Plant Circular RNA Database

Detail information of Os09g0568000_circ_g.6

			
						 General Information
					
						CircRNA Name
						Os09g0568000_circ_g.6
					
						ID in PlantcircBase
						osa_circ_040249
					
						Alias
						Os09circ11454/Os_ciR11954
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 22686800-22687250  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						PcircRNA_finder, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os09g0568000						
					
						Parent gene annotation
						
							Single-stranded nucleic acid binding R3H domain containing prote
in. (Os09t0568000-01);SUZ domain domain containing protein. (Os0
9t0568000-02);Conserved hypothetical protein. (Os09t0568000-03)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0568000_circ_g.4 Os09g0568000_circ_g.5 Os09g0568000_circ_g.7 						
					
						Support reads
						5/2/1
					
						Tissues
						leaf/root/seed
					
						Exon boundary  
						
							No-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
						Os09t0568000-02:1

General Information
CircRNA Name	Os09g0568000_circ_g.6
ID in PlantcircBase	osa_circ_040249
Alias	Os09circ11454/Os_ciR11954
Organism	Oryza sativa
Position	chr9: 22686800-22687250 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	PcircRNA_finder, SMALT, Segemehl, find_circ
Parent gene	Os09g0568000
Parent gene annotation	Single-stranded nucleic acid binding R3H domain containing prote in. (Os09t0568000-01);SUZ domain domain containing protein. (Os0 9t0568000-02);Conserved hypothetical protein. (Os09t0568000-03)
Parent gene strand	+
Alternative splicing	Os09g0568000_circ_g.4 Os09g0568000_circ_g.5 Os09g0568000_circ_g.7
Support reads	5/2/1
Tissues	leaf/root/seed
Exon boundary	No-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	Os09t0568000-02:1

			
						 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  
						
							ATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCTAGAGCTGCATCCATTCCGCTCACATCGCAGC
CTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTTGATgcagccagcagagacgaacaagcagaag
agtcaaagccaaagcaacaaaaggaagggaaagggaaggagatggaagggatgcgatgccgtca
tgatagct

									
								

					

						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: 259
Transcript exons: 22686800-22686903,22687096-22687250
GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA
AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGGCTGCTCCTTCCTTTTGCTTCTAT
AAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCT
AGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTT
GAT
Transcript length: 346
Transcript exons: 22686800-22686945,22687051-22687250
GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA
AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC
CTTTTGCCATCATTTTCCGATGACCATTCGAGCTGCTCACGTTACCTATGTCAATTCTGCACTG
CTGCTCCTTCCTTTTGCTTCTATAAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTT
CTTCACTAGCAGGAGCTGGAGCTAGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGA
GGAAGGAGGTGGTTTCTTGACTTGAT
Transcript length: 369
Transcript exons: 22686800-22686975,22687058-22687250
GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA
AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC
CTTTTGCCATCATTTTCCTTCCACGGCCTACAGAATCCAGCATATCTGATTCGAGCTGCTCACG
TTACCTATGTCAATTCTGCACTGCTGCTCCTTCCTTTTGCTTCTATAAATACCTTACCTTGTGC
TGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCTAGAGCTGCATCCATTCCG
CTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTTGAT
Transcript length: 394
Transcript exons: 22686800-22686996,22687054-22687250
GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA
AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC
CTTTTGCCATCATTTTCCTTCCACGGCCTACAGAATCCAGCATATCTGCTGCTCTCATGATGCT
CTTGCGACCATTCGAGCTGCTCACGTTACCTATGTCAATTCTGCACTGCTGCTCCTTCCTTTTG
CTTCTATAAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGC
TGGAGCTAGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTC
TTGACTTGAT
						
					

						Genomic sequence
						
							GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA
AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC
CTTTTGCCATCATTTTCCTTCCACGGCCTACAGAATCCAGCATATCTGCTGCTCTCATGATGCT
CTTGCACTGCCTCTGCCTTGCATTAATAGGCTCGCTCCGAGGGCTGGATCAAGTGAAATGATGA
CCATTCGAGCTGCTCACGTTACCTATGTCAATTCTGCACTGCTGCTCCTTCCTTTTGCTTCTAT
AAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCT
AGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTT
GAT
						
					

			
		

Sequences
Splice junction sequence	ATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCTAGAGCTGCATCCATTCCGCTCACATCGCAGC CTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTTGATgcagccagcagagacgaacaagcagaag agtcaaagccaaagcaacaaaaggaagggaaagggaaggagatggaagggatgcgatgccgtca tgatagct
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: 259 Transcript exons: 22686800-22686903,22687096-22687250 GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGGCTGCTCCTTCCTTTTGCTTCTAT AAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCT AGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTT GAT Transcript length: 346 Transcript exons: 22686800-22686945,22687051-22687250 GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC CTTTTGCCATCATTTTCCGATGACCATTCGAGCTGCTCACGTTACCTATGTCAATTCTGCACTG CTGCTCCTTCCTTTTGCTTCTATAAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTT CTTCACTAGCAGGAGCTGGAGCTAGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGA GGAAGGAGGTGGTTTCTTGACTTGAT Transcript length: 369 Transcript exons: 22686800-22686975,22687058-22687250 GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC CTTTTGCCATCATTTTCCTTCCACGGCCTACAGAATCCAGCATATCTGATTCGAGCTGCTCACG TTACCTATGTCAATTCTGCACTGCTGCTCCTTCCTTTTGCTTCTATAAATACCTTACCTTGTGC TGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCTAGAGCTGCATCCATTCCG CTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTTGAT Transcript length: 394 Transcript exons: 22686800-22686996,22687054-22687250 GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC CTTTTGCCATCATTTTCCTTCCACGGCCTACAGAATCCAGCATATCTGCTGCTCTCATGATGCT CTTGCGACCATTCGAGCTGCTCACGTTACCTATGTCAATTCTGCACTGCTGCTCCTTCCTTTTG CTTCTATAAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGC TGGAGCTAGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTC TTGACTTGAT
Genomic sequence	GCAGCCAGCAGAGACGAACAAGCAGAAGAGTCAAAGCCAAAGCAACAAAAGGAAGGGAAAGGGA AGGAGATGGAAGGGATGCGATGCCGTCATGATAGCTAGCGAATCTCGTGGTGGCCGGGCCTAAC CTTTTGCCATCATTTTCCTTCCACGGCCTACAGAATCCAGCATATCTGCTGCTCTCATGATGCT CTTGCACTGCCTCTGCCTTGCATTAATAGGCTCGCTCCGAGGGCTGGATCAAGTGAAATGATGA CCATTCGAGCTGCTCACGTTACCTATGTCAATTCTGCACTGCTGCTCCTTCCTTTTGCTTCTAT AAATACCTTACCTTGTGCTGTTGCTGCTTCAATCTTCAGTTCTTCACTAGCAGGAGCTGGAGCT AGAGCTGCATCCATTCCGCTCACATCGCAGCCTCGCAAGGAGGAAGGAGGTGGTTTCTTGACTT GAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008242* osi_circ_018786 						
					
						PMCS
						0.380465632

Conservation Information
Conserved circRNAs	osi_circ_008242* osi_circ_018786
PMCS	0.380465632

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

circRNA

Detail information of Os09g0568000_circ_g.6

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