Plant Circular RNA Database

Detail information of Os11g0170400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os11g0170400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_008607
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 3426241-3426756  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circseq_cup
					
						Parent gene
						
							Os11g0170400						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os11t0170400-01);Conserved hypo
thetical protein. (Os11t0170400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os11g0170400_circ_g.1 Os11g0170400_circ_g.2 Os11g0170400_circ_g.4 Os11g0170400_circ_g.5 Os11g0170400_circ_g.6 Os11g0170400_circ_g.7 						
					
						Support reads
						6/8
					
						Tissues
						root/shoot, 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  
						
							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
						Os11t0170400-01:3
Os11t0170400-02:3

General Information
CircRNA Name	Os11g0170400_circ_g.3
ID in PlantcircBase	osa_circ_008607
Alias	NA
Organism	Oryza sativa
Position	chr11: 3426241-3426756 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, CIRI, KNIFE, PcircRNA_finder, circseq_cup
Parent gene	Os11g0170400
Parent gene annotation	Conserved hypothetical protein. (Os11t0170400-01);Conserved hypo thetical protein. (Os11t0170400-02)
Parent gene strand	+
Alternative splicing	Os11g0170400_circ_g.1 Os11g0170400_circ_g.2 Os11g0170400_circ_g.4 Os11g0170400_circ_g.5 Os11g0170400_circ_g.6 Os11g0170400_circ_g.7
Support reads	6/8
Tissues	root/shoot, 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	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	Os11t0170400-01:3 Os11t0170400-02:3

			
						 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  
						
							TTGTATTGCAGTTCAACCATAACTCGAGCTGTCAACTTGCAAGGGTTTTCATCCTGTCTATATG
GTCAAATATTGCCACTCTGTAACTAAATGTTGTAAGtggctgcaagcctgcaagatggagctga
gttgggaggctgagcaagcagcaacaggaggaatcaaggaacaagggggaaaatgtgagggagg
aggaaact

						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: 358
Transcript exons: 3426241-3426445,3426537-3426600,3426668-3426756
TGGCTGCAAGCCTGCAAGATGGAGCTGAGTTGGGAGGCTGAGCAAGCAGCAACAGGAGGAATCA
AGGAACAAGGGGGAAAATGTGAGGGAGGAGGAAACTGGGATACCTAAGTAATTTGCTAATGCGT
TTTTAGGCTACCTATTCCAATCCCTCATCGTATGGTGTACATTCAGATTCAGATATGATTGGCT
TGATATTTAGGAGAGGCCAAATCAAGGAATGCAAATAACTATAGAGTTGTACAGGGTTCCTTAA
GCCCTCTATTAAGTTCAACCATAACTCGAGCTGTCAACTTGCAAGGGTTTTCATCCTGTCTATA
TGGTCAAATATTGCCACTCTGTAACTAAATGTTGTAAG
Transcript length: 365
Transcript exons: 3426241-3426756
TGGCTGCAAGCCTGCAAGATGGAGCTGAGTTGGGAGGCTGAGCAAGCAGCAACAGGAGGAATCA
AGGAACAAGGGGGAAAATGTGAGGGAGGAGGAAACTGGGATACCTAAGTAATTTGCTAATGCGT
TTTTAGGCTACCTATTCCAATCCCTCATCGTATGGTGTACATTCAGATTCAGATATGATTGGCT
TGATATTTAGGAGTCTTTAGAGGCCAAATCAAGGAATGCAAATAACTATAGAGTTGTACAGGGT
TCCTTAAGCCCTCTATTAAGTTCAACCATAACTCGAGCTGTCAACTTGCAAGGGTTTTCATCCT
GTCTATATGGTCAAATATTGCCACTCTGTAACTAAATGTTGTAAG
						
						Genomic sequence
						
							TGGCTGCAAGCCTGCAAGATGGAGCTGAGTTGGGAGGCTGAGCAAGCAGCAACAGGAGGAATCA
AGGAACAAGGGGGAAAATGTGAGGGAGGAGGAAACTGGGATACCTAAGTAATTTGCTAATGCGT
TTTTAGGCTACCTATTCCAATCCCTCATCGTATGGTGTACATTCAGATTCAGATATGATTGGCT
TGATATTTAGGAGGTAGGTTCGTGCTTTGTCCTAATTTCAGTTATTTGTTTTTATTTTCACAAA
ATTGTTCAATTTGGATATACCTAACTTTTTCAGTCTTTAGAGGCCAAATCAAGGAATGCAAATA
ACTATAGAGTTGTACAGGGTTCCTTAAGCCCTCTATTAAGGTAAAGAACATGGAAATCTACCAA
GTAGAATAGAAGTTATCACAATCTGAACTCTGTTGTATTGCAGTTCAACCATAACTCGAGCTGT
CAACTTGCAAGGGTTTTCATCCTGTCTATATGGTCAAATATTGCCACTCTGTAACTAAATGTTG
TAAG

Sequences
Splice junction sequence	TTGTATTGCAGTTCAACCATAACTCGAGCTGTCAACTTGCAAGGGTTTTCATCCTGTCTATATG GTCAAATATTGCCACTCTGTAACTAAATGTTGTAAGtggctgcaagcctgcaagatggagctga gttgggaggctgagcaagcagcaacaggaggaatcaaggaacaagggggaaaatgtgagggagg aggaaact
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: 358 Transcript exons: 3426241-3426445,3426537-3426600,3426668-3426756 TGGCTGCAAGCCTGCAAGATGGAGCTGAGTTGGGAGGCTGAGCAAGCAGCAACAGGAGGAATCA AGGAACAAGGGGGAAAATGTGAGGGAGGAGGAAACTGGGATACCTAAGTAATTTGCTAATGCGT TTTTAGGCTACCTATTCCAATCCCTCATCGTATGGTGTACATTCAGATTCAGATATGATTGGCT TGATATTTAGGAGAGGCCAAATCAAGGAATGCAAATAACTATAGAGTTGTACAGGGTTCCTTAA GCCCTCTATTAAGTTCAACCATAACTCGAGCTGTCAACTTGCAAGGGTTTTCATCCTGTCTATA TGGTCAAATATTGCCACTCTGTAACTAAATGTTGTAAG Transcript length: 365 Transcript exons: 3426241-3426756 TGGCTGCAAGCCTGCAAGATGGAGCTGAGTTGGGAGGCTGAGCAAGCAGCAACAGGAGGAATCA AGGAACAAGGGGGAAAATGTGAGGGAGGAGGAAACTGGGATACCTAAGTAATTTGCTAATGCGT TTTTAGGCTACCTATTCCAATCCCTCATCGTATGGTGTACATTCAGATTCAGATATGATTGGCT TGATATTTAGGAGTCTTTAGAGGCCAAATCAAGGAATGCAAATAACTATAGAGTTGTACAGGGT TCCTTAAGCCCTCTATTAAGTTCAACCATAACTCGAGCTGTCAACTTGCAAGGGTTTTCATCCT GTCTATATGGTCAAATATTGCCACTCTGTAACTAAATGTTGTAAG
Genomic sequence	TGGCTGCAAGCCTGCAAGATGGAGCTGAGTTGGGAGGCTGAGCAAGCAGCAACAGGAGGAATCA AGGAACAAGGGGGAAAATGTGAGGGAGGAGGAAACTGGGATACCTAAGTAATTTGCTAATGCGT TTTTAGGCTACCTATTCCAATCCCTCATCGTATGGTGTACATTCAGATTCAGATATGATTGGCT TGATATTTAGGAGGTAGGTTCGTGCTTTGTCCTAATTTCAGTTATTTGTTTTTATTTTCACAAA ATTGTTCAATTTGGATATACCTAACTTTTTCAGTCTTTAGAGGCCAAATCAAGGAATGCAAATA ACTATAGAGTTGTACAGGGTTCCTTAAGCCCTCTATTAAGGTAAAGAACATGGAAATCTACCAA GTAGAATAGAAGTTATCACAATCTGAACTCTGTTGTATTGCAGTTCAACCATAACTCGAGCTGT CAACTTGCAAGGGTTTTCATCCTGTCTATATGGTCAAATATTGCCACTCTGTAACTAAATGTTG TAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017834 						
					
						PMCS
						0.50362667

Conservation Information
Conserved circRNAs	osi_circ_017834
PMCS	0.50362667

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3426719-3426348(+)
						
						Potential amino acid sequence
						
							MVKYCHSVTKCCKWLQACKMELSWEAEQAATGGIKEQGGKCEGGGNWDT*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3426719-3426348(+)
Potential amino acid sequence	MVKYCHSVTKCCKWLQACKMELSWEAEQAATGGIKEQGGKCEGGGNWDT*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os11g0170400_circ_g.3

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