Plant Circular RNA Database

Detail information of Os09g0249700_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os09g0249700_circ_g.1
					
						ID in PlantcircBase
						osa_circ_038554
					
						Alias
						Os09circ01198/Os_ciR4166
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 3758543-3758829  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os09g0249700						
					
						Parent gene annotation
						
							Protein phosphatase 2A A subunit (Phosphatase 2A regulatory A su
bunit). (Os09t0249700-01);Similar to Phosphatase 2A regulatory A
 subunit. (Os09t0249700-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0249000_circ_ag.1 Os09g0249600_circ_ig.1 Os09g0249700_circ_g.2 Os09g0249700_circ_g.3 Os09g0249700_circ_g.4 Os09g0249700_circ_g.5 Os09g0249700_circ_g.6 Os09g0249700_circ_g.7 Os09g0249700_circ_g.8 Os09g0249700_circ_g.9 Os09g0249700_circ_g.10 Os09g0249700_circ_g.11 Os09g0249700_circ_g.12 Os09g0249700_circ_g.13 Os09g0249700_circ_g.14 Os09g0249700_circ_g.15 Os09g0249700_circ_g.16 						
					
						Support reads
						23/2
					
						Tissues
						leaf and panicle/root
					
						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
						Os09t0249700-01:2
Os09t0249700-02:2

General Information
CircRNA Name	Os09g0249700_circ_g.1
ID in PlantcircBase	osa_circ_038554
Alias	Os09circ01198/Os_ciR4166
Organism	Oryza sativa
Position	chr9: 3758543-3758829 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	SMALT, Segemehl, find_circ
Parent gene	Os09g0249700
Parent gene annotation	Protein phosphatase 2A A subunit (Phosphatase 2A regulatory A su bunit). (Os09t0249700-01);Similar to Phosphatase 2A regulatory A subunit. (Os09t0249700-02)
Parent gene strand	-
Alternative splicing	Os09g0249000_circ_ag.1 Os09g0249600_circ_ig.1 Os09g0249700_circ_g.2 Os09g0249700_circ_g.3 Os09g0249700_circ_g.4 Os09g0249700_circ_g.5 Os09g0249700_circ_g.6 Os09g0249700_circ_g.7 Os09g0249700_circ_g.8 Os09g0249700_circ_g.9 Os09g0249700_circ_g.10 Os09g0249700_circ_g.11 Os09g0249700_circ_g.12 Os09g0249700_circ_g.13 Os09g0249700_circ_g.14 Os09g0249700_circ_g.15 Os09g0249700_circ_g.16
Support reads	23/2
Tissues	leaf and panicle/root
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	Os09t0249700-01:2 Os09t0249700-02:2

			
						 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  
						
							GACAAGTGATTTCGGCACCCATGACAGGGGCCAGCAATGAAATAGCTTGCAGGATGGTCATGCG
GTAGAGATAATGCGGGTTGTTTATCTTCTCCAGCACagattgatcaaggatcggtataagtgcc
tgcagaaccttcgcaacattgaatttgatgtttggcactctgaaatttagaaaaatatttgtta
ataaggcc

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							AGATTGATCAAGGATCGGTATAAGTGCCTGCAGAACCTTCGCAACATTGAATTTGATGTTTGGC
ACTCTGAAATTTAGAAAAATATTTGTTAATAAGGCCTTGATCAGATGGGTAAACTATACATTTA
CAAATTACAAATTTTTCACCTGTCCTTTGAGGAATTAATCACAACAGGGAGCAGCTGTTGACAA
GTGATTTCGGCACCCATGACAGGGGCCAGCAATGAAATAGCTTGCAGGATGGTCATGCGGTAGA
GATAATGCGGGTTGTTTATCTTCTCCAGCAC

Sequences
Splice junction sequence	GACAAGTGATTTCGGCACCCATGACAGGGGCCAGCAATGAAATAGCTTGCAGGATGGTCATGCG GTAGAGATAATGCGGGTTGTTTATCTTCTCCAGCACagattgatcaaggatcggtataagtgcc tgcagaaccttcgcaacattgaatttgatgtttggcactctgaaatttagaaaaatatttgtta ataaggcc
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AGATTGATCAAGGATCGGTATAAGTGCCTGCAGAACCTTCGCAACATTGAATTTGATGTTTGGC ACTCTGAAATTTAGAAAAATATTTGTTAATAAGGCCTTGATCAGATGGGTAAACTATACATTTA CAAATTACAAATTTTTCACCTGTCCTTTGAGGAATTAATCACAACAGGGAGCAGCTGTTGACAA GTGATTTCGGCACCCATGACAGGGGCCAGCAATGAAATAGCTTGCAGGATGGTCATGCGGTAGA GATAATGCGGGTTGTTTATCTTCTCCAGCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.226686092

Conservation Information
Conserved circRNAs	NA
PMCS	0.226686092

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3758804-3758697(+)
3758792-3758545(-)
3758591-3758816(-)
						
						Potential amino acid sequence
						
							MRVVYLLQHRLIKDRYKCLQNLRNIEFDVWHSVL*(+)
MTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQALIPILDQSVLEKINNP
HYLYRMTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQALIPILDQSVLE
KINNPHYLYRMTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQALIPILD
QSVLEKINNPHYLYRMTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQAL
IPILDQS(-)
MLRRFCRHLYRSLINLCWRR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3758804-3758697(+) 3758792-3758545(-) 3758591-3758816(-)
Potential amino acid sequence	MRVVYLLQHRLIKDRYKCLQNLRNIEFDVWHSVL(+) MTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQALIPILDQSVLEKINNP HYLYRMTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQALIPILDQSVLE KINNPHYLYRMTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQALIPILD QSVLEKINNPHYLYRMTILQAISLLAPVMGAEITCQQLLPVVINSSKDRVPNIKFNVAKVLQAL IPILDQS(-) MLRRFCRHLYRSLINLCWRR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2015

circRNA

Detail information of Os09g0249700_circ_g.1

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