Plant Circular RNA Database

Detail information of Os09g0267600_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os09g0267600_circ_g.4
					
						ID in PlantcircBase
						osa_circ_038673
					
						Alias
						Os_ciR11993
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 5103873-5105175  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os09g0267600						
					
						Parent gene annotation
						
							Similar to Charged multivesicular body protein 4b. (Os09t0267600
-01);Similar to Charged multivesicular body protein 4b. (Os09t02
67600-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0267600_circ_g.2 Os09g0267600_circ_g.3 						
					
						Support reads
						2/5
					
						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
						Os09t0267600-02:5
Os09t0267600-01:6

General Information
CircRNA Name	Os09g0267600_circ_g.4
ID in PlantcircBase	osa_circ_038673
Alias	Os_ciR11993
Organism	Oryza sativa
Position	chr9: 5103873-5105175 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os09g0267600
Parent gene annotation	Similar to Charged multivesicular body protein 4b. (Os09t0267600 -01);Similar to Charged multivesicular body protein 4b. (Os09t02 67600-02)
Parent gene strand	+
Alternative splicing	Os09g0267600_circ_g.2 Os09g0267600_circ_g.3
Support reads	2/5
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	Os09t0267600-02:5 Os09t0267600-01:6

			
						 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  
						
							GTCCCAGGCACCAGGATACCAACTCGCCCTGCTCCACAGAAAGCATCAGCTGAGGAGGATGAGC
TTGCAGCCTTGCAAGCTGAAATGGCATTGTGATCAGagtttggatttaatattacaggcgcagc
catgttcaacaggctctttggtaagcccaaggagcaggccaatgctagtgcgttggccacgctt
gataagtt

									
								

					

						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: 696
Transcript exons: 5103873-5103979,5104165-5104264,5104416-5104501,5104582-
5104673,5104779-5104893,5104980-5105175
AGTTTGGATTTAATATTACAGGCGCAGCCATGTTCAACAGGCTCTTTGGTAAGCCCAAGGAGCA
GGCCAATGCTAGTGCGTTGGCCACGCTTGATAAGTTAAATGAGACCCTTGACATGCTGGAGAAG
AAGGAGAAAGTCTTAGAGAAAAAGGCAGCCGCAGAACTGGAGAGGGCTAAGGAGTTCTCAAAAG
CAAAGAATAAAAGAGCGGCTATCCAATCCTTGAAGAGAAAAAAGCTTTATGAACAACAAATTGA
GCAGCTAGGGAACTTCCAGTTGAGAATTCATGATCAGATGATCATGTTAGAAGCTGCAAAAGCT
ACGACAGAAACCGTTGATGCTTTGAGGACTGGAGCTGCAGCTATGAAAGCAATGCAAAAGGCGA
CAAATATTGATGACGTTGATAAGACTATGGATGAAATTAATGAACAGACTGAAAACATGAAACA
AATACAAGATGCTTTGTCAGCCCCTCTTGGAGCATCTGCTGATTTTGATGAGGACGAACTAGAG
GCAGAACTGGAAGAACTGGAGGGAGCAGAATTGGAATCTCAGCTTCTCGAGCCTGTTGCAGCTC
CACCTGTGCATCCAGTGCAGGTCCCAGGCACCAGGATACCAACTCGCCCTGCTCCACAGAAAGC
ATCAGCTGAGGAGGATGAGCTTGCAGCCTTGCAAGCTGAAATGGCATTGTGATCAG
						
					

						Genomic sequence
						
							AGTTTGGATTTAATATTACAGGCGCAGCCATGTTCAACAGGCTCTTTGGTAAGCCCAAGGAGCA
GGCCAATGCTAGTGCGTTGGCCACGCTTGATAAGTTAAATGAGGTAAAGCTTTCTTATTCCTCT
CCATTCTATGATCTTAGCCTTGATTCTCTTGTGCTATGCGCATTGTCTGAGTCTTATTTGGTCT
GCCTGAATAATTCAATTATTACTTTGTTACTCAATAATGCACATGTCCCAAGTCACTTGCAAAT
ATATTGGAACTGAAATCTTACTTTATGTGTATTTAGACCCTTGACATGCTGGAGAAGAAGGAGA
AAGTCTTAGAGAAAAAGGCAGCCGCAGAACTGGAGAGGGCTAAGGAGTTCTCAAAAGCAAAGAA
TAAAAGAGGTGTGGCTTATCTCCATAGTGCAAGTTGTATTATATATTTTTTGCTTTCTTTTGAT
CTGAACTGGATTGATGTATAACCGTTTTAATCTGGACTGAAGTGATACATAGCTGTGCTAATAT
TTAAGTTAATGAAATTGTTCTTGTTCACCAGCGGCTATCCAATCCTTGAAGAGAAAAAAGCTTT
ATGAACAACAAATTGAGCAGCTAGGGAACTTCCAGTTGAGAATTCATGATCAGGTTACTTCCAA
CTTAAAATTTTCACATCTGATTACTACATGTTATAAATGTTTATATTATAATAATATTGAAAAA
TACAGATGATCATGTTAGAAGCTGCAAAAGCTACGACAGAAACCGTTGATGCTTTGAGGACTGG
AGCTGCAGCTATGAAAGCAATGCAAAAGGCGACGTGAGTATTTTCTGAATCATTTCTTATTTTG
GGTTTAGTGGTTTATCCCCTGATTCTTTCAAGAAAATTATGTCTCAAAAATGACTATTTACTGT
TTTCCTGCAGAAATATTGATGACGTTGATAAGACTATGGATGAAATTAATGAACAGACTGAAAA
CATGAAACAAATACAAGATGCTTTGTCAGCCCCTCTTGGAGCATCTGCTGATTTTGATGAGGTA
ACTCACTGTGGACATTTACAATGTGTAATATCTTCATGGTTTTTTGTTTGCGGTGCACTTAATA
CGTACCATAAAACTGACAGGACGAACTAGAGGCAGAACTGGAAGAACTGGAGGGAGCAGAATTG
GAATCTCAGCTTCTCGAGCCTGTTGCAGCTCCACCTGTGCATCCAGTGCAGGTCCCAGGCACCA
GGATACCAACTCGCCCTGCTCCACAGAAAGCATCAGCTGAGGAGGATGAGCTTGCAGCCTTGCA
AGCTGAAATGGCATTGTGATCAG
						
					

			
		

Sequences
Splice junction sequence	GTCCCAGGCACCAGGATACCAACTCGCCCTGCTCCACAGAAAGCATCAGCTGAGGAGGATGAGC TTGCAGCCTTGCAAGCTGAAATGGCATTGTGATCAGagtttggatttaatattacaggcgcagc catgttcaacaggctctttggtaagcccaaggagcaggccaatgctagtgcgttggccacgctt gataagtt
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: 696 Transcript exons: 5103873-5103979,5104165-5104264,5104416-5104501,5104582- 5104673,5104779-5104893,5104980-5105175 AGTTTGGATTTAATATTACAGGCGCAGCCATGTTCAACAGGCTCTTTGGTAAGCCCAAGGAGCA GGCCAATGCTAGTGCGTTGGCCACGCTTGATAAGTTAAATGAGACCCTTGACATGCTGGAGAAG AAGGAGAAAGTCTTAGAGAAAAAGGCAGCCGCAGAACTGGAGAGGGCTAAGGAGTTCTCAAAAG CAAAGAATAAAAGAGCGGCTATCCAATCCTTGAAGAGAAAAAAGCTTTATGAACAACAAATTGA GCAGCTAGGGAACTTCCAGTTGAGAATTCATGATCAGATGATCATGTTAGAAGCTGCAAAAGCT ACGACAGAAACCGTTGATGCTTTGAGGACTGGAGCTGCAGCTATGAAAGCAATGCAAAAGGCGA CAAATATTGATGACGTTGATAAGACTATGGATGAAATTAATGAACAGACTGAAAACATGAAACA AATACAAGATGCTTTGTCAGCCCCTCTTGGAGCATCTGCTGATTTTGATGAGGACGAACTAGAG GCAGAACTGGAAGAACTGGAGGGAGCAGAATTGGAATCTCAGCTTCTCGAGCCTGTTGCAGCTC CACCTGTGCATCCAGTGCAGGTCCCAGGCACCAGGATACCAACTCGCCCTGCTCCACAGAAAGC ATCAGCTGAGGAGGATGAGCTTGCAGCCTTGCAAGCTGAAATGGCATTGTGATCAG
Genomic sequence	AGTTTGGATTTAATATTACAGGCGCAGCCATGTTCAACAGGCTCTTTGGTAAGCCCAAGGAGCA GGCCAATGCTAGTGCGTTGGCCACGCTTGATAAGTTAAATGAGGTAAAGCTTTCTTATTCCTCT CCATTCTATGATCTTAGCCTTGATTCTCTTGTGCTATGCGCATTGTCTGAGTCTTATTTGGTCT GCCTGAATAATTCAATTATTACTTTGTTACTCAATAATGCACATGTCCCAAGTCACTTGCAAAT ATATTGGAACTGAAATCTTACTTTATGTGTATTTAGACCCTTGACATGCTGGAGAAGAAGGAGA AAGTCTTAGAGAAAAAGGCAGCCGCAGAACTGGAGAGGGCTAAGGAGTTCTCAAAAGCAAAGAA TAAAAGAGGTGTGGCTTATCTCCATAGTGCAAGTTGTATTATATATTTTTTGCTTTCTTTTGAT CTGAACTGGATTGATGTATAACCGTTTTAATCTGGACTGAAGTGATACATAGCTGTGCTAATAT TTAAGTTAATGAAATTGTTCTTGTTCACCAGCGGCTATCCAATCCTTGAAGAGAAAAAAGCTTT ATGAACAACAAATTGAGCAGCTAGGGAACTTCCAGTTGAGAATTCATGATCAGGTTACTTCCAA CTTAAAATTTTCACATCTGATTACTACATGTTATAAATGTTTATATTATAATAATATTGAAAAA TACAGATGATCATGTTAGAAGCTGCAAAAGCTACGACAGAAACCGTTGATGCTTTGAGGACTGG AGCTGCAGCTATGAAAGCAATGCAAAAGGCGACGTGAGTATTTTCTGAATCATTTCTTATTTTG GGTTTAGTGGTTTATCCCCTGATTCTTTCAAGAAAATTATGTCTCAAAAATGACTATTTACTGT TTTCCTGCAGAAATATTGATGACGTTGATAAGACTATGGATGAAATTAATGAACAGACTGAAAA CATGAAACAAATACAAGATGCTTTGTCAGCCCCTCTTGGAGCATCTGCTGATTTTGATGAGGTA ACTCACTGTGGACATTTACAATGTGTAATATCTTCATGGTTTTTTGTTTGCGGTGCACTTAATA CGTACCATAAAACTGACAGGACGAACTAGAGGCAGAACTGGAAGAACTGGAGGGAGCAGAATTG GAATCTCAGCTTCTCGAGCCTGTTGCAGCTCCACCTGTGCATCCAGTGCAGGTCCCAGGCACCA GGATACCAACTCGCCCTGCTCCACAGAAAGCATCAGCTGAGGAGGATGAGCTTGCAGCCTTGCA AGCTGAAATGGCATTGTGATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018844 						
					
						PMCS
						0.408322237

Conservation Information
Conserved circRNAs	osi_circ_018844
PMCS	0.408322237

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							5105135-5103971(+)
5104177-5105032(-)
						
						Potential amino acid sequence
						
							MSLQPCKLKWHCDQSLDLILQAQPCSTGSLVSPRSRPMLVRWPRLIS*(+)
MSRVSFNLSSVANALALACSLGLPKSLLNMAAPVILNPNSDHNAISACKAASSSSSADAFCGAG
RVGILVPGTCTGCTGGAATGSRS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	5105135-5103971(+) 5104177-5105032(-)
Potential amino acid sequence	MSLQPCKLKWHCDQSLDLILQAQPCSTGSLVSPRSRPMLVRWPRLIS(+) MSRVSFNLSSVANALALACSLGLPKSLLNMAAPVILNPNSDHNAISACKAASSSSSADAFCGAG RVGILVPGTCTGCTGGAATGSRS(-)
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 Os09g0267600_circ_g.4

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