Plant Circular RNA Database

Detail information of Os11g0175900_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0175900_circ_g.3
					
						ID in PlantcircBase
						osa_circ_008683
					
						Alias
						Os_ciR1045
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 3785424-3786246  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os11g0175900						
					
						Parent gene annotation
						
							Similar to TPLATE; binding. (Os11t0175900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0175900_circ_g.1 Os11g0175900_circ_g.2 						
					
						Support reads
						15/10
					
						Tissues
						root/root, 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
						Os11t0175900-01:2

General Information
CircRNA Name	Os11g0175900_circ_g.3
ID in PlantcircBase	osa_circ_008683
Alias	Os_ciR1045
Organism	Oryza sativa
Position	chr11: 3785424-3786246 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os11g0175900
Parent gene annotation	Similar to TPLATE; binding. (Os11t0175900-01)
Parent gene strand	-
Alternative splicing	Os11g0175900_circ_g.1 Os11g0175900_circ_g.2
Support reads	15/10
Tissues	root/root, 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	Os11t0175900-01:2

			
						 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  
						
							GATCCTCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGC
CCATATCAACCGTGATGATATTCTTGGGGTATGGACctttagatgcagtgtgattctgccatca
gttggatctgccaaatgatacgcttcaatatagcatggatcactgctgccggtcaaagtatacg
cttttggg

									
								

					

						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: 170
Transcript exons: 3785424-3785521,3786175-3786246
CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT
GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGATCCAGACCTTCAAGATCGAAGTGTTCAGA
AATCGCCCATATCAACCGTGATGATATTCTTGGGGTATGGAC
Transcript length: 253
Transcript exons: 3785424-3785586,3786157-3786246
CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT
GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTT
TTGTCTGTAGCAGACTCAACTGTGTGGGACTTGGCGTCATCAGCTAAGAGAGGATCCAGACCTT
CAAGATCGAAGTGTTCAGAAATCGCCCATATCAACCGTGATGATATTCTTGGGGTATGGAC
Transcript length: 663
Transcript exons: 3785424-3785724,3785885-3786246
CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT
GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTT
TTGTCTGTAGCAGACTCAACTGTGTGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTAC
TAACCCCTCCAATTTCCTGTCTTGAGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGG
TGGCTAAATGGATAATCCCCTGTGGCATCACCTACGCCCACCCACCTGTTATCTGGATGGCTTG
TCACATATTTTATTATCTGCAAGACATAACGTGACTGATGTTTGGTGACAAAATCAGCTGAAGT
ACTTGCTCTATATTCTTCCAATTCTTTACTGAGGAGCTGGCCAGCTCTTGCATTTCTTGTTCCC
AAACGTTGGGCACATATGAGGACAGACTGCATATCTTGTATCCTATTCGATGTAGTGGTAGAGG
ATTCGGTGTTGAATAAAATCTTGTGCATGTTAGATATGATAATATTCAGTGGATCCTCTGGGTC
ATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGCCCATATCAACCGT
GATGATATTCTTGGGGTATGGAC
						
					

						Genomic sequence
						
							CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT
GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTT
TTGTCTGTAGCAGACTCAACTGTGTGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTAC
TAACCCCTCCAATTTCCTGTCTTGAGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGG
TGGCTAAATGGATAATCCCCTGTGGCATCACCTACGCCCACCCACCTGAATGACATATCAGAAA
AGTAGACAATTATTATATTTATTTCATAATGCATGTTCTAGTAGACAACTTTCTTTCAGGTATA
ATATTTTCGTTCTTTATCTATGTGAACACTTCAACCTCCGCGGAGAATTTGTTACTCAAGTTCC
AAAATACACTCACCTGTTATCTGGATGGCTTGTCACATATTTTATTATCTGCAAGACATAACGT
GACTGATGTTTGGTGACAAAATCAGCTGAAGTACTTGCTCTATATTCTTCCAATTCTTTACTGA
GGAGCTGGCCAGCTCTTGCATTTCTTGTTCCCAAACGTTGGGCACATATGAGGACAGACTGCAT
ATCTTGTATCCTATTCGATGTAGTGGTAGAGGATTCGGTGTTGAATAAAATCTTGTGCATGTTA
GATATGATAATATTCAGTGGATCCTCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGAT
CGAAGTGTTCAGAAATCGCCCATATCAACCGTGATGATATTCTTGGGGTATGGAC
						
					

			
		

Sequences
Splice junction sequence	GATCCTCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGC CCATATCAACCGTGATGATATTCTTGGGGTATGGACctttagatgcagtgtgattctgccatca gttggatctgccaaatgatacgcttcaatatagcatggatcactgctgccggtcaaagtatacg cttttggg
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: 170 Transcript exons: 3785424-3785521,3786175-3786246 CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGATCCAGACCTTCAAGATCGAAGTGTTCAGA AATCGCCCATATCAACCGTGATGATATTCTTGGGGTATGGAC Transcript length: 253 Transcript exons: 3785424-3785586,3786157-3786246 CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTT TTGTCTGTAGCAGACTCAACTGTGTGGGACTTGGCGTCATCAGCTAAGAGAGGATCCAGACCTT CAAGATCGAAGTGTTCAGAAATCGCCCATATCAACCGTGATGATATTCTTGGGGTATGGAC Transcript length: 663 Transcript exons: 3785424-3785724,3785885-3786246 CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTT TTGTCTGTAGCAGACTCAACTGTGTGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTAC TAACCCCTCCAATTTCCTGTCTTGAGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGG TGGCTAAATGGATAATCCCCTGTGGCATCACCTACGCCCACCCACCTGTTATCTGGATGGCTTG TCACATATTTTATTATCTGCAAGACATAACGTGACTGATGTTTGGTGACAAAATCAGCTGAAGT ACTTGCTCTATATTCTTCCAATTCTTTACTGAGGAGCTGGCCAGCTCTTGCATTTCTTGTTCCC AAACGTTGGGCACATATGAGGACAGACTGCATATCTTGTATCCTATTCGATGTAGTGGTAGAGG ATTCGGTGTTGAATAAAATCTTGTGCATGTTAGATATGATAATATTCAGTGGATCCTCTGGGTC ATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGCCCATATCAACCGT GATGATATTCTTGGGGTATGGAC
Genomic sequence	CTTTAGATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCAT GGATCACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTT TTGTCTGTAGCAGACTCAACTGTGTGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTAC TAACCCCTCCAATTTCCTGTCTTGAGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGG TGGCTAAATGGATAATCCCCTGTGGCATCACCTACGCCCACCCACCTGAATGACATATCAGAAA AGTAGACAATTATTATATTTATTTCATAATGCATGTTCTAGTAGACAACTTTCTTTCAGGTATA ATATTTTCGTTCTTTATCTATGTGAACACTTCAACCTCCGCGGAGAATTTGTTACTCAAGTTCC AAAATACACTCACCTGTTATCTGGATGGCTTGTCACATATTTTATTATCTGCAAGACATAACGT GACTGATGTTTGGTGACAAAATCAGCTGAAGTACTTGCTCTATATTCTTCCAATTCTTTACTGA GGAGCTGGCCAGCTCTTGCATTTCTTGTTCCCAAACGTTGGGCACATATGAGGACAGACTGCAT ATCTTGTATCCTATTCGATGTAGTGGTAGAGGATTCGGTGTTGAATAAAATCTTGTGCATGTTA GATATGATAATATTCAGTGGATCCTCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGAT CGAAGTGTTCAGAAATCGCCCATATCAACCGTGATGATATTCTTGGGGTATGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003040* osi_circ_009301 						
					
						PMCS
						0.570639378

Conservation Information
Conserved circRNAs	osi_circ_003040* osi_circ_009301
PMCS	0.570639378

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3786048-3785466(+)
3786125-3785426(-)
						
						Potential amino acid sequence
						
							MRTDCISCILFDVVVEDSVLNKILCMLDMIIFSGSSGSSAKRGSRPSRSKCSEIAHINRDDILG
VWTFRCSVILPSVGSAK*(+)
MHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFVTKHQSR
YVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAILELWRPS
PTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKVHTPRISSRLIW
AISEHFDLEGLDPLLADDPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRN
ARAGQLLSKELEEYRASTSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLT
VQFSEASAAQDRKLEGLVHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIE
AYHLADPTDGRITLHLKVHTPRISSRLIWAISEHFDLEGLDPLLADDPEDPLNIIISNMHKILF
NTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFVTKHQSRYVLQII
KYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAILELWRPSPTQLSL
LQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKVHTPRISSRLIWAISEHF
DLEGLDPLLADDPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQL
LSKELEEYRASTSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEA
SAAQDRKLEGLVHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLAD
PTDGRITLHLK(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3786048-3785466(+) 3786125-3785426(-)
Potential amino acid sequence	MRTDCISCILFDVVVEDSVLNKILCMLDMIIFSGSSGSSAKRGSRPSRSKCSEIAHINRDDILG VWTFRCSVILPSVGSAK*(+) MHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFVTKHQSR YVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAILELWRPS PTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKVHTPRISSRLIW AISEHFDLEGLDPLLADDPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRN ARAGQLLSKELEEYRASTSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLT VQFSEASAAQDRKLEGLVHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIE AYHLADPTDGRITLHLKVHTPRISSRLIWAISEHFDLEGLDPLLADDPEDPLNIIISNMHKILF NTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFVTKHQSRYVLQII KYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAILELWRPSPTQLSL LQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKVHTPRISSRLIWAISEHF DLEGLDPLLADDPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQL LSKELEEYRASTSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEA SAAQDRKLEGLVHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLAD PTDGRITLHLK(-)
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 Os11g0175900_circ_g.3

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