTAAGGTAACAGAGTTAGCAGATTATGTCTCTC
TAGTTTCTGTTCTATGTTCTGTTTGTTGACCCTTTTACATTTGTTGAATGGAGAAAGTGGAGAA
AAATACAGCATAAAAAATATTTCTTGGGAAGATGCCTTTCAAAAAAAAAAACTGGCTGGTTATA
TTGATGTCTTTGTAGCATCAATAGTACTTCACAAATATTGTTTTTTTCTTCCCACAGCGCTGTT
CCAACATGCTTTTAGATGAGAAATTGTATGAAGATCACTTGAGGAAGATGCGGAATCCCAGAAT
GGAGCCATTGAAGAAGACAGAATTGGCAAAAGCCGTTGTCAAGAAGTGCAGTACGATGGCGAGC
CAGAGAATTATAACGTGCAAAAAATGTGGCTACCTGAATG
						
					

			
		

Sequences
Splice junction sequence	CCATTGAAGAAGACAGAATTGGCAAAAGCCGTTGTCAAGAAGTGCAGTACGATGGCGAGCCAGA GAATTATAACGTGCAAAAAATGTGGCTACCTGAATGaaaaagcataaacttctctgtgctttct gatcttgaggtcatgaaagccgctgaagttcaagtctggaacatcggtttatacgaccacagtt ttaaaccc
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: 455 Transcript exons: 24174068-24174197,24174402-24174551,24174765-24174939 AAAAAGCATAAACTTCTCTGTGCTTTCTGATCTTGAGGTCATGAAAGCCGCTGAAGTTCAAGTC TGGAACATCGGTTTATACGACCACAGTTTTAAACCCTATGAAAACGGCTTGTTGGATCCTCGAA TGGGTCCTCCAAACAAAAAGTCTATATGCACAACCTGTGAAGGAAACTTCCAAAATTGTCCGGG ACACTATGGATATCTGAAGCTTGACCTCCCAGTTTACAACGTTGGATACTTTAATTTTATCCTT GATATTTTGAAGTGCATTTGTAAGCGCTGTTCCAACATGCTTTTAGATGAGAAATTGTATGAAG ATCACTTGAGGAAGATGCGGAATCCCAGAATGGAGCCATTGAAGAAGACAGAATTGGCAAAAGC CGTTGTCAAGAAGTGCAGTACGATGGCGAGCCAGAGAATTATAACGTGCAAAAAATGTGGCTAC CTGAATG Transcript length: 485 Transcript exons: 24174068-24174197,24174402-24174581,24174765-24174939 AAAAAGCATAAACTTCTCTGTGCTTTCTGATCTTGAGGTCATGAAAGCCGCTGAAGTTCAAGTC TGGAACATCGGTTTATACGACCACAGTTTTAAACCCTATGAAAACGGCTTGTTGGATCCTCGAA TGGGTCCTCCAAACAAAAAGTCTATATGCACAACCTGTGAAGGAAACTTCCAAAATTGTCCGGG ACACTATGGATATCTGAAGCTTGACCTCCCAGTTTACAACGTTGGATACTTTAATTTTATCCTT GATATTTTGAAGTGCATTTGTAAGGTAACAGAGTTAGCAGATTATGTCTCTCTACGCTGTTCCA ACATGCTTTTAGATGAGAAATTGTATGAAGATCACTTGAGGAAGATGCGGAATCCCAGAATGGA GCCATTGAAGAAGACAGAATTGGCAAAAGCCGTTGTCAAGAAGTGCAGTACGATGGCGAGCCAG AGAATTATAACGTGCAAAAAATGTGGCTACCTGAATG
Genomic sequence	AAAAAGCATAAACTTCTCTGTGCTTTCTGATCTTGAGGTCATGAAAGCCGCTGAAGTTCAAGTC TGGAACATCGGTTTATACGACCACAGTTTTAAACCCTATGAAAACGGCTTGTTGGATCCTCGAA TGGTATCCGATTTTCTTATATACACCTACTATCTTTTGGTTTAACTTCTCTTATGCCAATAACC ATGGCAAGTATTGTATGTCATGTTTTTGCCTCCTGCAGTTATTTGCATCAGTATATGTGATTCT AAACATTCTATACTCCAAGATATTTTTTTCATTGTAAGAAGATAAGTACTAAATGGTTTGTTCA TTATGATTTTGCAGGGTCCTCCAAACAAAAAGTCTATATGCACAACCTGTGAAGGAAACTTCCA AAATTGTCCGGGACACTATGGATATCTGAAGCTTGACCTCCCAGTTTACAACGTTGGATACTTT AATTTTATCCTTGATATTTTGAAGTGCATTTGTAAGGTAACAGAGTTAGCAGATTATGTCTCTC TAGTTTCTGTTCTATGTTCTGTTTGTTGACCCTTTTACATTTGTTGAATGGAGAAAGTGGAGAA AAATACAGCATAAAAAATATTTCTTGGGAAGATGCCTTTCAAAAAAAAAAACTGGCTGGTTATA TTGATGTCTTTGTAGCATCAATAGTACTTCACAAATATTGTTTTTTTCTTCCCACAGCGCTGTT CCAACATGCTTTTAGATGAGAAATTGTATGAAGATCACTTGAGGAAGATGCGGAATCCCAGAAT GGAGCCATTGAAGAAGACAGAATTGGCAAAAGCCGTTGTCAAGAAGTGCAGTACGATGGCGAGC CAGAGAATTATAACGTGCAAAAAATGTGGCTACCTGAATG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.178692825

Conservation Information
Conserved circRNAs	NA
PMCS	0.178692825

			
						 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 AT5G60040_circ_g.1

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