Plant Circular RNA Database

Detail information of AT1G09660_circ_g.2

			
						 General Information
					
						CircRNA Name
						AT1G09660_circ_g.2
					
						ID in PlantcircBase
						ath_circ_001720
					
						Alias
						1:3128259-3130799
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 3128259-3130799  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ; CIRI2
					
						Parent gene
						
							AT1G09660						
					
						Parent gene annotation
						
							KH domain-containing protein At1g09660/At1g09670
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G09470_circ_g.1 AT1G09470_circ_g.2 AT1G09470_circ_g.3 1_circ_ag.4 AT1G09470_circ_g.5 AT1G09480_circ_g.1 1_circ_ag.2 1_circ_ag.3 1_circ_ag.4 1_circ_igg.5 AT1G09490_circ_g.1 AT1G09530_circ_g.1 AT1G09560_circ_g.1 AT1G09560_circ_g.2 AT1G09570_circ_g.1 AT1G09570_circ_g.2 AT1G09580_circ_g.1 AT1G09590_circ_g.1 AT1G09590_circ_g.2 AT1G09620_circ_g.1 AT1G09620_circ_g.2 AT1G09620_circ_g.3 AT1G09620_circ_g.4 AT1G09640_circ_g.1 AT1G09640_circ_g.2 AT1G09640_circ_g.3 AT1G09640_circ_g.4 AT1G09640_circ_g.5 AT1G09640_circ_g.6 AT1G09640_circ_g.7 AT1G09640_circ_g.8 AT1G09640_circ_g.9 AT1G09640_circ_g.10 AT1G09660_circ_g.1 AT1G09660_circ_g.3 AT1G09660_circ_g.4 AT1G09660_circ_g.5 AT1G09660_circ_g.6 AT1G09660_circ_g.7 						
					
						Support reads
						1/2
					
						Tissues
						seedling;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  
						
							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
						AT1G09660.1:6
AT1G09660.2:6
AT1G09660.3:6

General Information
CircRNA Name	AT1G09660_circ_g.2
ID in PlantcircBase	ath_circ_001720
Alias	1:3128259-3130799
Organism	Arabidpsis thaliana
Position	chr1: 3128259-3130799 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	find_circ; CIRI2
Parent gene	AT1G09660
Parent gene annotation	KH domain-containing protein At1g09660/At1g09670
Parent gene strand	-
Alternative splicing	AT1G09470_circ_g.1 AT1G09470_circ_g.2 AT1G09470_circ_g.3 1_circ_ag.4 AT1G09470_circ_g.5 AT1G09480_circ_g.1 1_circ_ag.2 1_circ_ag.3 1_circ_ag.4 1_circ_igg.5 AT1G09490_circ_g.1 AT1G09530_circ_g.1 AT1G09560_circ_g.1 AT1G09560_circ_g.2 AT1G09570_circ_g.1 AT1G09570_circ_g.2 AT1G09580_circ_g.1 AT1G09590_circ_g.1 AT1G09590_circ_g.2 AT1G09620_circ_g.1 AT1G09620_circ_g.2 AT1G09620_circ_g.3 AT1G09620_circ_g.4 AT1G09640_circ_g.1 AT1G09640_circ_g.2 AT1G09640_circ_g.3 AT1G09640_circ_g.4 AT1G09640_circ_g.5 AT1G09640_circ_g.6 AT1G09640_circ_g.7 AT1G09640_circ_g.8 AT1G09640_circ_g.9 AT1G09640_circ_g.10 AT1G09660_circ_g.1 AT1G09660_circ_g.3 AT1G09660_circ_g.4 AT1G09660_circ_g.5 AT1G09660_circ_g.6 AT1G09660_circ_g.7
Support reads	1/2
Tissues	seedling;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	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	AT1G09660.1:6 AT1G09660.2:6 AT1G09660.3:6

			
						 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  
						
							GAAGCACGGAATCCAGAAAGAGGATACTGGAAGAAACTTCCAGGAGAGATCCTCTCTTCCATGG
CCACGAAACCAGCGCCAGATTCCATCATCTTTAACAcatcggcttcaggagtgattccaggaaa
tgcactgcatgctccaatcgagagtttattatgtcttctggaagctcggcctcgatcagtacat
gtagtggc

									
								

					

						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
						
							CATCGGCTTCAGGAGTGATTCCAGGAAATGCACTGCATGCTCCAATCGAGAGTTTATTATGTCT
TCTGGAAGCTCGGCCTCGATCAGTACATGTAGTGGCTCGCAGAGATGCTCGTACCCTGGCTTAC
CTTTTAATTTTTCCTCCTGCAGGGAAGTAAAGAACTAAATGGATAAGCTTTCACACCGCATGGT
AGATTGTCAGAGAATATATAAGAGTCAGAAAAAAATGAATTTCAAAACTTTCTCTATTTACTTC
TGATGATGTAAGAACCTAAAACTTTAACAGTTTATTTCTTATACAGGCTGCCAAAATTTACATA
TCTTCAAATGTAAACAAGAGTAGTAGCTGCTGATGCAGTAAAAAATGTATCATTACTTCAACAA
TAAGCTTGATATGCTAAAAGACGTAAGCTTATACACAAAAGGAAAACAAATTGCTCCTAAAGGC
CGGAAGAAAATTGTGCGTATTCAAAACATGGTTATAAAACTGATTAACAGGTAAAAACATGACA
TAAAGTGAAGTTTTGAACTGTAAGAATAAAACAGAGACAAAATGGAATCCTTCAGAGAATTAAT
AAACAAGGAGCCATACCTTGACAGTATCCTTCACAGATCCTCGTCCTCTGATAAACACCCTGCA
GTGGGTTGCTAGCTCAACTCTTTTTAGGGAGTTTCCACGTGGCCCAAGAATCCTCCCAACAAAA
TTATACTGCAACGCTCAATGGATTTAAACTCTAGAACAATCCAATTATAATAACCTATTTGGGT
AAAGATTTAAGACATACGCTTGGATATTTATCCACTGGGACATCAAGTCTAATCACTTTTTTCA
CAATGGGTGGGTTAGGGAGTCCCGGCATCCCAATCCAGCCCACTGGGGAAGGACCGCGAAATGG
AGAAGCTCTCTGGAGGTGACAGTTTTCCTGAAGAAAGCAAAAGCAATCAATATCGGTAAAGCCC
ACTCTTGATTATAAAAATTATTAGTATCACCATTACAATTCAACATGAATCAGTTAATTGACTA
CAACTATCAGCAGTGGCTTACCTCGGCTTGCATCATCGACCATCCCTCTAAATCAAGCTTTCCA
TTTGTCGGCTGACCAAGCGATCTAAATGGACTGCCATGCTCATATCTATCAAGATCAGGAAAAC
TAGAGACCCTCCTGATTTCTGCACAGACGTCAGCAATGTTGGCAGTTAAGCAAACGTATAAAAG
AAACTGTAAGAGTTATACATCAGGGGCATCTTCAGTCTCTTATCTTTAATGCCAATAATGAAAC
AAAAGGCTCGGGTTCTAATAGGTTAGAATGATGAAAACTTCAAACACATCTTTGTCTTTTAAGG
TTCACACATCCCTTAAGGGCATGATGGACAACTAAAAGCTAGGTAAACAAGTCTGGAAACAAGC
TTCTAATCACCATATGCATATTTACGGACAAATAGGCTTCCTAGTATAAATTAGTTGGTGATCA
TTTGCTTAACGATCATTATCATTTGCAAACACATAGACTTAATTCATTTTCACATAACATAACT
CATCAAGGATGATCATTTAGCAATAAGTTGCAATTAAAAACTGTTTCTAAATGCTAAAAGTAAC
ATAGACTTTGATTGGCTATATATATATTAAGAAGGCCATAACAAAGAGAATAAAAAGTTGCATG
TAGATACATTTTTGTTACTCAACTATCCTTACCCAATTTCTGTAAACCTTTAACTGGAAAAAAG
CCAGGGTGATGCGCACTAAGGCTTTGTTCACGTGGGAAATTTCTTAAGTTCGTGTGCACACACT
CTAAGGAAATACTAAATTCAAAATCACATAGCTTAATAAGATAGCTCACCATGATTAAGCAGTC
TGCAGCAATTTGGCATAACTTGCAAAAAGGGACCCAACTTTTGTCTCTCTTGCAATAATTCAGT
CAAGTACCTGCACAAGGTTAAGAACAAAAAAAACTTAAGTTTCAGTGGATGTTGCGTGTGAATC
GAGTGGGTGACATTGGAATCAGCACTCAGTCACATGTAAACTAAGCTTCTAAAAATACATCAGT
ACGTTCATTTCTAAAACATTGATAAAATATAGCTATCTTGTTAAAATCCTTAAGAGTACATTGT
ATAGAATCCAATAATAAGTGAGCTAATTGTGAAAAAGGCGACATGTTGAGGTGAGAGAGTATGA
TCGAGAATTTGGATCTGTGTAAGCAGTTCATGAAAATACAAACTTGACAGAATCATTTTTAAAC
ACTGATCCAATCAAAGGCAACAATACCCACCAATCACAAAGAGACACACTTGAAGTTGTGCTAA
AGCAACAAGTCCAGAAGAAGAAACGGGTCCACAACAATCAAGCTAACACAGATTCACAAATAGC
AAAAAGGTTGAGAAAGAAGAGAGAAAATAGAAACCTTTCACGATCAGAGGGAGGACAAGGGGAT
CGATTAGGAGAAGCACGGAATCCAGAAAGAGGATACTGGAAGAAACTTCCAGGAGAGATCCTCT
CTTCCATGGCCACGAAACCAGCGCCAGATTCCATCATCTTTAACA
						
					

			
		

Sequences
Splice junction sequence	GAAGCACGGAATCCAGAAAGAGGATACTGGAAGAAACTTCCAGGAGAGATCCTCTCTTCCATGG CCACGAAACCAGCGCCAGATTCCATCATCTTTAACAcatcggcttcaggagtgattccaggaaa tgcactgcatgctccaatcgagagtttattatgtcttctggaagctcggcctcgatcagtacat gtagtggc
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	CATCGGCTTCAGGAGTGATTCCAGGAAATGCACTGCATGCTCCAATCGAGAGTTTATTATGTCT TCTGGAAGCTCGGCCTCGATCAGTACATGTAGTGGCTCGCAGAGATGCTCGTACCCTGGCTTAC CTTTTAATTTTTCCTCCTGCAGGGAAGTAAAGAACTAAATGGATAAGCTTTCACACCGCATGGT AGATTGTCAGAGAATATATAAGAGTCAGAAAAAAATGAATTTCAAAACTTTCTCTATTTACTTC TGATGATGTAAGAACCTAAAACTTTAACAGTTTATTTCTTATACAGGCTGCCAAAATTTACATA TCTTCAAATGTAAACAAGAGTAGTAGCTGCTGATGCAGTAAAAAATGTATCATTACTTCAACAA TAAGCTTGATATGCTAAAAGACGTAAGCTTATACACAAAAGGAAAACAAATTGCTCCTAAAGGC CGGAAGAAAATTGTGCGTATTCAAAACATGGTTATAAAACTGATTAACAGGTAAAAACATGACA TAAAGTGAAGTTTTGAACTGTAAGAATAAAACAGAGACAAAATGGAATCCTTCAGAGAATTAAT AAACAAGGAGCCATACCTTGACAGTATCCTTCACAGATCCTCGTCCTCTGATAAACACCCTGCA GTGGGTTGCTAGCTCAACTCTTTTTAGGGAGTTTCCACGTGGCCCAAGAATCCTCCCAACAAAA TTATACTGCAACGCTCAATGGATTTAAACTCTAGAACAATCCAATTATAATAACCTATTTGGGT AAAGATTTAAGACATACGCTTGGATATTTATCCACTGGGACATCAAGTCTAATCACTTTTTTCA CAATGGGTGGGTTAGGGAGTCCCGGCATCCCAATCCAGCCCACTGGGGAAGGACCGCGAAATGG AGAAGCTCTCTGGAGGTGACAGTTTTCCTGAAGAAAGCAAAAGCAATCAATATCGGTAAAGCCC ACTCTTGATTATAAAAATTATTAGTATCACCATTACAATTCAACATGAATCAGTTAATTGACTA CAACTATCAGCAGTGGCTTACCTCGGCTTGCATCATCGACCATCCCTCTAAATCAAGCTTTCCA TTTGTCGGCTGACCAAGCGATCTAAATGGACTGCCATGCTCATATCTATCAAGATCAGGAAAAC TAGAGACCCTCCTGATTTCTGCACAGACGTCAGCAATGTTGGCAGTTAAGCAAACGTATAAAAG AAACTGTAAGAGTTATACATCAGGGGCATCTTCAGTCTCTTATCTTTAATGCCAATAATGAAAC AAAAGGCTCGGGTTCTAATAGGTTAGAATGATGAAAACTTCAAACACATCTTTGTCTTTTAAGG TTCACACATCCCTTAAGGGCATGATGGACAACTAAAAGCTAGGTAAACAAGTCTGGAAACAAGC TTCTAATCACCATATGCATATTTACGGACAAATAGGCTTCCTAGTATAAATTAGTTGGTGATCA TTTGCTTAACGATCATTATCATTTGCAAACACATAGACTTAATTCATTTTCACATAACATAACT CATCAAGGATGATCATTTAGCAATAAGTTGCAATTAAAAACTGTTTCTAAATGCTAAAAGTAAC ATAGACTTTGATTGGCTATATATATATTAAGAAGGCCATAACAAAGAGAATAAAAAGTTGCATG TAGATACATTTTTGTTACTCAACTATCCTTACCCAATTTCTGTAAACCTTTAACTGGAAAAAAG CCAGGGTGATGCGCACTAAGGCTTTGTTCACGTGGGAAATTTCTTAAGTTCGTGTGCACACACT CTAAGGAAATACTAAATTCAAAATCACATAGCTTAATAAGATAGCTCACCATGATTAAGCAGTC TGCAGCAATTTGGCATAACTTGCAAAAAGGGACCCAACTTTTGTCTCTCTTGCAATAATTCAGT CAAGTACCTGCACAAGGTTAAGAACAAAAAAAACTTAAGTTTCAGTGGATGTTGCGTGTGAATC GAGTGGGTGACATTGGAATCAGCACTCAGTCACATGTAAACTAAGCTTCTAAAAATACATCAGT ACGTTCATTTCTAAAACATTGATAAAATATAGCTATCTTGTTAAAATCCTTAAGAGTACATTGT ATAGAATCCAATAATAAGTGAGCTAATTGTGAAAAAGGCGACATGTTGAGGTGAGAGAGTATGA TCGAGAATTTGGATCTGTGTAAGCAGTTCATGAAAATACAAACTTGACAGAATCATTTTTAAAC ACTGATCCAATCAAAGGCAACAATACCCACCAATCACAAAGAGACACACTTGAAGTTGTGCTAA AGCAACAAGTCCAGAAGAAGAAACGGGTCCACAACAATCAAGCTAACACAGATTCACAAATAGC AAAAAGGTTGAGAAAGAAGAGAGAAAATAGAAACCTTTCACGATCAGAGGGAGGACAAGGGGAT CGATTAGGAGAAGCACGGAATCCAGAAAGAGGATACTGGAAGAAACTTCCAGGAGAGATCCTCT CTTCCATGGCCACGAAACCAGCGCCAGATTCCATCATCTTTAACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.095943133

Conservation Information
Conserved circRNAs	NA
PMCS	0.095943133

			
						 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 AT1G09660_circ_g.2

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