Plant Circular RNA Database

Detail information of Os11g0539800_circ_ag.3

			
						 General Information
					
						CircRNA Name
						Os11g0539800_circ_ag.3
					
						ID in PlantcircBase
						osa_circ_009514
					
						Alias
						Os_ciR135
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 19712670-19726827  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
						
							Os11g0539800_circ_ag.1 Os11g0539800_circ_g.1 Os11g0539800_circ_g.2 Os11g0539800_circ_g.4 Os11g0539800_circ_ag.5 Os11g0539800_circ_ag.6 Os11g0539800_circ_ag.7 Os11g0539800_circ_ag.8 EPlOSAG00000016968_circ_ig.1 EPlOSAG00000016968_circ_ig.2 Os11g0540100_circ_g.1 						
					
						Support reads
						495/15
					
						Tissues
						root/seed, pistil
					
						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	Os11g0539800_circ_ag.3
ID in PlantcircBase	osa_circ_009514
Alias	Os_ciR135
Organism	Oryza sativa
Position	chr11: 19712670-19726827 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	Os11g0539800_circ_ag.1 Os11g0539800_circ_g.1 Os11g0539800_circ_g.2 Os11g0539800_circ_g.4 Os11g0539800_circ_ag.5 Os11g0539800_circ_ag.6 Os11g0539800_circ_ag.7 Os11g0539800_circ_ag.8 EPlOSAG00000016968_circ_ig.1 EPlOSAG00000016968_circ_ig.2 Os11g0540100_circ_g.1
Support reads	495/15
Tissues	root/seed, pistil
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  
						
							GTGGTGAAACAGAACTTACAGCTGTGTAGCATGACTTTTCATGCTCAGATGGTTTGCCAAAATG
TACAGTTCTTGTGATGTCTGTAGTACCATCAAGATActgagccccagagtcacagagatatatt
ttatcagcatcaagttcagcacatgaacttgcttcaggtgaatagtgaatcactgctgcatttg
gtcccacg

						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: 927
Transcript exons: 19712670-19712802,19714028-19714085,19714253-19714341,19
715418-19715621,19715835-19715911,19716034-19716227,1972
5039-19725156,19725248-19725267,19726794-19726827
CTGAGCCCCAGAGTCACAGAGATATATTTTATCAGCATCAAGTTCAGCACATGAACTTGCTTCA
GGTGAATAGTGAATCACTGCTGCATTTGGTCCCACGGATGAAATCGTAGGGAAACTCAGACCTT
TGAAGTCTGTGATCCCTTGGCCTCACTAAAGTAACCAGAAGCTCCATAGTTCTCTTGCATCTGC
TGATTGTCAAGCCAAGCCAGGTATTGCACAACAGCAGCACCATCTCGAATATGTGCCTTCCTCA
AACCATCCAGCTCCACGGGATTCTCTTCACAGCCTTTGGAAGAGCAATAGGTGATTGCAGCATC
AGAACTTGATCTTGATCCAGTTTTGAGTACAGTGCAAGACAGCATGAATTTGAATCAATCCAAA
CTTTTGAATTCTCATTCATATCATTTTCCCCATACGAGCTACCATTAACTGCAGAACCTTTTAG
CTGTCCAGATGCAAGCAAGCTTGCATCTGATTGAACGGTTACAATAGAATAAGAATGGACCACT
GGGCTGTAGTGCACATCATCTCCTCTAATATTGTACAACCAAGCAACCTTACCTCATCAAGTGC
AGCAATTATAATGCCCCTAGCCTTTTCATGTAGAAATTTTTCTCTTAATTCCTTAAGTTTTTCG
GTAACAGTACGGCCAGCATACTCTACAGGTTGCACAAATACAGGTAGAGCCTCGGCCGAAGGAC
GATCCTTCCATATTTCATCTATCAAGTCAGAAGAAAGCTGAAACAGTGTCTGTCCTATTGAAAT
AAATAGTGATCCAGTTAGGATATGCACTGACCATCTGTTACAGTCATCGATGCTTGTAGTGGTA
CATTTCTAGCAGAAGGTCTGAAGCTAATTTGATGAGGACCTGACCTTCATGAACAGTCAAACAG
TTCTTGTGATGTCTGTAGTACCATCAAGATA
						
						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	GTGGTGAAACAGAACTTACAGCTGTGTAGCATGACTTTTCATGCTCAGATGGTTTGCCAAAATG TACAGTTCTTGTGATGTCTGTAGTACCATCAAGATActgagccccagagtcacagagatatatt ttatcagcatcaagttcagcacatgaacttgcttcaggtgaatagtgaatcactgctgcatttg gtcccacg
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: 927 Transcript exons: 19712670-19712802,19714028-19714085,19714253-19714341,19 715418-19715621,19715835-19715911,19716034-19716227,1972 5039-19725156,19725248-19725267,19726794-19726827 CTGAGCCCCAGAGTCACAGAGATATATTTTATCAGCATCAAGTTCAGCACATGAACTTGCTTCA GGTGAATAGTGAATCACTGCTGCATTTGGTCCCACGGATGAAATCGTAGGGAAACTCAGACCTT TGAAGTCTGTGATCCCTTGGCCTCACTAAAGTAACCAGAAGCTCCATAGTTCTCTTGCATCTGC TGATTGTCAAGCCAAGCCAGGTATTGCACAACAGCAGCACCATCTCGAATATGTGCCTTCCTCA AACCATCCAGCTCCACGGGATTCTCTTCACAGCCTTTGGAAGAGCAATAGGTGATTGCAGCATC AGAACTTGATCTTGATCCAGTTTTGAGTACAGTGCAAGACAGCATGAATTTGAATCAATCCAAA CTTTTGAATTCTCATTCATATCATTTTCCCCATACGAGCTACCATTAACTGCAGAACCTTTTAG CTGTCCAGATGCAAGCAAGCTTGCATCTGATTGAACGGTTACAATAGAATAAGAATGGACCACT GGGCTGTAGTGCACATCATCTCCTCTAATATTGTACAACCAAGCAACCTTACCTCATCAAGTGC AGCAATTATAATGCCCCTAGCCTTTTCATGTAGAAATTTTTCTCTTAATTCCTTAAGTTTTTCG GTAACAGTACGGCCAGCATACTCTACAGGTTGCACAAATACAGGTAGAGCCTCGGCCGAAGGAC GATCCTTCCATATTTCATCTATCAAGTCAGAAGAAAGCTGAAACAGTGTCTGTCCTATTGAAAT AAATAGTGATCCAGTTAGGATATGCACTGACCATCTGTTACAGTCATCGATGCTTGTAGTGGTA CATTTCTAGCAGAAGGTCTGAAGCTAATTTGATGAGGACCTGACCTTCATGAACAGTCAAACAG TTCTTGTGATGTCTGTAGTACCATCAAGATA
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
						0.6850244

Conservation Information
Conserved circRNAs	NA
PMCS	0.6850244

			
						 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 Os11g0539800_circ_ag.3

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