Plant Circular RNA Database

Detail information of Os09g0475400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0475400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_039560
					
						Alias
						Os_ciR11848
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 18209460-18209666  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os09g0475400						
					
						Parent gene annotation
						
							Helix-loop-helix DNA-binding domain containing protein. (Os09t04
75400-01);Similar to cDNA clone:J023084K14, full insert sequence
. (Os09t0475400-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0475400_circ_g.1 Os09g0475400_circ_g.2 Os09g0475400_circ_g.4 Os09g0475400_circ_g.5 Os09g0475400_circ_g.6 Os09g0475400_circ_g.7 Os09g0475400_circ_g.8 Os09g0475400_circ_g.9 Os09g0475400_circ_g.10 						
					
						Support reads
						2/1
					
						Tissues
						root/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  
						
							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
						Os09t0475400-02:1
Os09t0475400-01:1

General Information
CircRNA Name	Os09g0475400_circ_g.3
ID in PlantcircBase	osa_circ_039560
Alias	Os_ciR11848
Organism	Oryza sativa
Position	chr9: 18209460-18209666 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os09g0475400
Parent gene annotation	Helix-loop-helix DNA-binding domain containing protein. (Os09t04 75400-01);Similar to cDNA clone:J023084K14, full insert sequence . (Os09t0475400-02)
Parent gene strand	+
Alternative splicing	Os09g0475400_circ_g.1 Os09g0475400_circ_g.2 Os09g0475400_circ_g.4 Os09g0475400_circ_g.5 Os09g0475400_circ_g.6 Os09g0475400_circ_g.7 Os09g0475400_circ_g.8 Os09g0475400_circ_g.9 Os09g0475400_circ_g.10
Support reads	2/1
Tissues	root/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	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	Os09t0475400-02:1 Os09t0475400-01:1

			
						 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  
						
							GGCGGGTTCATGGACTCTGGCTCCAGATCCAGTGGCGGCGCCGGGTTCGACGACGACGATGGCG
TGGCCGCGCGGCGTGAGGTCTCGTCCTCGCTCAAAGggcaccaccaccaccaccaccagtggac
gctccccttcgccggcgtcgggcaggtggccgccaccgcggcgaggcagcagcaggagtggaag
gggcgagt

						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
						
							GGCACCACCACCACCACCACCAGTGGACGCTCCCCTTCGCCGGCGTCGGGCAGGTGGCCGCCAC
CGCGGCGAGGCAGCAGCAGGAGTGGAAGGGGCGAGTCGGGGGAGGCGGGTTCATGGACTCTGGC
TCCAGATCCAGTGGCGGCGCCGGGTTCGACGACGACGATGGCGTGGCCGCGCGGCGTGAGGTCT
CGTCCTCGCTCAAAG

Sequences
Splice junction sequence	GGCGGGTTCATGGACTCTGGCTCCAGATCCAGTGGCGGCGCCGGGTTCGACGACGACGATGGCG TGGCCGCGCGGCGTGAGGTCTCGTCCTCGCTCAAAGggcaccaccaccaccaccaccagtggac gctccccttcgccggcgtcgggcaggtggccgccaccgcggcgaggcagcagcaggagtggaag gggcgagt
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	GGCACCACCACCACCACCACCAGTGGACGCTCCCCTTCGCCGGCGTCGGGCAGGTGGCCGCCAC CGCGGCGAGGCAGCAGCAGGAGTGGAAGGGGCGAGTCGGGGGAGGCGGGTTCATGGACTCTGGC TCCAGATCCAGTGGCGGCGCCGGGTTCGACGACGACGATGGCGTGGCCGCGCGGCGTGAGGTCT CGTCCTCGCTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.297475121

Conservation Information
Conserved circRNAs	NA
PMCS	0.297475121

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							18209626-18209663(+)
18209577-18209663(+)
18209579-18209462(-)
						
						Potential amino acid sequence
						
							MAWPRGVRSRPRSKGTTTTTTSGRSPSPASGRWPPPRRGSSRSGRGESGEAGSWTLAPDPVAAP
GSTTTMAWPRGVRSRPRSKGTTTTTTSGRSPSPASGRWPPPRRGSSRSGRGESGEAGSWTLAPD
PVAAPGSTTTMAWPRGVRSRPRSKGTTTTTTSGRSPSPASGRWPPPRRGSSRSGRGESGEAGSW
TLAPDPVAAPGSTTTMAWPRGVRSRPRSK(+)
MDSGSRSSGGAGFDDDDGVAARREVSSSLKGHHHHHHQWTLPFAGVGQVAATAARQQQEWKGRV
GGGGFMDSGSRSSGGAGFDDDDGVAARREVSSSLKGHHHHHHQWTLPFAGVGQVAATAARQQQE
WKGRVGGGGFMDSGSRSSGGAGFDDDDGVAARREVSSSLKGHHHHHHQWTLPFAGVGQVAATAA
RQQQEWKGRVGGGGFMDSGSRSSGGAGFDDDDGVAARREVSSSLK(+)
MNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWCPLSEDETSRRAATPSSSSNPAPPLD
LEPESMNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWCPLSEDETSRRAATPSSSSNP
APPLDLEPESMNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWCPLSEDETSRRAATPS
SSSNPAPPLDLEPESMNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWC(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	18209626-18209663(+) 18209577-18209663(+) 18209579-18209462(-)
Potential amino acid sequence	MAWPRGVRSRPRSKGTTTTTTSGRSPSPASGRWPPPRRGSSRSGRGESGEAGSWTLAPDPVAAP GSTTTMAWPRGVRSRPRSKGTTTTTTSGRSPSPASGRWPPPRRGSSRSGRGESGEAGSWTLAPD PVAAPGSTTTMAWPRGVRSRPRSKGTTTTTTSGRSPSPASGRWPPPRRGSSRSGRGESGEAGSW TLAPDPVAAPGSTTTMAWPRGVRSRPRSK(+) MDSGSRSSGGAGFDDDDGVAARREVSSSLKGHHHHHHQWTLPFAGVGQVAATAARQQQEWKGRV GGGGFMDSGSRSSGGAGFDDDDGVAARREVSSSLKGHHHHHHQWTLPFAGVGQVAATAARQQQE WKGRVGGGGFMDSGSRSSGGAGFDDDDGVAARREVSSSLKGHHHHHHQWTLPFAGVGQVAATAA RQQQEWKGRVGGGGFMDSGSRSSGGAGFDDDDGVAARREVSSSLK(+) MNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWCPLSEDETSRRAATPSSSSNPAPPLD LEPESMNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWCPLSEDETSRRAATPSSSSNP APPLDLEPESMNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWCPLSEDETSRRAATPS SSSNPAPPLDLEPESMNPPPPTRPFHSCCCLAAVAATCPTPAKGSVHWWWWWWC(-)
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 Os09g0475400_circ_g.3

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