Plant Circular RNA Database

Detail information of AT3G56160_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT3G56160_circ_g.2
					
						ID in PlantcircBase
						ath_circ_027816
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr3: 20838067-20840903  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT3G56160						
					
						Parent gene annotation
						
							Probable sodium/metabolite cotransporter BASS4, chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT3G56160_circ_g.1 AT3G56160_circ_g.3 AT3G56160_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						whole_plant
					
						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
						AT3G56160.3:10
AT3G56160.2:10
AT3G56160.5:9
AT3G56160.4:10
AT3G56160.1:10

General Information
CircRNA Name	AT3G56160_circ_g.2
ID in PlantcircBase	ath_circ_027816
Alias	NA
Organism	Arabidpsis thaliana
Position	chr3: 20838067-20840903 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT3G56160
Parent gene annotation	Probable sodium/metabolite cotransporter BASS4, chloroplastic
Parent gene strand	-
Alternative splicing	AT3G56160_circ_g.1 AT3G56160_circ_g.3 AT3G56160_circ_g.4
Support reads	2
Tissues	whole_plant
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	AT3G56160.3:10 AT3G56160.2:10 AT3G56160.5:9 AT3G56160.4:10 AT3G56160.1:10

			
						 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  
						
							ATAAATATCCCGCATGTGCTGATCTTAGTGAAAGAGTACTTGTCTGCAAGACAGCCTAGAGTCG
GATTTGCAAAGCCCAACCCCACTCCACTAACAAGAGctggcttgaaacgagcaaaactgcagtg
ctgttttccttggagctcttgctaccacctgtaagaccggagaggatgcggattgaaacagcat
tgaatgct

									
								

					

						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
						
							CTGGCTTGAAACGAGCAAAACTGCAGTGCTGTTTTCCTTGGAGCTCTTGCTACCACCTGTAAGA
CCGGAGAGGATGCGGATTGAAACAGCATTGAATGCTAGTAGAGAAAGATGCAGCAATCTGTAAG
AAGACGTAAGAATCTTCTGTCAAACGTAATCCGCATTTCTAACACACAAGCCAAATATTTCCAT
GAGCTTCTTCACTTGGTATCTTTTCTATATGTTAAAAGAAGAATGCGTACATTCCAATGCCAAC
TGCTGCAAGGAAAACCTTAGGTTGAACGGATAGTAGCAGTGATCTTGACCTGCTCACTTGGATC
CATGGCACCTAGAATATTAATCATGGAATAAACACTATTAAGTTCCCAAAATAACCAGGTAAAT
GCAATAACAAAGTCAGACCAGTTGAAGTAGCCAGGGAAGCAGAGGTTAAACTATAAAAAGGAAA
AAAGTATTAAGTCCTTCTATCTCCAAAGTCATAACCGTGACTGCAAATATGGTTTTTGCAATTT
AGTAAAAGCTTTGGATTGGCACATCAATGCCACGGAATGTTGAAATCCCAAGCTATCATACAAG
AAAAGAGAAAGTTTTAAGTACAGGCATCTAAAATGCCAAGTTTAAGATTCCTGCAACAAAGCAA
AACTCCAAGGATATGACTTCAGAAAGTTATTCAAGGGGTGTAGAAATTACGGGAGACTAACATT
TCATATCTTACCAAACTGAGGCAGATTGCGTTGATTTTCGAAAAGAGTTTACGGTTATTGTCAA
CAAAGTTTGCGAAACCTGTATCACACATTTCAACAAGAGTTTCAACAAGGTCAGAAAGTAGGCA
GCGATAAGCATATATATTTATTATAAACAGAACCATTTTGATCCATTGTCACGATAAAGTGACT
GCTAACTATTTAAAATGGTATGTATTCAATTACTTTCACCAGAGAAGTAAAATATAACAAATGG
CGCTCACCTTTGAATGATTCTCGAATAACCTATAACAGAAGAAACCAAGTATGTCAAAGCTCGA
TTTTAAAAACGTGTGCAAAATGGCAAGTGATAGAACTTCATGCTGAAATGACTGTTTGTGAAAG
GTTCATATAAACATCAGGGAAAGTAACAAATAATAGAGAGTAAGCTTTCTTCATTTTCAAATGA
GCCACGCAACAACCCTATTATAATTTCCAATAAAGTATTCACATATCTTTTGGCAACAACCACC
TCTGCAAATTTAGCTTTCACAATTGTACCGTATATCAGAATTTATATTGATTCATCATTGCAAG
AACAGGACAAACAGAAAGATTGTCTCACCTTGCCAATGATTAAAGGAATTAACAGAGTAACTAT
AAGACTTCTGAATAGTTGGTCAGTAGGAAACGAAACCCCTACTCCCCCAGCTATGTATCTTGAT
ACCCAAAATGGAATCTGATTAGAGGTCAAACCACGTTAACTTCAGTGTCAGAAGACGCAATACT
CATTCTTAATAGAAGACTTTGAAGTTTGAATCCTACTCATAGTCATAGATACAAGATCATGAGT
TGTTTTGAGAACAAATTGCTAAGCAATTCGGAAATATAGACCAGGAAACAATCTTACTAAAAAT
ACCCCTGATTCTGCATGATCAACTAGTTTCAAAGGAGGAACAATAATATGCAAGTCGTTCGGCT
TACAGTTAAAATTCCTAATAAGTTAGATGCCACTGTCACAGCAAGAGCAAGAGCAGCATTACCA
CCAGCAAGCTGAATTGGCAATATGATAAGTCAGTGGAACGCAAGAAAAACAGTTTTGCACAAAA
TATTGATTAGACTTATATCAAATTGAGTACGTGAGTAAGGGCAACACCACTTGATAAGGTGGTT
GGCATACAGCAAAATATACCCAGCCCTGTAAAGAGCAAAAGGACATACATAAGTTTTGGACTCC
TCAATCACTAACTCACTACTGAGCTGGAACTGAAGAATAAGGTATTCAAAATTGAACCATAAAT
GTAAGAAACGGATCAAGATTCAAAGACAACGTCAAAGTGGAACTGTTGGATACAAGATCACAAA
GGCAATCAGATTACTACTTAATAACGCAGCTATAGTTGATCAATTAGTTGTCAGATATTATATA
ACGAGAGACAATTTAACAAAAACTGTAGATGTAATGTAAATCAATGGAAGCCGATACAATATAA
GCAGTAACAAGTTCAGGAAAGAACGTGGTCTTTGAAGTTTTACTTGACACTAAGTTTAAGATAG
AGAAAGAGTAACCTGTAACAAGTTCACGAGGTTGGAGTTGGACCAACATAATTAGCCTTGAGAA
GGATGGAGTGAGCAACAAAATAGAGATCTGAAAGAAAAAGAGAAATAGTTTGCGTTTAAGTATG
TAGTATAACTAACAGGAGTTAAAAAAAGGAAAAGCATTACCAAAAGGTTTCTATTCATTAGATT
TTCTTATTTTCAGAACTTAGCAGAAGAGATCTACAGAAGAGGAAACATTCACAGAACATATGAA
AGCTAAAGATGAGTCAAGATCATACTAGCCCAAAGAGTCCAAGAGGCCACCCTTTGACAGCAGC
ACCAATCGCTTCGGTACGTAAAGTCAACCCTGCTCCACAATACATGAAAAGAGTACACATTTGA
TAAGCTATTCGACAGAAACAAAGTGATTGCTTCCATCACCCTTTAACATAGAAAAAGAAGAAGA
ACAAAGCAATTGTACACTTATGCCACAGCTGATAGAATCACCTGATATAATAAATATCCCGCAT
GTGCTGATCTTAGTGAAAGAGTACTTGTCTGCAAGACAGCCTAGAGTCGGATTTGCAAAGCCCA
ACCCCACTCCACTAACAAGAG
						
					

			
		

Sequences
Splice junction sequence	ATAAATATCCCGCATGTGCTGATCTTAGTGAAAGAGTACTTGTCTGCAAGACAGCCTAGAGTCG GATTTGCAAAGCCCAACCCCACTCCACTAACAAGAGctggcttgaaacgagcaaaactgcagtg ctgttttccttggagctcttgctaccacctgtaagaccggagaggatgcggattgaaacagcat tgaatgct
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	CTGGCTTGAAACGAGCAAAACTGCAGTGCTGTTTTCCTTGGAGCTCTTGCTACCACCTGTAAGA CCGGAGAGGATGCGGATTGAAACAGCATTGAATGCTAGTAGAGAAAGATGCAGCAATCTGTAAG AAGACGTAAGAATCTTCTGTCAAACGTAATCCGCATTTCTAACACACAAGCCAAATATTTCCAT GAGCTTCTTCACTTGGTATCTTTTCTATATGTTAAAAGAAGAATGCGTACATTCCAATGCCAAC TGCTGCAAGGAAAACCTTAGGTTGAACGGATAGTAGCAGTGATCTTGACCTGCTCACTTGGATC CATGGCACCTAGAATATTAATCATGGAATAAACACTATTAAGTTCCCAAAATAACCAGGTAAAT GCAATAACAAAGTCAGACCAGTTGAAGTAGCCAGGGAAGCAGAGGTTAAACTATAAAAAGGAAA AAAGTATTAAGTCCTTCTATCTCCAAAGTCATAACCGTGACTGCAAATATGGTTTTTGCAATTT AGTAAAAGCTTTGGATTGGCACATCAATGCCACGGAATGTTGAAATCCCAAGCTATCATACAAG AAAAGAGAAAGTTTTAAGTACAGGCATCTAAAATGCCAAGTTTAAGATTCCTGCAACAAAGCAA AACTCCAAGGATATGACTTCAGAAAGTTATTCAAGGGGTGTAGAAATTACGGGAGACTAACATT TCATATCTTACCAAACTGAGGCAGATTGCGTTGATTTTCGAAAAGAGTTTACGGTTATTGTCAA CAAAGTTTGCGAAACCTGTATCACACATTTCAACAAGAGTTTCAACAAGGTCAGAAAGTAGGCA GCGATAAGCATATATATTTATTATAAACAGAACCATTTTGATCCATTGTCACGATAAAGTGACT GCTAACTATTTAAAATGGTATGTATTCAATTACTTTCACCAGAGAAGTAAAATATAACAAATGG CGCTCACCTTTGAATGATTCTCGAATAACCTATAACAGAAGAAACCAAGTATGTCAAAGCTCGA TTTTAAAAACGTGTGCAAAATGGCAAGTGATAGAACTTCATGCTGAAATGACTGTTTGTGAAAG GTTCATATAAACATCAGGGAAAGTAACAAATAATAGAGAGTAAGCTTTCTTCATTTTCAAATGA GCCACGCAACAACCCTATTATAATTTCCAATAAAGTATTCACATATCTTTTGGCAACAACCACC TCTGCAAATTTAGCTTTCACAATTGTACCGTATATCAGAATTTATATTGATTCATCATTGCAAG AACAGGACAAACAGAAAGATTGTCTCACCTTGCCAATGATTAAAGGAATTAACAGAGTAACTAT AAGACTTCTGAATAGTTGGTCAGTAGGAAACGAAACCCCTACTCCCCCAGCTATGTATCTTGAT ACCCAAAATGGAATCTGATTAGAGGTCAAACCACGTTAACTTCAGTGTCAGAAGACGCAATACT CATTCTTAATAGAAGACTTTGAAGTTTGAATCCTACTCATAGTCATAGATACAAGATCATGAGT TGTTTTGAGAACAAATTGCTAAGCAATTCGGAAATATAGACCAGGAAACAATCTTACTAAAAAT ACCCCTGATTCTGCATGATCAACTAGTTTCAAAGGAGGAACAATAATATGCAAGTCGTTCGGCT TACAGTTAAAATTCCTAATAAGTTAGATGCCACTGTCACAGCAAGAGCAAGAGCAGCATTACCA CCAGCAAGCTGAATTGGCAATATGATAAGTCAGTGGAACGCAAGAAAAACAGTTTTGCACAAAA TATTGATTAGACTTATATCAAATTGAGTACGTGAGTAAGGGCAACACCACTTGATAAGGTGGTT GGCATACAGCAAAATATACCCAGCCCTGTAAAGAGCAAAAGGACATACATAAGTTTTGGACTCC TCAATCACTAACTCACTACTGAGCTGGAACTGAAGAATAAGGTATTCAAAATTGAACCATAAAT GTAAGAAACGGATCAAGATTCAAAGACAACGTCAAAGTGGAACTGTTGGATACAAGATCACAAA GGCAATCAGATTACTACTTAATAACGCAGCTATAGTTGATCAATTAGTTGTCAGATATTATATA ACGAGAGACAATTTAACAAAAACTGTAGATGTAATGTAAATCAATGGAAGCCGATACAATATAA GCAGTAACAAGTTCAGGAAAGAACGTGGTCTTTGAAGTTTTACTTGACACTAAGTTTAAGATAG AGAAAGAGTAACCTGTAACAAGTTCACGAGGTTGGAGTTGGACCAACATAATTAGCCTTGAGAA GGATGGAGTGAGCAACAAAATAGAGATCTGAAAGAAAAAGAGAAATAGTTTGCGTTTAAGTATG TAGTATAACTAACAGGAGTTAAAAAAAGGAAAAGCATTACCAAAAGGTTTCTATTCATTAGATT TTCTTATTTTCAGAACTTAGCAGAAGAGATCTACAGAAGAGGAAACATTCACAGAACATATGAA AGCTAAAGATGAGTCAAGATCATACTAGCCCAAAGAGTCCAAGAGGCCACCCTTTGACAGCAGC ACCAATCGCTTCGGTACGTAAAGTCAACCCTGCTCCACAATACATGAAAAGAGTACACATTTGA TAAGCTATTCGACAGAAACAAAGTGATTGCTTCCATCACCCTTTAACATAGAAAAAGAAGAAGA ACAAAGCAATTGTACACTTATGCCACAGCTGATAGAATCACCTGATATAATAAATATCCCGCAT GTGCTGATCTTAGTGAAAGAGTACTTGTCTGCAAGACAGCCTAGAGTCGGATTTGCAAAGCCCA ACCCCACTCCACTAACAAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.102884696

Conservation Information
Conserved circRNAs	NA
PMCS	0.102884696

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

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of AT3G56160_circ_g.2

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