Plant Circular RNA Database

Detail information of AT1G72320_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G72320_circ_g.3
					
						ID in PlantcircBase
						ath_circ_009749
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 27229635-27230947  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
					
						Parent gene
						
							AT1G72320						
					
						Parent gene annotation
						
							Pumilio homolog 23
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G72320_circ_g.2 						
					
						Support reads
						6/3
					
						Tissues
						inflorescences, whole_plant/seedlings
					
						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
						AT1G72320.4:5
AT1G72320.2:5
AT1G72320.1:5
AT1G72320.3:5

General Information
CircRNA Name	AT1G72320_circ_g.3
ID in PlantcircBase	ath_circ_009749
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 27229635-27230947 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, circRNA_finder, find_circ
Parent gene	AT1G72320
Parent gene annotation	Pumilio homolog 23
Parent gene strand	-
Alternative splicing	AT1G72320_circ_g.2
Support reads	6/3
Tissues	inflorescences, whole_plant/seedlings
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	AT1G72320.4:5 AT1G72320.2:5 AT1G72320.1:5 AT1G72320.3:5

			
						 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  
						
							AATTTGCACACCGATCAACTGAAAGCTCAAATAAAGAATTCTTGAAAACTTTGTTGAACATTTC
GTTATACAAACTTTCAGGGGCCACTTCCAAAATAACccatcgatatcaagtttcctaagcagat
aaggcccttgctttgttttcgagagatcaactttcacatccaacagttcagatgctatggcttc
ccttagtg

									
								

					

						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: 782
Transcript exons: 27229635-27229817,27230012-27230160,27230276-27230461,27
230554-27230673,27230804-27230947
CCATCGATATCAAGTTTCCTAAGCAGATAAGGCCCTTGCTTTGTTTTCGAGAGATCAACTTTCA
CATCCAACAGTTCAGATGCTATGGCTTCCCTTAGTGTCAAATTACATGCATCGAAGCACTTCTC
AACTGTAAATGAACCAGACGTGTGTAATGAGAGCTCGCCAAAATGTCCACGTAATTTTATAATT
AGTCTACGTTTCTGTTTTGTAGCAGCATCTGAGGCAAGAAAGGCCTCGATGACACGTGCTCCAC
TGGAATCTTTTGCCGTTTCAGTGATATACTCAGCTTTCATAGAAGTTAAGCTTGTTATGTATGG
CTGTATATGATCACTAGAAAACTTAAAAATCCCCTGAAGTATCAAACAACCCATGACATGCATC
TTTGCACCAGGTGCCCACTCCCATGTAGACTTATCTCGACAACCAAAGTAGTAATCAAGAAACA
GCAACCGTGGAAGAATGGAGATACGGGATTCATTTGTGGAGCATACTGCACCAACAAGGGCCTC
ACAACACTTATTTTCATGACTTTGAAGCCTTTGGCTAACTGCTATCAGAGAAGCCACAACACCT
GACTTCCCTTGCTCAAGAAGATCCTTGAATCTTGGAGCTAATTCTTCCCACATAATACCCATCT
GCTCTTGGTCTCTTGCATGGGAGATTAATGCTTGAATAACAAAATTTGCACACCGATCAACTGA
AAGCTCAAATAAAGAATTCTTGAAAACTTTGTTGAACATTTCGTTATACAAACTTTCAGGGGCC
ACTTCCAAAATAAC
						
					

						Genomic sequence
						
							CCATCGATATCAAGTTTCCTAAGCAGATAAGGCCCTTGCTTTGTTTTCGAGAGATCAACTTTCA
CATCCAACAGTTCAGATGCTATGGCTTCCCTTAGTGTCAAATTACATGCATCGAAGCACTTCTC
AACTGTAAATGAACCAGACGTGTGTAATGAGAGCTCGCCAAAATGTCCACGTAATCTGTGACGA
AATCATTGGTGAAAAGAAACATCATCAAAATATGAAGAATTGCTTGAAAAAAAAAACTGACAAG
CAGCCTAAGAGACTGAATGAAGAAAAAACAGAATGAAGGAAATCATATAAACAAGCTACTGTGG
AATCTATCGGTCTTGAGATAAACATATCCCCATATAAAATCAAGAAGCAGTGCATACTTTATAA
TTAGTCTACGTTTCTGTTTTGTAGCAGCATCTGAGGCAAGAAAGGCCTCGATGACACGTGCTCC
ACTGGAATCTTTTGCCGTTTCAGTGATATACTCAGCTTTCATAGAAGTTAAGCTTGTTATGTAT
GGCTGTATATGATCCTGTGAAATTGAGAAAAAGTTGGGAGTTACTGTGAATGCACATGAAAAGC
CAAAAATTTGGAAGTTAAAAGCACTGAAGCTATTTTTGTCAACACAAGAAGAGAAGGAAACATA
CACTAGAAAACTTAAAAATCCCCTGAAGTATCAAACAACCCATGACATGCATCTTTGCACCAGG
TGCCCACTCCCATGTAGACTTATCTCGACAACCAAAGTAGTAATCAAGAAACAGCAACCGTGGA
AGAATGGAGATACGGGATTCATTTGTGGAGCATACTGCACCAACAAGGGCCTCACAACACTGTC
AAATCAGTAAAAATCAGCTGTATAAGAACACAATTTTGAAACTAGAAAAGAAATAAATTTTCAT
CTAAATTTAGAAAACATAGAAACCTTATTTTCATGACTTTGAAGCCTTTGGCTAACTGCTATCA
GAGAAGCCACAACACCTGACTTCCCTTGCTCAAGAAGATCCTTGAATCTTGGAGCTAATTCTTC
CCACATAATACCCATCTTGTAAACAAAATCAATTGAACGTAAGTTTACTGGCTTCACGGAAATA
GCACAAATAAATTCGAAGTTAAGAAGACCTGGAATGAAATTTTGATGTCACAGAAAAAGATGAA
GTGTATGATAAAGATACCTGCTCTTGGTCTCTTGCATGGGAGATTAATGCTTGAATAACAAAAT
TTGCACACCGATCAACTGAAAGCTCAAATAAAGAATTCTTGAAAACTTTGTTGAACATTTCGTT
ATACAAACTTTCAGGGGCCACTTCCAAAATAAC
						
					

			
		

Sequences
Splice junction sequence	AATTTGCACACCGATCAACTGAAAGCTCAAATAAAGAATTCTTGAAAACTTTGTTGAACATTTC GTTATACAAACTTTCAGGGGCCACTTCCAAAATAACccatcgatatcaagtttcctaagcagat aaggcccttgctttgttttcgagagatcaactttcacatccaacagttcagatgctatggcttc ccttagtg
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: 782 Transcript exons: 27229635-27229817,27230012-27230160,27230276-27230461,27 230554-27230673,27230804-27230947 CCATCGATATCAAGTTTCCTAAGCAGATAAGGCCCTTGCTTTGTTTTCGAGAGATCAACTTTCA CATCCAACAGTTCAGATGCTATGGCTTCCCTTAGTGTCAAATTACATGCATCGAAGCACTTCTC AACTGTAAATGAACCAGACGTGTGTAATGAGAGCTCGCCAAAATGTCCACGTAATTTTATAATT AGTCTACGTTTCTGTTTTGTAGCAGCATCTGAGGCAAGAAAGGCCTCGATGACACGTGCTCCAC TGGAATCTTTTGCCGTTTCAGTGATATACTCAGCTTTCATAGAAGTTAAGCTTGTTATGTATGG CTGTATATGATCACTAGAAAACTTAAAAATCCCCTGAAGTATCAAACAACCCATGACATGCATC TTTGCACCAGGTGCCCACTCCCATGTAGACTTATCTCGACAACCAAAGTAGTAATCAAGAAACA GCAACCGTGGAAGAATGGAGATACGGGATTCATTTGTGGAGCATACTGCACCAACAAGGGCCTC ACAACACTTATTTTCATGACTTTGAAGCCTTTGGCTAACTGCTATCAGAGAAGCCACAACACCT GACTTCCCTTGCTCAAGAAGATCCTTGAATCTTGGAGCTAATTCTTCCCACATAATACCCATCT GCTCTTGGTCTCTTGCATGGGAGATTAATGCTTGAATAACAAAATTTGCACACCGATCAACTGA AAGCTCAAATAAAGAATTCTTGAAAACTTTGTTGAACATTTCGTTATACAAACTTTCAGGGGCC ACTTCCAAAATAAC
Genomic sequence	CCATCGATATCAAGTTTCCTAAGCAGATAAGGCCCTTGCTTTGTTTTCGAGAGATCAACTTTCA CATCCAACAGTTCAGATGCTATGGCTTCCCTTAGTGTCAAATTACATGCATCGAAGCACTTCTC AACTGTAAATGAACCAGACGTGTGTAATGAGAGCTCGCCAAAATGTCCACGTAATCTGTGACGA AATCATTGGTGAAAAGAAACATCATCAAAATATGAAGAATTGCTTGAAAAAAAAAACTGACAAG CAGCCTAAGAGACTGAATGAAGAAAAAACAGAATGAAGGAAATCATATAAACAAGCTACTGTGG AATCTATCGGTCTTGAGATAAACATATCCCCATATAAAATCAAGAAGCAGTGCATACTTTATAA TTAGTCTACGTTTCTGTTTTGTAGCAGCATCTGAGGCAAGAAAGGCCTCGATGACACGTGCTCC ACTGGAATCTTTTGCCGTTTCAGTGATATACTCAGCTTTCATAGAAGTTAAGCTTGTTATGTAT GGCTGTATATGATCCTGTGAAATTGAGAAAAAGTTGGGAGTTACTGTGAATGCACATGAAAAGC CAAAAATTTGGAAGTTAAAAGCACTGAAGCTATTTTTGTCAACACAAGAAGAGAAGGAAACATA CACTAGAAAACTTAAAAATCCCCTGAAGTATCAAACAACCCATGACATGCATCTTTGCACCAGG TGCCCACTCCCATGTAGACTTATCTCGACAACCAAAGTAGTAATCAAGAAACAGCAACCGTGGA AGAATGGAGATACGGGATTCATTTGTGGAGCATACTGCACCAACAAGGGCCTCACAACACTGTC AAATCAGTAAAAATCAGCTGTATAAGAACACAATTTTGAAACTAGAAAAGAAATAAATTTTCAT CTAAATTTAGAAAACATAGAAACCTTATTTTCATGACTTTGAAGCCTTTGGCTAACTGCTATCA GAGAAGCCACAACACCTGACTTCCCTTGCTCAAGAAGATCCTTGAATCTTGGAGCTAATTCTTC CCACATAATACCCATCTTGTAAACAAAATCAATTGAACGTAAGTTTACTGGCTTCACGGAAATA GCACAAATAAATTCGAAGTTAAGAAGACCTGGAATGAAATTTTGATGTCACAGAAAAAGATGAA GTGTATGATAAAGATACCTGCTCTTGGTCTCTTGCATGGGAGATTAATGCTTGAATAACAAAAT TTGCACACCGATCAACTGAAAGCTCAAATAAAGAATTCTTGAAAACTTTGTTGAACATTTCGTT ATACAAACTTTCAGGGGCCACTTCCAAAATAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.382052545

Conservation Information
Conserved circRNAs	NA
PMCS	0.382052545

			
						 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;Pan et al., 2017

circRNA

Detail information of AT1G72320_circ_g.3

Address

Any questions?

Supported by