Plant Circular RNA Database

Detail information of AT5G46340_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT5G46340_circ_g.4
					
						ID in PlantcircBase
						ath_circ_042681
					
						Alias
						5:18797074-18798395
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr5: 18797074-18798395  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT5G46340						
					
						Parent gene annotation
						
							RWA1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT5G46340_circ_g.2 AT5G46340_circ_g.3 AT5G46340_circ_g.5 AT5G46340_circ_g.6 						
					
						Support reads
						3
					
						Tissues
						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  
						
							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
						AT5G46340.1:6
AT5G46340.2:6

General Information
CircRNA Name	AT5G46340_circ_g.4
ID in PlantcircBase	ath_circ_042681
Alias	5:18797074-18798395
Organism	Arabidpsis thaliana
Position	chr5: 18797074-18798395 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT5G46340
Parent gene annotation	RWA1
Parent gene strand	-
Alternative splicing	AT5G46340_circ_g.2 AT5G46340_circ_g.3 AT5G46340_circ_g.5 AT5G46340_circ_g.6
Support reads	3
Tissues	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	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	AT5G46340.1:6 AT5G46340.2:6

			
						 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  
						
							CAGATATGGGTGACTTGTCATTGTGTTTTCTGAGAGATGTCATGGCTGATACTATGATGAGAAG
AACGTAGAGAAAAAGGAAAAGGTCGCGGTTGTAATTgtgatggggatccatgatgtgtacggat
gatacatgttgtaactggtcctgtccagcttgtagatacattcataccacacatagccaaccta
aaatgtga

									
								

					

						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: 857
Transcript exons: 18797074-18797162,18797251-18797337,18797416-18797531,18
797641-18797896,18797974-18798123,18798237-18798395
GTGATGGGGATCCATGATGTGTACGGATGATACATGTTGTAACTGGTCCTGTCCAGCTTGTAGA
TACATTCATACCACACATAGCCAACAAGCACAGTAATAGTAACAATAGCGGCCTTTATGGATAG
TCTTTTCTTCGTTTCACAGTCCTCTAACTTCTCCATCCATCTCTCTACAGTTGGGTGATAATAG
GCATAAATCATTCCGATGATCCATATGTAGCGATCAAGGCCTGATCTAAAGTGCCATTCATGCA
GCCGATGAAGATCGGGCTTGGCAGGGTCATTGTAACCTAGCAAAAATGTTAAGGGACCCCAAAA
TATTTCAAAAGCTCCAGGAATTTCCCACAACAAAAAGACAACGAGGAAGCATGAAAATATCTTC
AGAGCCATCACCGATCCTATCTCATTGTACTTGCTGAAGATACCCAGAGCTCCATATACCATTA
GGGTGAAAAGAGTGTGCATTGGGCAGATGTAGTATAACATATAGTCGTTGTTGAGAACAATACA
GCAAAACGCTACAAAGAAGTTCAGCCTCCACATCATCTGCGCAAAACGTGCAACAGAGAAATCC
TTTCTGACATAGTAGTAAGAGAAGTTTCCAAAACCAGTCATCCAAACATAAGCAGCAATAAAGA
TACGGATTGCGTTGTATATCTCGGCCGCAGCAAAGTAGTGATACATTAAGAACAAAACCTGCAT
CCATCCTTTCCATTCTTCAGTTTGGTGGCGATTAAGGTAAAGAATGGACTTCCCAGATATGGGT
GACTTGTCATTGTGTTTTCTGAGAGATGTCATGGCTGATACTATGATGAGAAGAACGTAGAGAA
AAAGGAAAAGGTCGCGGTTGTAATT
						
					

						Genomic sequence
						
							GTGATGGGGATCCATGATGTGTACGGATGATACATGTTGTAACTGGTCCTGTCCAGCTTGTAGA
TACATTCATACCACACATAGCCAACCTAAAATGTGACCAAACGGGAAAATTATATCAATCTGTA
CAATGGGAATGGTGCAATTACCAAGCTAAAAGATGACTAAATGACTTACAAGCACAGTAATAGT
AACAATAGCGGCCTTTATGGATAGTCTTTTCTTCGTTTCACAGTCCTCTAACTTCTCCATCCAT
CTCTCTACCTAGAGAATGATCCCAAGTTTTGAAGTTTATTACATCGACACTACAAAAAACGGAA
AAAAATGGAAGTAAGAACTTACAGTTGGGTGATAATAGGCATAAATCATTCCGATGATCCATAT
GTAGCGATCAAGGCCTGATCTAAAGTGCCATTCATGCAGCCGATGAAGATCGGGCTTGGCAGGG
TCATTGTAACCTGGAGTTATTCACAAGTAATATACAAATATTAGAAACTTCTTCTAATTCCATT
ATGAATAATCTCATTCCACATTGGGAATTCAATCAATTTCGGATAAGCTAACCACCTAGCAAAA
ATGTTAAGGGACCCCAAAATATTTCAAAAGCTCCAGGAATTTCCCACAACAAAAAGACAACGAG
GAAGCATGAAAATATCTTCAGAGCCATCACCGATCCTATCTCATTGTACTTGCTGAAGATACCC
AGAGCTCCATATACCATTAGGGTGAAAAGAGTGTGCATTGGGCAGATGTAGTATAACATATAGT
CGTTGTTGAGAACAATACAGCAAAACGCTACAAAGAAGTTCAGCCTCCACATCATCTGCAAGAG
AACCAAGATTTTAGATGCGGATTATCAAGTACAATGACGAGAGCTTTTTGTGGAATGAATTGTA
TCACCTGCGCAAAACGTGCAACAGAGAAATCCTTTCTGACATAGTAGTAAGAGAAGTTTCCAAA
ACCAGTCATCCAAACATAAGCAGCAATAAAGATACGGATTGCGTTGTATATCTCGGCCGCAGCA
AAGTAGTGATACATTAAGAACAAAACCTGTTAAAAAGTAAGTCATGAGACTGTATATAGCCAGC
GGCAGTAAGAGCTCCATACAGTTACCGGCCAGAAAAAGGAAATGATCATATTGGGAATAATCAA
GAGAAACTTGCCTGCATCCATCCTTTCCATTCTTCAGTTTGGTGGCGATTAAGGTAAAGAATGG
ACTTCCCAGATATGGGTGACTTGTCATTGTGTTTTCTGAGAGATGTCATGGCTGATACTATGAT
GAGAAGAACGTAGAGAAAAAGGAAAAGGTCGCGGTTGTAATT
						
					

			
		

Sequences
Splice junction sequence	CAGATATGGGTGACTTGTCATTGTGTTTTCTGAGAGATGTCATGGCTGATACTATGATGAGAAG AACGTAGAGAAAAAGGAAAAGGTCGCGGTTGTAATTgtgatggggatccatgatgtgtacggat gatacatgttgtaactggtcctgtccagcttgtagatacattcataccacacatagccaaccta aaatgtga
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: 857 Transcript exons: 18797074-18797162,18797251-18797337,18797416-18797531,18 797641-18797896,18797974-18798123,18798237-18798395 GTGATGGGGATCCATGATGTGTACGGATGATACATGTTGTAACTGGTCCTGTCCAGCTTGTAGA TACATTCATACCACACATAGCCAACAAGCACAGTAATAGTAACAATAGCGGCCTTTATGGATAG TCTTTTCTTCGTTTCACAGTCCTCTAACTTCTCCATCCATCTCTCTACAGTTGGGTGATAATAG GCATAAATCATTCCGATGATCCATATGTAGCGATCAAGGCCTGATCTAAAGTGCCATTCATGCA GCCGATGAAGATCGGGCTTGGCAGGGTCATTGTAACCTAGCAAAAATGTTAAGGGACCCCAAAA TATTTCAAAAGCTCCAGGAATTTCCCACAACAAAAAGACAACGAGGAAGCATGAAAATATCTTC AGAGCCATCACCGATCCTATCTCATTGTACTTGCTGAAGATACCCAGAGCTCCATATACCATTA GGGTGAAAAGAGTGTGCATTGGGCAGATGTAGTATAACATATAGTCGTTGTTGAGAACAATACA GCAAAACGCTACAAAGAAGTTCAGCCTCCACATCATCTGCGCAAAACGTGCAACAGAGAAATCC TTTCTGACATAGTAGTAAGAGAAGTTTCCAAAACCAGTCATCCAAACATAAGCAGCAATAAAGA TACGGATTGCGTTGTATATCTCGGCCGCAGCAAAGTAGTGATACATTAAGAACAAAACCTGCAT CCATCCTTTCCATTCTTCAGTTTGGTGGCGATTAAGGTAAAGAATGGACTTCCCAGATATGGGT GACTTGTCATTGTGTTTTCTGAGAGATGTCATGGCTGATACTATGATGAGAAGAACGTAGAGAA AAAGGAAAAGGTCGCGGTTGTAATT
Genomic sequence	GTGATGGGGATCCATGATGTGTACGGATGATACATGTTGTAACTGGTCCTGTCCAGCTTGTAGA TACATTCATACCACACATAGCCAACCTAAAATGTGACCAAACGGGAAAATTATATCAATCTGTA CAATGGGAATGGTGCAATTACCAAGCTAAAAGATGACTAAATGACTTACAAGCACAGTAATAGT AACAATAGCGGCCTTTATGGATAGTCTTTTCTTCGTTTCACAGTCCTCTAACTTCTCCATCCAT CTCTCTACCTAGAGAATGATCCCAAGTTTTGAAGTTTATTACATCGACACTACAAAAAACGGAA AAAAATGGAAGTAAGAACTTACAGTTGGGTGATAATAGGCATAAATCATTCCGATGATCCATAT GTAGCGATCAAGGCCTGATCTAAAGTGCCATTCATGCAGCCGATGAAGATCGGGCTTGGCAGGG TCATTGTAACCTGGAGTTATTCACAAGTAATATACAAATATTAGAAACTTCTTCTAATTCCATT ATGAATAATCTCATTCCACATTGGGAATTCAATCAATTTCGGATAAGCTAACCACCTAGCAAAA ATGTTAAGGGACCCCAAAATATTTCAAAAGCTCCAGGAATTTCCCACAACAAAAAGACAACGAG GAAGCATGAAAATATCTTCAGAGCCATCACCGATCCTATCTCATTGTACTTGCTGAAGATACCC AGAGCTCCATATACCATTAGGGTGAAAAGAGTGTGCATTGGGCAGATGTAGTATAACATATAGT CGTTGTTGAGAACAATACAGCAAAACGCTACAAAGAAGTTCAGCCTCCACATCATCTGCAAGAG AACCAAGATTTTAGATGCGGATTATCAAGTACAATGACGAGAGCTTTTTGTGGAATGAATTGTA TCACCTGCGCAAAACGTGCAACAGAGAAATCCTTTCTGACATAGTAGTAAGAGAAGTTTCCAAA ACCAGTCATCCAAACATAAGCAGCAATAAAGATACGGATTGCGTTGTATATCTCGGCCGCAGCA AAGTAGTGATACATTAAGAACAAAACCTGTTAAAAAGTAAGTCATGAGACTGTATATAGCCAGC GGCAGTAAGAGCTCCATACAGTTACCGGCCAGAAAAAGGAAATGATCATATTGGGAATAATCAA GAGAAACTTGCCTGCATCCATCCTTTCCATTCTTCAGTTTGGTGGCGATTAAGGTAAAGAATGG ACTTCCCAGATATGGGTGACTTGTCATTGTGTTTTCTGAGAGATGTCATGGCTGATACTATGAT GAGAAGAACGTAGAGAAAAAGGAAAAGGTCGCGGTTGTAATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.295211824

Conservation Information
Conserved circRNAs	NA
PMCS	0.295211824

			
						 Functional Information
					
						Coding potential
						NA
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							ath-miR5021 						
					
						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	ath-miR5021
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Philips et al., 2020

circRNA

Detail information of AT5G46340_circ_g.4

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