Plant Circular RNA Database

Detail information of Os11g0139900_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os11g0139900_circ_g.2
					
						ID in PlantcircBase
						osa_circ_008414
					
						Alias
						Os11circ00243/Os_ciR543
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 1842847-1843432  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ei-circRNA							
									
						Identification method
						SMALT, Segemehl, circseq_cup, find_circ
					
						Parent gene
						
							Os11g0139900						
					
						Parent gene annotation
						
							Mitochondrial glycoprotein domain containing protein. (Os11t0139
900-00)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0139900_circ_g.3 						
					
						Support reads
						6/74/24
					
						Tissues
						leaf and panicle/root/root
					
						Exon boundary  
						
							Yes-No							"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
						Os11t0139900-00:2

General Information
CircRNA Name	Os11g0139900_circ_g.2
ID in PlantcircBase	osa_circ_008414
Alias	Os11circ00243/Os_ciR543
Organism	Oryza sativa
Position	chr11: 1842847-1843432 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ei-circRNA
Identification method	SMALT, Segemehl, circseq_cup, find_circ
Parent gene	Os11g0139900
Parent gene annotation	Mitochondrial glycoprotein domain containing protein. (Os11t0139 900-00)
Parent gene strand	-
Alternative splicing	Os11g0139900_circ_g.3
Support reads	6/74/24
Tissues	leaf and panicle/root/root
Exon boundary	Yes-No "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	Os11t0139900-00:2

			
						 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  
						
							GGTGCCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGC
TCCACTGGAGTTTGGACGCTCCTCATCTTTACTCACttggccgcgtgttccatggtatactcgc
cgatctcagctgcctcgccaccgcagcgcagccacagggcctccatgtagctcgtgtgtgcgaa
ataggcct

									
								

					

						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: 217
Transcript exons: 1842847-1842881,1843251-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCCCGGGGTGGCGGTGGAGGCAGCACCAACC
AAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCTTCAGGGTGCCGTACA
CGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGT
TTGGACGCTCCTCATCTTTACTCAC
Transcript length: 228
Transcript exons: 1842847-1843026,1843385-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC
CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCCCTCAATTTCTGC
TCCACTGGAGTTTGGACGCTCCTCATCTTTACTCAC
Transcript length: 279
Transcript exons: 1842847-1842960,1843251-1843351,1843369-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCCCGGGGTGGCGGTG
GAGGCAGCACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCT
TCAGGGTGCCGTACACGAACACCTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGTTT
GGACGCTCCTCATCTTTACTCAC
Transcript length: 288
Transcript exons: 1842847-1843023,1843322-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC
CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCACGCTTCAGGGTG
CCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCA
CTGGAGTTTGGACGCTCCTCATCTTTACTCAC
Transcript length: 290
Transcript exons: 1842847-1842949,1843236-1843353,1843364-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCACAACAAGCGAGGCCGGGGTGGC
GGTGGAGGCAGCACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCA
CGCTTCAGGGTGCCGTACACGAACACCATTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTC
CACTGGAGTTTGGACGCTCCTCATCTTTACTCAC
Transcript length: 302
Transcript exons: 1842847-1842998,1843283-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC
CTCAACTACCACGGTCACTTTGCGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAAC
CACGCTTCAGGGTGCCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCT
CAATTTCTGCTCCACTGGAGTTTGGACGCTCCTCATCTTTACTCAC
Transcript length: 341
Transcript exons: 1842847-1843002,1843236-1843336,1843349-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC
CTCAACTACCACGGTCACTTTGCGCCGCCCACAACAAGCGAGGCCGGGGTGGCGGTGGAGGCAG
CACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCTTCAGGGT
GACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGTTTGG
ACGCTCCTCATCTTTACTCAC
Transcript length: 495
Transcript exons: 1842847-1843432
TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC
CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCCTCGAGGGCATCG
AGGTCAACTAGGGCGCGGGGGGACACGGCGTAGAGCTCGCCGGAGACGAGATGGCTACCGGAGG
ATGAACTTGGCCTGGGGAGGAGGAACGGAACAGAGTAGGGCCCCACAACAAGCGAGGCCGGGGT
GGCGGTGGAGGCAGCACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAA
CCACGCTTCAGGGTGCCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGC
TCAATTTCTGCTCCACTGGAGTTTGGACGCTCCTCATCTTTACTCAC
						
					

						Genomic sequence
						
							TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA
GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC
CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCCTGCAGATGCAAT
TCCGCTCCATCCAAATCATGCATCTAGCCATCTAGGTGAATAGGTGATCGAGGACTGATCAGGA
ATATATGTACGTACCTCGAGGGCATCGAGGTCAACTAGGGCGCGGGGGGACACGGCGTAGAGCT
CGCCGGAGACGAGATGGCTACCGGAGGATGAACTTGGCCTGGGGAGGAGGAACGGAACAGAGTA
GGGCCCCACAACAAGCGAGGCCGGGGTGGCGGTGGAGGCAGCACCAACCAAGGGGGAACCGGAG
GCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCTTCAGGGTGCCGTACACGAACACCATTGTCG
CCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGTTTGGACGCTCCTCAT
CTTTACTCAC
						
					

			
		

Sequences
Splice junction sequence	GGTGCCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGC TCCACTGGAGTTTGGACGCTCCTCATCTTTACTCACttggccgcgtgttccatggtatactcgc cgatctcagctgcctcgccaccgcagcgcagccacagggcctccatgtagctcgtgtgtgcgaa ataggcct
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: 217 Transcript exons: 1842847-1842881,1843251-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCCCGGGGTGGCGGTGGAGGCAGCACCAACC AAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCTTCAGGGTGCCGTACA CGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGT TTGGACGCTCCTCATCTTTACTCAC Transcript length: 228 Transcript exons: 1842847-1843026,1843385-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCCCTCAATTTCTGC TCCACTGGAGTTTGGACGCTCCTCATCTTTACTCAC Transcript length: 279 Transcript exons: 1842847-1842960,1843251-1843351,1843369-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCCCGGGGTGGCGGTG GAGGCAGCACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCT TCAGGGTGCCGTACACGAACACCTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGTTT GGACGCTCCTCATCTTTACTCAC Transcript length: 288 Transcript exons: 1842847-1843023,1843322-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCACGCTTCAGGGTG CCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCA CTGGAGTTTGGACGCTCCTCATCTTTACTCAC Transcript length: 290 Transcript exons: 1842847-1842949,1843236-1843353,1843364-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCACAACAAGCGAGGCCGGGGTGGC GGTGGAGGCAGCACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCA CGCTTCAGGGTGCCGTACACGAACACCATTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTC CACTGGAGTTTGGACGCTCCTCATCTTTACTCAC Transcript length: 302 Transcript exons: 1842847-1842998,1843283-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC CTCAACTACCACGGTCACTTTGCGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAAC CACGCTTCAGGGTGCCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCT CAATTTCTGCTCCACTGGAGTTTGGACGCTCCTCATCTTTACTCAC Transcript length: 341 Transcript exons: 1842847-1843002,1843236-1843336,1843349-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC CTCAACTACCACGGTCACTTTGCGCCGCCCACAACAAGCGAGGCCGGGGTGGCGGTGGAGGCAG CACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCTTCAGGGT GACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGTTTGG ACGCTCCTCATCTTTACTCAC Transcript length: 495 Transcript exons: 1842847-1843432 TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCCTCGAGGGCATCG AGGTCAACTAGGGCGCGGGGGGACACGGCGTAGAGCTCGCCGGAGACGAGATGGCTACCGGAGG ATGAACTTGGCCTGGGGAGGAGGAACGGAACAGAGTAGGGCCCCACAACAAGCGAGGCCGGGGT GGCGGTGGAGGCAGCACCAACCAAGGGGGAACCGGAGGCGGCGAGGAGAGGGTGGTTGGGGAAA CCACGCTTCAGGGTGCCGTACACGAACACCATTGTCGCCGCCTCCACTCCTCCCCCTCCATTGC TCAATTTCTGCTCCACTGGAGTTTGGACGCTCCTCATCTTTACTCAC
Genomic sequence	TTGGCCGCGTGTTCCATGGTATACTCGCCGATCTCAGCTGCCTCGCCACCGCAGCGCAGCCACA GGGCCTCCATGTAGCTCGTGTGTGCGAAATAGGCCTCCGCCTCCACTACCTCTCCTGATCCTCC CTCAACTACCACGGTCACTTTGCGCCGCTCATACACACCCAGGTGGGTGCCCTGCAGATGCAAT TCCGCTCCATCCAAATCATGCATCTAGCCATCTAGGTGAATAGGTGATCGAGGACTGATCAGGA ATATATGTACGTACCTCGAGGGCATCGAGGTCAACTAGGGCGCGGGGGGACACGGCGTAGAGCT CGCCGGAGACGAGATGGCTACCGGAGGATGAACTTGGCCTGGGGAGGAGGAACGGAACAGAGTA GGGCCCCACAACAAGCGAGGCCGGGGTGGCGGTGGAGGCAGCACCAACCAAGGGGGAACCGGAG GCGGCGAGGAGAGGGTGGTTGGGGAAACCACGCTTCAGGGTGCCGTACACGAACACCATTGTCG CCGCCTCCACTCCTCCCCCTCCATTGCTCAATTTCTGCTCCACTGGAGTTTGGACGCTCCTCAT CTTTACTCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_003000* osi_circ_009065 						
					
						PMCS
						0.456582907

Conservation Information
Conserved circRNAs	osi_circ_003000* osi_circ_009065
PMCS	0.456582907

			
						 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;Ye et al., 2016

circRNA

Detail information of Os11g0139900_circ_g.2

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