Plant Circular RNA Database

Detail information of Os09g0525600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0525600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_039906
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 20536361-20537138  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ie-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0525650						
					
						Parent gene annotation
						
							Hypothetical protein. (Os09t0525650-00)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0525600_circ_g.4 Os09g0525600_circ_g.5 						
					
						Support reads
						6
					
						Tissues
						shoot, 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
						Os09t0525600-03:2
Os09t0525600-01:2
Os09t0525600-02:1
Os09t0525600-03:2
Os09t0525600-01:2
Os09t0525600-02:1
Os09t0525650-00:2

General Information
CircRNA Name	Os09g0525600_circ_g.3
ID in PlantcircBase	osa_circ_039906
Alias	NA
Organism	Oryza sativa
Position	chr9: 20536361-20537138 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ie-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0525650
Parent gene annotation	Hypothetical protein. (Os09t0525650-00)
Parent gene strand	+
Alternative splicing	Os09g0525600_circ_g.4 Os09g0525600_circ_g.5
Support reads	6
Tissues	shoot, 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	Os09t0525600-03:2 Os09t0525600-01:2 Os09t0525600-02:1 Os09t0525600-03:2 Os09t0525600-01:2 Os09t0525600-02:1 Os09t0525650-00:2

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: AAGCATCATTGCCGTCAGAG
 R: TTGCAGCAGTTTCTTCCAGG
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	Yes 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	F: AAGCATCATTGCCGTCAGAG R: TTGCAGCAGTTTCTTCCAGG 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  
						
							CTCTTGCAGCAGTTTCTTCCAGGCGACGAAGCTCGGCCTCCTGTAGGGCCTTCAACTCTTTTTC
TTGATCAGCTTGGAGTGATGCAAGGTATTCATCATCctgaagtttatgagatttcagaaagcga
cgcccctgtcgactaccatcaggcatgcggactacaagtgtgacagcaccttcctcgtctgcag
ctggctct

						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: 309
Transcript exons: 20536361-20536504,20536974-20537138
CTGAAGTTTATGAGATTTCAGAAAGCGACGCCCCTGTCGACTACCATCAGGCATGCGGACTACA
AGTGTGACAGCACCTTCCTCGTCTGCAGCTGGCTCTGACGGCAATGATGCTTGTTTGGATGCAA
GACTGGACTCTAGCTCCTCTTCCTCCAGTTGTTTTTTACGCCTTTCCTCTTCCTCTTGCTTCTG
TTTTTCAAGGGCAGCTTCTCTTGCAGCAGTTTCTTCCAGGCGACGAAGCTCGGCCTCCTGTAGG
GCCTTCAACTCTTTTTCTTGATCAGCTTGGAGTGATGCAAGGTATTCATCATC
						
						Genomic sequence
						
							CTGAAGTTTATGAGATTTCAGAAAGCGACGCCCCTGTCGACTACCATCAGGCATGCGGACTACA
AGTGTGACAGCACCTTCCTCGTCTGCAGCTGGCTCTGACGGCAATGATGCTTGTTTGGATGCAA
GACTGGACTCTAGCTCCTGTTTGCATAAAACGTCAGGAACCACATCACACACATTACAAATGGT
GCAGAATACAAGTGCAATATGAATTAAGGAAATAATGGACAAAGCCTCAATGGAACTGCAGAAA
GAAAGCACCAGGTTTGTCATACAGCTTTATAAGAACTTGATACTGCTTTAGCGAATTGCTTGTC
AACAAAATGTAGAAAATATCAATATAATAATACAAAATGTCAGGAAAGAAGATGCCATGATGCT
AGGTAGTATCCATCTAGACTTTATGCAGAGTTTCATCAAGTATATCAACCAGCAGCTAAGCCTC
AAAGTAGAACCCTTTGTAACATATAAAATAGAGCAGATCACCAGAGCACCAAGTTTCATATGCT
CAAAATGTGAACTTATGATCTAAATACCTAGCATTCAAGTATTGAAAAGACTGTTGTTGATGAT
CAATTAATTCCATAATTATTTTTAACGAAAGGTTTACCTCTTCCTCCAGTTGTTTTTTACGCCT
TTCCTCTTCCTCTTGCTTCTGTTTTTCAAGGGCAGCTTCTCTTGCAGCAGTTTCTTCCAGGCGA
CGAAGCTCGGCCTCCTGTAGGGCCTTCAACTCTTTTTCTTGATCAGCTTGGAGTGATGCAAGGT
ATTCATCATC

Sequences
Splice junction sequence	CTCTTGCAGCAGTTTCTTCCAGGCGACGAAGCTCGGCCTCCTGTAGGGCCTTCAACTCTTTTTC TTGATCAGCTTGGAGTGATGCAAGGTATTCATCATCctgaagtttatgagatttcagaaagcga cgcccctgtcgactaccatcaggcatgcggactacaagtgtgacagcaccttcctcgtctgcag ctggctct
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: 309 Transcript exons: 20536361-20536504,20536974-20537138 CTGAAGTTTATGAGATTTCAGAAAGCGACGCCCCTGTCGACTACCATCAGGCATGCGGACTACA AGTGTGACAGCACCTTCCTCGTCTGCAGCTGGCTCTGACGGCAATGATGCTTGTTTGGATGCAA GACTGGACTCTAGCTCCTCTTCCTCCAGTTGTTTTTTACGCCTTTCCTCTTCCTCTTGCTTCTG TTTTTCAAGGGCAGCTTCTCTTGCAGCAGTTTCTTCCAGGCGACGAAGCTCGGCCTCCTGTAGG GCCTTCAACTCTTTTTCTTGATCAGCTTGGAGTGATGCAAGGTATTCATCATC
Genomic sequence	CTGAAGTTTATGAGATTTCAGAAAGCGACGCCCCTGTCGACTACCATCAGGCATGCGGACTACA AGTGTGACAGCACCTTCCTCGTCTGCAGCTGGCTCTGACGGCAATGATGCTTGTTTGGATGCAA GACTGGACTCTAGCTCCTGTTTGCATAAAACGTCAGGAACCACATCACACACATTACAAATGGT GCAGAATACAAGTGCAATATGAATTAAGGAAATAATGGACAAAGCCTCAATGGAACTGCAGAAA GAAAGCACCAGGTTTGTCATACAGCTTTATAAGAACTTGATACTGCTTTAGCGAATTGCTTGTC AACAAAATGTAGAAAATATCAATATAATAATACAAAATGTCAGGAAAGAAGATGCCATGATGCT AGGTAGTATCCATCTAGACTTTATGCAGAGTTTCATCAAGTATATCAACCAGCAGCTAAGCCTC AAAGTAGAACCCTTTGTAACATATAAAATAGAGCAGATCACCAGAGCACCAAGTTTCATATGCT CAAAATGTGAACTTATGATCTAAATACCTAGCATTCAAGTATTGAAAAGACTGTTGTTGATGAT CAATTAATTCCATAATTATTTTTAACGAAAGGTTTACCTCTTCCTCCAGTTGTTTTTTACGCCT TTCCTCTTCCTCTTGCTTCTGTTTTTCAAGGGCAGCTTCTCTTGCAGCAGTTTCTTCCAGGCGA CGAAGCTCGGCCTCCTGTAGGGCCTTCAACTCTTTTTCTTGATCAGCTTGGAGTGATGCAAGGT ATTCATCATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008181* osi_circ_018660 						
					
						PMCS
						0.285527624

Conservation Information
Conserved circRNAs	osi_circ_008181* osi_circ_018660
PMCS	0.285527624

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							20536469-20536428(+)
20536416-20536363(-)
						
						Potential amino acid sequence
						
							MMLVWMQDWTLAPLPPVVFYAFPLPLASVFQGQLLLQQFLPGDEARPPVGPSTLFLDQLGVMQG
IHHPEVYEISESDAPVDYHQACGLQV*(+)
MPDGSRQGRRFLKSHKLQDDEYLASLQADQEKELKALQEAELRRLEETAAREAALEKQKQEEEE
RRKKQLEEEELESSLASKQASLPSEPAADEEGAVTLVVRMPDGSRQGRRFLKSHKLQDDEYLAS
LQADQEKELKALQEAELRRLEETAAREAALEKQKQEEEERRKKQLEEEELESSLASKQASLPSE
PAADEEGAVTLVVRMPDGSRQGRRFLKSHKLQDDEYLASLQADQEKELKALQEAELRRLEETAA
REAALEKQKQEEEERRKKQLEEEELESSLASKQASLPSEPAADEEGAVTLVVRMPDGSRQGRRF
LKSHKLQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	20536469-20536428(+) 20536416-20536363(-)
Potential amino acid sequence	MMLVWMQDWTLAPLPPVVFYAFPLPLASVFQGQLLLQQFLPGDEARPPVGPSTLFLDQLGVMQG IHHPEVYEISESDAPVDYHQACGLQV*(+) MPDGSRQGRRFLKSHKLQDDEYLASLQADQEKELKALQEAELRRLEETAAREAALEKQKQEEEE RRKKQLEEEELESSLASKQASLPSEPAADEEGAVTLVVRMPDGSRQGRRFLKSHKLQDDEYLAS LQADQEKELKALQEAELRRLEETAAREAALEKQKQEEEERRKKQLEEEELESSLASKQASLPSE PAADEEGAVTLVVRMPDGSRQGRRFLKSHKLQDDEYLASLQADQEKELKALQEAELRRLEETAA REAALEKQKQEEEERRKKQLEEEELESSLASKQASLPSEPAADEEGAVTLVVRMPDGSRQGRRF LKSHKLQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0525600_circ_g.3

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