Plant Circular RNA Database

Detail information of Os09g0437500_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os09g0437500_circ_g.4
					
						ID in PlantcircBase
						osa_circ_039306
					
						Alias
						Os09circ06057
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 16153454-16154026  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, circseq_cup
					
						Parent gene
						
							Os09g0437500						
					
						Parent gene annotation
						
							Dormancyauxin associated family protein. (Os09t0437500-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0437500_circ_g.5 Os09g0437500_circ_g.6 Os09g0437500_circ_g.7 						
					
						Support reads
						5/21/29
					
						Tissues
						leaf and panicle/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
						Os09t0437500-01:2

General Information
CircRNA Name	Os09g0437500_circ_g.4
ID in PlantcircBase	osa_circ_039306
Alias	Os09circ06057
Organism	Oryza sativa
Position	chr9: 16153454-16154026 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, circseq_cup
Parent gene	Os09g0437500
Parent gene annotation	Dormancyauxin associated family protein. (Os09t0437500-01)
Parent gene strand	+
Alternative splicing	Os09g0437500_circ_g.5 Os09g0437500_circ_g.6 Os09g0437500_circ_g.7
Support reads	5/21/29
Tissues	leaf and panicle/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	Os09t0437500-01:2

			
						 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  
						
							CGGAGGGCTGGAAGAAGCTGCGCCGTGGGGCGGCGAGGATGGCCGACGGCGTGGACGCCAGCGC
CGGCGGCCAGCCGAGAAGCCCCACCGTATACGACTGgtgatcttgggttagcttagctagctaa
attaagctgcgtgcagcatggggctcctcgaccagctctgggacgacacggtggccgggccgcg
gccggact

						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: 458
Transcript exons: 16153454-16153793,16153909-16154026
GTGATCTTGGGTTAGCTTAGCTAGCTAAATTAAGCTGCGTGCAGCATGGGGCTCCTCGACCAGC
TCTGGGACGACACGGTGGCCGGGCCGCGGCCGGACTCCGGCCTCGGCAAGCTCCGCAAGTACGC
CTCCTTCTCCCCTTCCTCCTCCTCCTCGACGATGGCGGCGTCGCCGTCGCCCATCTCGGCGGCG
GCGGCGGCGGCCGACGCGCCGGCCGTGACGCGCAGCATCACCATCCTCCGCCCGCCGGCGCTGT
CCGTGACGTCGCCGCGCGGCAGCGAGTCGGGCCCCTCCACGCCGTCGTCGCCGGCCAGCGTCCC
GGACTCCCCCTTCGGCTCAGCACCGACGCCGAAGGGATCGGAGGGCTGGAAGAAGCTGCGCCGT
GGGGCGGCGAGGATGGCCGACGGCGTGGACGCCAGCGCCGGCGGCCAGCCGAGAAGCCCCACCG
TATACGACTG
						
						Genomic sequence
						
							GTGATCTTGGGTTAGCTTAGCTAGCTAAATTAAGCTGCGTGCAGCATGGGGCTCCTCGACCAGC
TCTGGGACGACACGGTGGCCGGGCCGCGGCCGGACTCCGGCCTCGGCAAGCTCCGCAAGTACGC
CTCCTTCTCCCCTTCCTCCTCCTCCTCGACGATGGCGGCGTCGCCGTCGCCCATCTCGGCGGCG
GCGGCGGCGGCCGACGCGCCGGCCGTGACGCGCAGCATCACCATCCTCCGCCCGCCGGCGCTGT
CCGTGACGTCGCCGCGCGGCAGCGAGTCGGGCCCCTCCACGCCGTCGTCGCCGGCCAGCGTCCC
GGACTCCCCCTTCGGCTCAGGTGGTGACCAGGCCACCATAATCTCTTCTTGAATCTTGATCTTT
TTGCACACGCATATATCGTAATCTCGATCTTAATTATATCTATGCATCGTCGACTTGTGCATGG
CATGCAGCACCGACGCCGAAGGGATCGGAGGGCTGGAAGAAGCTGCGCCGTGGGGCGGCGAGGA
TGGCCGACGGCGTGGACGCCAGCGCCGGCGGCCAGCCGAGAAGCCCCACCGTATACGACTG

Sequences
Splice junction sequence	CGGAGGGCTGGAAGAAGCTGCGCCGTGGGGCGGCGAGGATGGCCGACGGCGTGGACGCCAGCGC CGGCGGCCAGCCGAGAAGCCCCACCGTATACGACTGgtgatcttgggttagcttagctagctaa attaagctgcgtgcagcatggggctcctcgaccagctctgggacgacacggtggccgggccgcg gccggact
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: 458 Transcript exons: 16153454-16153793,16153909-16154026 GTGATCTTGGGTTAGCTTAGCTAGCTAAATTAAGCTGCGTGCAGCATGGGGCTCCTCGACCAGC TCTGGGACGACACGGTGGCCGGGCCGCGGCCGGACTCCGGCCTCGGCAAGCTCCGCAAGTACGC CTCCTTCTCCCCTTCCTCCTCCTCCTCGACGATGGCGGCGTCGCCGTCGCCCATCTCGGCGGCG GCGGCGGCGGCCGACGCGCCGGCCGTGACGCGCAGCATCACCATCCTCCGCCCGCCGGCGCTGT CCGTGACGTCGCCGCGCGGCAGCGAGTCGGGCCCCTCCACGCCGTCGTCGCCGGCCAGCGTCCC GGACTCCCCCTTCGGCTCAGCACCGACGCCGAAGGGATCGGAGGGCTGGAAGAAGCTGCGCCGT GGGGCGGCGAGGATGGCCGACGGCGTGGACGCCAGCGCCGGCGGCCAGCCGAGAAGCCCCACCG TATACGACTG
Genomic sequence	GTGATCTTGGGTTAGCTTAGCTAGCTAAATTAAGCTGCGTGCAGCATGGGGCTCCTCGACCAGC TCTGGGACGACACGGTGGCCGGGCCGCGGCCGGACTCCGGCCTCGGCAAGCTCCGCAAGTACGC CTCCTTCTCCCCTTCCTCCTCCTCCTCGACGATGGCGGCGTCGCCGTCGCCCATCTCGGCGGCG GCGGCGGCGGCCGACGCGCCGGCCGTGACGCGCAGCATCACCATCCTCCGCCCGCCGGCGCTGT CCGTGACGTCGCCGCGCGGCAGCGAGTCGGGCCCCTCCACGCCGTCGTCGCCGGCCAGCGTCCC GGACTCCCCCTTCGGCTCAGGTGGTGACCAGGCCACCATAATCTCTTCTTGAATCTTGATCTTT TTGCACACGCATATATCGTAATCTCGATCTTAATTATATCTATGCATCGTCGACTTGTGCATGG CATGCAGCACCGACGCCGAAGGGATCGGAGGGCTGGAAGAAGCTGCGCCGTGGGGCGGCGAGGA TGGCCGACGGCGTGGACGCCAGCGCCGGCGGCCAGCCGAGAAGCCCCACCGTATACGACTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_008080* osi_circ_018515 						
					
						PMCS
						0.415426687

Conservation Information
Conserved circRNAs	osi_circ_008080* osi_circ_018515
PMCS	0.415426687

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							16153500-16153454(+)
						
						Potential amino acid sequence
						
							MGLLDQLWDDTVAGPRPDSGLGKLRKYASFSPSSSSSTMAASPSPISAAAAAADAPAVTRSITI
LRPPALSVTSPRGSESGPSTPSSPASVPDSPFGSAPTPKGSEGWKKLRRGAARMADGVDASAGG
QPRSPTVYDW*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	16153500-16153454(+)
Potential amino acid sequence	MGLLDQLWDDTVAGPRPDSGLGKLRKYASFSPSSSSSTMAASPSPISAAAAAADAPAVTRSITI LRPPALSVTSPRGSESGPSTPSSPASVPDSPFGSAPTPKGSEGWKKLRRGAARMADGVDASAGG QPRSPTVYDW*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os09g0437500_circ_g.4

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