Plant Circular RNA Database

Detail information of AT1G08060_circ_g.4

			
						 General Information
					
						CircRNA Name
						AT1G08060_circ_g.4
					
						ID in PlantcircBase
						ath_circ_001277
					
						Alias
						NA
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 2508676-2510493  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder
					
						Parent gene
						
							AT1G08060						
					
						Parent gene annotation
						
							ATP-dependent helicase family protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							AT1G08060_circ_g.5 AT1G08060_circ_g.6 						
					
						Support reads
						12
					
						Tissues
						leaf, inflorescences
					
						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
						AT1G08060.2:3
AT1G08060.3:3
AT1G08060.1:3

General Information
CircRNA Name	AT1G08060_circ_g.4
ID in PlantcircBase	ath_circ_001277
Alias	NA
Organism	Arabidpsis thaliana
Position	chr1: 2508676-2510493 JBrowse»
Reference genome	TAIR10.38
Type	ue-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder
Parent gene	AT1G08060
Parent gene annotation	ATP-dependent helicase family protein
Parent gene strand	-
Alternative splicing	AT1G08060_circ_g.5 AT1G08060_circ_g.6
Support reads	12
Tissues	leaf, inflorescences
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	AT1G08060.2:3 AT1G08060.3:3 AT1G08060.1:3

			
						 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  
						
							GGGGTTTCTTGTTCAACTGAGGCAGGAATTGAAGCTGCTAGGGATCTGGTGTAAATGGTTCTCC
CCGTCAAACCAATCTTTTCATCTTTCTTCATATTCAttttcttacagaattgagagtttcttct
agagctccaagatcaatcttcgaaagtgaagaaagagataaggatttggagaagagagtctgac
agtattgc

									
								

					

						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: 1580
Transcript exons: 2508676-2508921,2509037-2509115,2509239-2510493
TTTTCTTACAGAATTGAGAGTTTCTTCTAGAGCTCCAAGATCAATCTTCGAAAGTGAAGAAAGA
GATAAGGATTTGGAGAAGAGAGTCTGACAGTATTGCTCCAGCTGTACATCTGATAGCTGCACAG
GAACCCAATACTCTGGGTACACCGAAGAATAGAATTTGGGATCACTTGATTTACCATGTTGTAT
TTGCCCGTTCTCCTCATATTCTCTGCTCGTAACTGGTCCAGTTTCTTTCATATCCTGTGTCACG
TTATCAGATTCTTCAACTGGCTGGACAATGCAGGAGCAAACACTCCTATTTTGACAATCACCGT
TGACCTTTTGCCGTTTTTTACACGTGTTGCACATTTCAGGTCGATTATCATTTTTGCACCCAGA
TGGAGATGGAATGACCCCATCAGAACTCATAACGTGATCATCTCCATTTGCAACTGTAGCACAT
GCATCCAGCTCAATTTCTGCAGTGTCTCTTTTTCTTTTCAAAGGCAAAACTATGTCGGTTTCTA
AGCCAGTTTTACTGACAAGAAGCTTTTGGGTTTCTAAATTTGTAGATGGTGAACATATAACGCT
GTCATCCCTAGTTTCAACTATGGGGGATGCATAAAGAACCATCTTTCCAGTCTCCGTAGTTGAT
TTCAAAGGAAAATCAGTGTCCTTTTCTAAACTAGTTTCGCCAACTGGCAGCCTTTTTGATTCTG
CATTTGCAGGTGGTAGACAATCTGTGTTATCATCTTGAAACTTTTGTGGATATTCTTTTTCTAA
ACTAGTTTCACCAACTGGCAGCGTTTTCGATTCTGCATTTGCAGGTGGTGAACAATCTGTCTTA
CCATCTTGAAGCTTTTGTGTCTCTAAATTCTCAGATGGTGAACCTATAACACTGTCATCCCCAG
TTTCAACTATGGGGGATGCATCAAGCACTATCTTCTCGGTCTCCGTAACTGATTTCAAAGGAAA
ATCAGTGCCCTTGTCCAAACTAGTTTCGTCAACTGGCAGCCTTTTTGATCCTGCATCTGCAGGT
GGTGGACAATCTGTTTTACCTTGAACATCATCATTGCCTGCAGGTATGCGGCGAGAACAACCAA
CAACTACTAGTTCCTCTTCATTTGGGGAAGCATCAACTAATGCCTCAGATTCCTTGAGCTTCCC
TCTAAACAATGCCCTGTAACTTCGGGCTGACATTATAGGCTTGATCTTATCTGTCGACTCTTCA
ACACTATCCTTTCTCTGCTCAATATCCGGTGAAGTATCTCCTTTCCTGATAGAATTATCTGATC
CTTTGGAACTCTGCAAGGATACTTCAGTCTTCCCCCTATTGGACCTTCGCAAAGAACTTGGTGT
GGAATTCTTGACGATTCCACCGGACTTTTTTGAAACTGAAGCAGGTGAGGGAGCCAGTCTCTCT
GACTTTCTAGTAGCAGAAGCTGGAGTTATTACCTTCGTAGATGGTGTCCCCCGGCTTGACCTCC
TCAAACCAGGGGTTTCTTGTTCAACTGAGGCAGGAATTGAAGCTGCTAGGGATCTGGTGTAAAT
GGTTCTCCCCGTCAAACCAATCTTTTCATCTTTCTTCATATTCA
						
					

						Genomic sequence
						
							TTTTCTTACAGAATTGAGAGTTTCTTCTAGAGCTCCAAGATCAATCTTCGAAAGTGAAGAAAGA
GATAAGGATTTGGAGAAGAGAGTCTGACAGTATTGCTCCAGCTGTACATCTGATAGCTGCACAG
GAACCCAATACTCTGGGTACACCGAAGAATAGAATTTGGGATCACTTGATTTACCATGTTGTAT
TTGCCCGTTCTCCTCATATTCTCTGCTCGTAACTGGTCCAGTTTCTTTCATATCCTAATCAAAT
GCAAAATAGAATTGCAGATTACAAGTAAAAGGATAAGTAAATCTAGTATCTAACTATTTAAGAG
TCCACTGATTAACGGGTCTCCGAAAGTAATTAGAAACCAACCTGTGTCACGTTATCAGATTCTT
CAACTGGCTGGACAATGCAGGAGCAAACACTCCTATTTTGACAATCACCGTTGACCCTTCAAAA
TTTTGAACAACTCATTACAATACAGAACATATATCCTAAGAATCAAACCCATCTGCCCAACATT
CAACATTGGCAGATCGTTTCAATAGACAGACAACACTAAAAAAACTCTTACTTTTGCCGTTTTT
TACACGTGTTGCACATTTCAGGTCGATTATCATTTTTGCACCCAGATGGAGATGGAATGACCCC
ATCAGAACTCATAACGTGATCATCTCCATTTGCAACTGTAGCACATGCATCCAGCTCAATTTCT
GCAGTGTCTCTTTTTCTTTTCAAAGGCAAAACTATGTCGGTTTCTAAGCCAGTTTTACTGACAA
GAAGCTTTTGGGTTTCTAAATTTGTAGATGGTGAACATATAACGCTGTCATCCCTAGTTTCAAC
TATGGGGGATGCATAAAGAACCATCTTTCCAGTCTCCGTAGTTGATTTCAAAGGAAAATCAGTG
TCCTTTTCTAAACTAGTTTCGCCAACTGGCAGCCTTTTTGATTCTGCATTTGCAGGTGGTAGAC
AATCTGTGTTATCATCTTGAAACTTTTGTGGATATTCTTTTTCTAAACTAGTTTCACCAACTGG
CAGCGTTTTCGATTCTGCATTTGCAGGTGGTGAACAATCTGTCTTACCATCTTGAAGCTTTTGT
GTCTCTAAATTCTCAGATGGTGAACCTATAACACTGTCATCCCCAGTTTCAACTATGGGGGATG
CATCAAGCACTATCTTCTCGGTCTCCGTAACTGATTTCAAAGGAAAATCAGTGCCCTTGTCCAA
ACTAGTTTCGTCAACTGGCAGCCTTTTTGATCCTGCATCTGCAGGTGGTGGACAATCTGTTTTA
CCTTGAACATCATCATTGCCTGCAGGTATGCGGCGAGAACAACCAACAACTACTAGTTCCTCTT
CATTTGGGGAAGCATCAACTAATGCCTCAGATTCCTTGAGCTTCCCTCTAAACAATGCCCTGTA
ACTTCGGGCTGACATTATAGGCTTGATCTTATCTGTCGACTCTTCAACACTATCCTTTCTCTGC
TCAATATCCGGTGAAGTATCTCCTTTCCTGATAGAATTATCTGATCCTTTGGAACTCTGCAAGG
ATACTTCAGTCTTCCCCCTATTGGACCTTCGCAAAGAACTTGGTGTGGAATTCTTGACGATTCC
ACCGGACTTTTTTGAAACTGAAGCAGGTGAGGGAGCCAGTCTCTCTGACTTTCTAGTAGCAGAA
GCTGGAGTTATTACCTTCGTAGATGGTGTCCCCCGGCTTGACCTCCTCAAACCAGGGGTTTCTT
GTTCAACTGAGGCAGGAATTGAAGCTGCTAGGGATCTGGTGTAAATGGTTCTCCCCGTCAAACC
AATCTTTTCATCTTTCTTCATATTCA
						
					

			
		

Sequences
Splice junction sequence	GGGGTTTCTTGTTCAACTGAGGCAGGAATTGAAGCTGCTAGGGATCTGGTGTAAATGGTTCTCC CCGTCAAACCAATCTTTTCATCTTTCTTCATATTCAttttcttacagaattgagagtttcttct agagctccaagatcaatcttcgaaagtgaagaaagagataaggatttggagaagagagtctgac agtattgc
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: 1580 Transcript exons: 2508676-2508921,2509037-2509115,2509239-2510493 TTTTCTTACAGAATTGAGAGTTTCTTCTAGAGCTCCAAGATCAATCTTCGAAAGTGAAGAAAGA GATAAGGATTTGGAGAAGAGAGTCTGACAGTATTGCTCCAGCTGTACATCTGATAGCTGCACAG GAACCCAATACTCTGGGTACACCGAAGAATAGAATTTGGGATCACTTGATTTACCATGTTGTAT TTGCCCGTTCTCCTCATATTCTCTGCTCGTAACTGGTCCAGTTTCTTTCATATCCTGTGTCACG TTATCAGATTCTTCAACTGGCTGGACAATGCAGGAGCAAACACTCCTATTTTGACAATCACCGT TGACCTTTTGCCGTTTTTTACACGTGTTGCACATTTCAGGTCGATTATCATTTTTGCACCCAGA TGGAGATGGAATGACCCCATCAGAACTCATAACGTGATCATCTCCATTTGCAACTGTAGCACAT GCATCCAGCTCAATTTCTGCAGTGTCTCTTTTTCTTTTCAAAGGCAAAACTATGTCGGTTTCTA AGCCAGTTTTACTGACAAGAAGCTTTTGGGTTTCTAAATTTGTAGATGGTGAACATATAACGCT GTCATCCCTAGTTTCAACTATGGGGGATGCATAAAGAACCATCTTTCCAGTCTCCGTAGTTGAT TTCAAAGGAAAATCAGTGTCCTTTTCTAAACTAGTTTCGCCAACTGGCAGCCTTTTTGATTCTG CATTTGCAGGTGGTAGACAATCTGTGTTATCATCTTGAAACTTTTGTGGATATTCTTTTTCTAA ACTAGTTTCACCAACTGGCAGCGTTTTCGATTCTGCATTTGCAGGTGGTGAACAATCTGTCTTA CCATCTTGAAGCTTTTGTGTCTCTAAATTCTCAGATGGTGAACCTATAACACTGTCATCCCCAG TTTCAACTATGGGGGATGCATCAAGCACTATCTTCTCGGTCTCCGTAACTGATTTCAAAGGAAA ATCAGTGCCCTTGTCCAAACTAGTTTCGTCAACTGGCAGCCTTTTTGATCCTGCATCTGCAGGT GGTGGACAATCTGTTTTACCTTGAACATCATCATTGCCTGCAGGTATGCGGCGAGAACAACCAA CAACTACTAGTTCCTCTTCATTTGGGGAAGCATCAACTAATGCCTCAGATTCCTTGAGCTTCCC TCTAAACAATGCCCTGTAACTTCGGGCTGACATTATAGGCTTGATCTTATCTGTCGACTCTTCA ACACTATCCTTTCTCTGCTCAATATCCGGTGAAGTATCTCCTTTCCTGATAGAATTATCTGATC CTTTGGAACTCTGCAAGGATACTTCAGTCTTCCCCCTATTGGACCTTCGCAAAGAACTTGGTGT GGAATTCTTGACGATTCCACCGGACTTTTTTGAAACTGAAGCAGGTGAGGGAGCCAGTCTCTCT GACTTTCTAGTAGCAGAAGCTGGAGTTATTACCTTCGTAGATGGTGTCCCCCGGCTTGACCTCC TCAAACCAGGGGTTTCTTGTTCAACTGAGGCAGGAATTGAAGCTGCTAGGGATCTGGTGTAAAT GGTTCTCCCCGTCAAACCAATCTTTTCATCTTTCTTCATATTCA
Genomic sequence	TTTTCTTACAGAATTGAGAGTTTCTTCTAGAGCTCCAAGATCAATCTTCGAAAGTGAAGAAAGA GATAAGGATTTGGAGAAGAGAGTCTGACAGTATTGCTCCAGCTGTACATCTGATAGCTGCACAG GAACCCAATACTCTGGGTACACCGAAGAATAGAATTTGGGATCACTTGATTTACCATGTTGTAT TTGCCCGTTCTCCTCATATTCTCTGCTCGTAACTGGTCCAGTTTCTTTCATATCCTAATCAAAT GCAAAATAGAATTGCAGATTACAAGTAAAAGGATAAGTAAATCTAGTATCTAACTATTTAAGAG TCCACTGATTAACGGGTCTCCGAAAGTAATTAGAAACCAACCTGTGTCACGTTATCAGATTCTT CAACTGGCTGGACAATGCAGGAGCAAACACTCCTATTTTGACAATCACCGTTGACCCTTCAAAA TTTTGAACAACTCATTACAATACAGAACATATATCCTAAGAATCAAACCCATCTGCCCAACATT CAACATTGGCAGATCGTTTCAATAGACAGACAACACTAAAAAAACTCTTACTTTTGCCGTTTTT TACACGTGTTGCACATTTCAGGTCGATTATCATTTTTGCACCCAGATGGAGATGGAATGACCCC ATCAGAACTCATAACGTGATCATCTCCATTTGCAACTGTAGCACATGCATCCAGCTCAATTTCT GCAGTGTCTCTTTTTCTTTTCAAAGGCAAAACTATGTCGGTTTCTAAGCCAGTTTTACTGACAA GAAGCTTTTGGGTTTCTAAATTTGTAGATGGTGAACATATAACGCTGTCATCCCTAGTTTCAAC TATGGGGGATGCATAAAGAACCATCTTTCCAGTCTCCGTAGTTGATTTCAAAGGAAAATCAGTG TCCTTTTCTAAACTAGTTTCGCCAACTGGCAGCCTTTTTGATTCTGCATTTGCAGGTGGTAGAC AATCTGTGTTATCATCTTGAAACTTTTGTGGATATTCTTTTTCTAAACTAGTTTCACCAACTGG CAGCGTTTTCGATTCTGCATTTGCAGGTGGTGAACAATCTGTCTTACCATCTTGAAGCTTTTGT GTCTCTAAATTCTCAGATGGTGAACCTATAACACTGTCATCCCCAGTTTCAACTATGGGGGATG CATCAAGCACTATCTTCTCGGTCTCCGTAACTGATTTCAAAGGAAAATCAGTGCCCTTGTCCAA ACTAGTTTCGTCAACTGGCAGCCTTTTTGATCCTGCATCTGCAGGTGGTGGACAATCTGTTTTA CCTTGAACATCATCATTGCCTGCAGGTATGCGGCGAGAACAACCAACAACTACTAGTTCCTCTT CATTTGGGGAAGCATCAACTAATGCCTCAGATTCCTTGAGCTTCCCTCTAAACAATGCCCTGTA ACTTCGGGCTGACATTATAGGCTTGATCTTATCTGTCGACTCTTCAACACTATCCTTTCTCTGC TCAATATCCGGTGAAGTATCTCCTTTCCTGATAGAATTATCTGATCCTTTGGAACTCTGCAAGG ATACTTCAGTCTTCCCCCTATTGGACCTTCGCAAAGAACTTGGTGTGGAATTCTTGACGATTCC ACCGGACTTTTTTGAAACTGAAGCAGGTGAGGGAGCCAGTCTCTCTGACTTTCTAGTAGCAGAA GCTGGAGTTATTACCTTCGTAGATGGTGTCCCCCGGCTTGACCTCCTCAAACCAGGGGTTTCTT GTTCAACTGAGGCAGGAATTGAAGCTGCTAGGGATCTGGTGTAAATGGTTCTCCCCGTCAAACC AATCTTTTCATCTTTCTTCATATTCA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.222698799

Conservation Information
Conserved circRNAs	NA
PMCS	0.222698799

			
						 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 AT1G08060_circ_g.4

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