Plant Circular RNA Database

Detail information of Os09g0478100_circ_ag.1

			
						 General Information
					
						CircRNA Name
						Os09g0478100_circ_ag.1
					
						ID in PlantcircBase
						osa_circ_039578
					
						Alias
						Os_ciR144
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 18308860-18316604  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							Os09g0477900_circ_ag.1 Os09g0477900_circ_g.2 Os09g0478100_circ_ag.3 Os09g0477900_circ_g.4 Os09g0478100_circ_ag.5 Os09g0478300_circ_g.1 Os09g0478300_circ_g.2 						
					
						Support reads
						230/4
					
						Tissues
						root/shoot, seed
					
						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
						NA

General Information
CircRNA Name	Os09g0478100_circ_ag.1
ID in PlantcircBase	osa_circ_039578
Alias	Os_ciR144
Organism	Oryza sativa
Position	chr9: 18308860-18316604 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ag-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	Os09g0477900_circ_ag.1 Os09g0477900_circ_g.2 Os09g0478100_circ_ag.3 Os09g0477900_circ_g.4 Os09g0478100_circ_ag.5 Os09g0478300_circ_g.1 Os09g0478300_circ_g.2
Support reads	230/4
Tissues	root/shoot, seed
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	NA

			
						 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  
						
							ATCCTTTCAATGTATCCCCAGATAATAATGCCTCATAAAGACTGTAGAGGGTCTTCACACAAAA
TACATATATGAAGGGTGTAGCCCATGGACTCATAATctgtgggaataggggggtgcccttaaca
agacctagtgatggaatcacaacataatagagtgtaggcagtgagttggctgcccataatccac
atatgcag

						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: 450
Transcript exons: 18308860-18309013,18310759-18310833,18310855-18310955,18
316485-18316604
CTGTGGGAATAGGGGGGTGCCCTTAACAAGACCTAGTGATGGAATCACAACATAATAGAGTGTA
GGCAGTGAGTTGGCTGCCCATAATCCACATATGCAGTAGCCCATCTGTAGTTGTAACTTGATTT
TTCCATGTCCAAACAAGAAGGAGCAGATCAGTGCCCATTCTTTTGGGATGCACAGATTGTGATG
CACTTTTGACTCTGAGAAGTAAGCAGCTGGTGACCTTCAGAATGGTAGCCATTTCTTTGCAAAT
ATGGAGGCCTCCCATAAAGCATAGAAAGTAAGAATTGAACCTCCATCATCGGAAAGGTACACAC
TTATTTTTTCCATCCTTTGTCCATTCCACCATCCTTTCAATGTATCCCCAGATAATAATGCCTC
ATAAAGACTGTAGAGGGTCTTCACACAAAATACATATATGAAGGGTGTAGCCCATGGACTCATA
AT
Transcript length: 516
Transcript exons: 18308860-18309059,18309709-18309752,18310205-18310322,18
310755-18310908
CTGTGGGAATAGGGGGGTGCCCTTAACAAGACCTAGTGATGGAATCACAACATAATAGAGTGTA
GGCAGTGAGTTGGCTGCCCATAATCCACATATGCAGTAGCCCATCTGTAGTTGTAACTTGATTT
TTCCATGTCCAAACAAGAAGGAGCAGTACTTCGAAAGAAAAATTGTGAGATTACCCTCACTCCA
TCTCTTATTCAAGATAACAGGGCTGTCACTTATCACTGATGATACCCTTATCCAAAGCGTTCAA
TGCCCCAGCTTTGAAGTTATGGTGGTACTGAGGCCTCTTCTCGCGCGCCACGTATACCATTGTT
GGTAGCACATTTCTATCATCATCAATTGCATTTCGGTTTTTCCTTGATCAGTGCCCATTCTTTT
GGGATGCACAGATTGTGATGCACTTTTGACTCTGAGAAGTAAGCAGCTGGTGACCTTGGCTCAA
TGTTATATCTTTTGCAGAATGGTAGCCATTTCTTTGCAAATATGGAGGCCTCCCATAAAGCATA
GAAA
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	ATCCTTTCAATGTATCCCCAGATAATAATGCCTCATAAAGACTGTAGAGGGTCTTCACACAAAA TACATATATGAAGGGTGTAGCCCATGGACTCATAATctgtgggaataggggggtgcccttaaca agacctagtgatggaatcacaacataatagagtgtaggcagtgagttggctgcccataatccac atatgcag
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: 450 Transcript exons: 18308860-18309013,18310759-18310833,18310855-18310955,18 316485-18316604 CTGTGGGAATAGGGGGGTGCCCTTAACAAGACCTAGTGATGGAATCACAACATAATAGAGTGTA GGCAGTGAGTTGGCTGCCCATAATCCACATATGCAGTAGCCCATCTGTAGTTGTAACTTGATTT TTCCATGTCCAAACAAGAAGGAGCAGATCAGTGCCCATTCTTTTGGGATGCACAGATTGTGATG CACTTTTGACTCTGAGAAGTAAGCAGCTGGTGACCTTCAGAATGGTAGCCATTTCTTTGCAAAT ATGGAGGCCTCCCATAAAGCATAGAAAGTAAGAATTGAACCTCCATCATCGGAAAGGTACACAC TTATTTTTTCCATCCTTTGTCCATTCCACCATCCTTTCAATGTATCCCCAGATAATAATGCCTC ATAAAGACTGTAGAGGGTCTTCACACAAAATACATATATGAAGGGTGTAGCCCATGGACTCATA AT Transcript length: 516 Transcript exons: 18308860-18309059,18309709-18309752,18310205-18310322,18 310755-18310908 CTGTGGGAATAGGGGGGTGCCCTTAACAAGACCTAGTGATGGAATCACAACATAATAGAGTGTA GGCAGTGAGTTGGCTGCCCATAATCCACATATGCAGTAGCCCATCTGTAGTTGTAACTTGATTT TTCCATGTCCAAACAAGAAGGAGCAGTACTTCGAAAGAAAAATTGTGAGATTACCCTCACTCCA TCTCTTATTCAAGATAACAGGGCTGTCACTTATCACTGATGATACCCTTATCCAAAGCGTTCAA TGCCCCAGCTTTGAAGTTATGGTGGTACTGAGGCCTCTTCTCGCGCGCCACGTATACCATTGTT GGTAGCACATTTCTATCATCATCAATTGCATTTCGGTTTTTCCTTGATCAGTGCCCATTCTTTT GGGATGCACAGATTGTGATGCACTTTTGACTCTGAGAAGTAAGCAGCTGGTGACCTTGGCTCAA TGTTATATCTTTTGCAGAATGGTAGCCATTTCTTTGCAAATATGGAGGCCTCCCATAAAGCATA GAAA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.987748148

Conservation Information
Conserved circRNAs	NA
PMCS	0.987748148

			
						 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
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os09g0478100_circ_ag.1

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