Plant Circular RNA Database

Detail information of AT1G55810_circ_g.1

			
						 General Information
					
						CircRNA Name
						AT1G55810_circ_g.1
					
						ID in PlantcircBase
						ath_circ_007605
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 20861271-20863734  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G55810						
					
						Parent gene annotation
						
							uridine kinase-like 3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G55810_circ_g.2 AT1G55810_circ_g.3 AT1G55810_circ_g.4 AT1G55810_circ_g.5 AT1G55810_circ_g.6 AT1G55810_circ_g.7 						
					
						Support reads
						5
					
						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  
						
							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
						AT1G55810.5:12
AT1G55810.6:13
AT1G55810.3:13
AT1G55810.7:13
AT1G55810.2:13
AT1G55810.4:12
AT1G55810.1:13

General Information
CircRNA Name	AT1G55810_circ_g.1
ID in PlantcircBase	ath_circ_007605
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 20861271-20863734 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	KNIFE, PcircRNA_finder
Parent gene	AT1G55810
Parent gene annotation	uridine kinase-like 3
Parent gene strand	+
Alternative splicing	AT1G55810_circ_g.2 AT1G55810_circ_g.3 AT1G55810_circ_g.4 AT1G55810_circ_g.5 AT1G55810_circ_g.6 AT1G55810_circ_g.7
Support reads	5
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	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	AT1G55810.5:12 AT1G55810.6:13 AT1G55810.3:13 AT1G55810.7:13 AT1G55810.2:13 AT1G55810.4:12 AT1G55810.1:13

			
						 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  
						
							CATGTTTTGTATAGCAGGAAACTCGGCGGTGCAAGCGATAAGACTGCTCATAAGTAAAGGCGTG
CCTGAATCCAACATCATATTTCTCAATTTGATATCTgaatggcttcaaagtcggatgtgaatat
aatagagacatcctcaaaggttcatttctcaggatttcatcaaatggatggtttagcttcaaat
agaccaga

									
								

					

						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
						
							GAATGGCTTCAAAGTCGGATGTGAATATAATAGAGACATCCTCAAAGGTTCATTTCTCAGGATT
TCATCAAATGGATGGTTTAGCTTCAAATAGACCAGAGCAAATGGCTGAGGAAGAAGAACATGGT
CAACCTTTTGTGATCGGTGAGAGTCGTGGTGGATTTTAGTTTACCAAAGATGGTTAGAAACAGA
AAATGTTAAATAGAAAATGTTGTTTTCAGGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACT
GTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAGGTGATTC
TTGTCCTCGATATGATTATGCAACAATATAAACCATTTTTTTAAAGCTCTTGTAAGTCGATATA
TAATGCACCGAGGTTGATCTTTGTTTGCAGGATTCTTTCTACCATAATGTAAATGAAGTGGAGC
TTGTAAGAGTTCATGATTACAATTTTGACCATCCTGGTTAGTAAGTTTTTGAAAAACTAATGGG
TCTTTTGATCTAATGCACGCTGTTCTGTGTCCCTTAGCCTTTTGAATCTACGAATTGTGTGTCA
TATGCTTCCTTGTCTTGTAGACGCTTTCGATACTGAGCAATTATTGTCTTCCATGGAGAAGTTA
AGAAAAGGACAAGCAGTAGATATTCCTAATTATGACTTCAAAAGTTACAAGAACAATGTTTTTC
CACCTAGAAGGGTAAGAATCTTTACTTGTCAATTAGTCACTTCTGACATTTAAAGTTTTCTGCT
AATTTCTGAAGCTCAAACTCATGATCAAGTGGTTAGCTTTCTTGTGTATTCCATACTAATTACA
TGCACTCTTGTTTGTCAGATACATAAACTTGTCATCATAGCCTATATAAGAATCATGCTTATAC
TAATATTTCTCTGTTTATGATATATTTGCAGGTGAATCCTTCTGACGTTATAATTCTGGAAGGT
ATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG
GTCTTTCCCATACCAAACCTGTTAACACTTATGTAGTCAAATCCGTAGCATATATGAGACGCTG
CACTTGTATATGTACTCATGAAGGTAACACATTGGTCTCTTATTTTACATCATGGCGTTATCTA
TGCAGATGCCGATGTGCGTCTAGCGAGAAGGATAAAACGCGATACTGTTGAGAAGGGCAGAGAT
ATTGCCACTGTTCTTGACCAGGTTTTGTGTGGCTGTATATTCTTGTTTTGCAAATAATTTCTTT
ATTTATGTTTTCATGTGTGAAACTCTTATGCAGTACTCAAAGTTTGTGAAGCCAGCATTTGAGG
ATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGT
TGCTATTGATTTGATTGTGCAACACATCCATACGAAGCTCGGTCAACATGATCTCTGTAAAATT
TATCCAAATCTTTATGTTATTCAATCAACTTTTCAGGTTTTACTTATTCCCCTTTTCTCGTCTA
CTCAACAACAATCATTTTCTTGTTTAGTCACCCAAAAGACTGATCCTTTGGCCGCTGCTTGCAG
ATACGTGGTATGCACACTCTAATCCGCGACTCTAAAACAACAAAGCATGACTTTATCTTCTACT
CCGATCGATTGATACGTTTGGTGGGTGCAAGATTTGATTTCTGTTCGTTTTATTTCACCATGTT
TGCTGACTCTAACAATGAGCTCTCGCCAGGTCGTTGAACATGGCCTCGGACACCTTCCCTTTAC
AGAAAAGCAAGTGGTTACTCCAACAGGTAAGCTAATGAAAAAGATTATACCTTACTACAATCTT
GGAGAAGAACTCTCCAATCATAGTAATATTATAAACTCATGTTGAGTTTTTGGATTTCTGTAAT
TGTAGGATCTGTGTATTCGGGTGTGGACTTCTGTAAGAAACTGTGTGGTGTCTCAGTTATCAGA
AGGTAAAGAAATCAGCTTAAACACTAATAGTTAACGTCAATACTATATAATGATTTTGTCTCTG
AACATAGCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAA
GATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGGTTTGTGTTCTTTCTCTGCTCATCACT
TCTCCTAACTATTTACTAACAACAAATGGCACTCACCAGCTTATCTACGAGAAGCTACCCTCAG
ACATTTCAGAAAGGCATGTGCTTTTACTGGATCCAATCCTCGGGACAGGTCTGACTCATTGTTT
TGTGAACTCTGTACTATACTGGTAGAGTAAAAGACTATGTACATAGAAACATAACAAAAGCATG
TTTTGTATAGCAGGAAACTCGGCGGTGCAAGCGATAAGACTGCTCATAAGTAAAGGCGTGCCTG
AATCCAACATCATATTTCTCAATTTGATATCT
						
					

			
		

Sequences
Splice junction sequence	CATGTTTTGTATAGCAGGAAACTCGGCGGTGCAAGCGATAAGACTGCTCATAAGTAAAGGCGTG CCTGAATCCAACATCATATTTCTCAATTTGATATCTgaatggcttcaaagtcggatgtgaatat aatagagacatcctcaaaggttcatttctcaggatttcatcaaatggatggtttagcttcaaat agaccaga
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	GAATGGCTTCAAAGTCGGATGTGAATATAATAGAGACATCCTCAAAGGTTCATTTCTCAGGATT TCATCAAATGGATGGTTTAGCTTCAAATAGACCAGAGCAAATGGCTGAGGAAGAAGAACATGGT CAACCTTTTGTGATCGGTGAGAGTCGTGGTGGATTTTAGTTTACCAAAGATGGTTAGAAACAGA AAATGTTAAATAGAAAATGTTGTTTTCAGGAGTTGCTGGAGGTGCAGCATCCGGGAAAACAACT GTCTGTGATATGATTATGCAGCAACTGCATGATCAGAGAGCTGTTGTTGTAAATCAGGTGATTC TTGTCCTCGATATGATTATGCAACAATATAAACCATTTTTTTAAAGCTCTTGTAAGTCGATATA TAATGCACCGAGGTTGATCTTTGTTTGCAGGATTCTTTCTACCATAATGTAAATGAAGTGGAGC TTGTAAGAGTTCATGATTACAATTTTGACCATCCTGGTTAGTAAGTTTTTGAAAAACTAATGGG TCTTTTGATCTAATGCACGCTGTTCTGTGTCCCTTAGCCTTTTGAATCTACGAATTGTGTGTCA TATGCTTCCTTGTCTTGTAGACGCTTTCGATACTGAGCAATTATTGTCTTCCATGGAGAAGTTA AGAAAAGGACAAGCAGTAGATATTCCTAATTATGACTTCAAAAGTTACAAGAACAATGTTTTTC CACCTAGAAGGGTAAGAATCTTTACTTGTCAATTAGTCACTTCTGACATTTAAAGTTTTCTGCT AATTTCTGAAGCTCAAACTCATGATCAAGTGGTTAGCTTTCTTGTGTATTCCATACTAATTACA TGCACTCTTGTTTGTCAGATACATAAACTTGTCATCATAGCCTATATAAGAATCATGCTTATAC TAATATTTCTCTGTTTATGATATATTTGCAGGTGAATCCTTCTGACGTTATAATTCTGGAAGGT ATACTCATTTTCCATGACCCTCGGGTGCGAGATTTGATGAACATGAAGATATTTGTAGACGCAG GTCTTTCCCATACCAAACCTGTTAACACTTATGTAGTCAAATCCGTAGCATATATGAGACGCTG CACTTGTATATGTACTCATGAAGGTAACACATTGGTCTCTTATTTTACATCATGGCGTTATCTA TGCAGATGCCGATGTGCGTCTAGCGAGAAGGATAAAACGCGATACTGTTGAGAAGGGCAGAGAT ATTGCCACTGTTCTTGACCAGGTTTTGTGTGGCTGTATATTCTTGTTTTGCAAATAATTTCTTT ATTTATGTTTTCATGTGTGAAACTCTTATGCAGTACTCAAAGTTTGTGAAGCCAGCATTTGAGG ATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGT TGCTATTGATTTGATTGTGCAACACATCCATACGAAGCTCGGTCAACATGATCTCTGTAAAATT TATCCAAATCTTTATGTTATTCAATCAACTTTTCAGGTTTTACTTATTCCCCTTTTCTCGTCTA CTCAACAACAATCATTTTCTTGTTTAGTCACCCAAAAGACTGATCCTTTGGCCGCTGCTTGCAG ATACGTGGTATGCACACTCTAATCCGCGACTCTAAAACAACAAAGCATGACTTTATCTTCTACT CCGATCGATTGATACGTTTGGTGGGTGCAAGATTTGATTTCTGTTCGTTTTATTTCACCATGTT TGCTGACTCTAACAATGAGCTCTCGCCAGGTCGTTGAACATGGCCTCGGACACCTTCCCTTTAC AGAAAAGCAAGTGGTTACTCCAACAGGTAAGCTAATGAAAAAGATTATACCTTACTACAATCTT GGAGAAGAACTCTCCAATCATAGTAATATTATAAACTCATGTTGAGTTTTTGGATTTCTGTAAT TGTAGGATCTGTGTATTCGGGTGTGGACTTCTGTAAGAAACTGTGTGGTGTCTCAGTTATCAGA AGGTAAAGAAATCAGCTTAAACACTAATAGTTAACGTCAATACTATATAATGATTTTGTCTCTG AACATAGCGGTGAGAGTATGGAGAACGCTCTTAGAGCATGCTGCAAAGGCATCAAAATTGGGAA GATTCTGATTCATAGAGAAGGCGACAATGGTCAACAGGTTTGTGTTCTTTCTCTGCTCATCACT TCTCCTAACTATTTACTAACAACAAATGGCACTCACCAGCTTATCTACGAGAAGCTACCCTCAG ACATTTCAGAAAGGCATGTGCTTTTACTGGATCCAATCCTCGGGACAGGTCTGACTCATTGTTT TGTGAACTCTGTACTATACTGGTAGAGTAAAAGACTATGTACATAGAAACATAACAAAAGCATG TTTTGTATAGCAGGAAACTCGGCGGTGCAAGCGATAAGACTGCTCATAAGTAAAGGCGTGCCTG AATCCAACATCATATTTCTCAATTTGATATCT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.171272633

Conservation Information
Conserved circRNAs	NA
PMCS	0.171272633

			
						 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 AT1G55810_circ_g.1

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