Plant Circular RNA Database

Detail information of Os06g0233400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0233400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_030312
					
						Alias
						Os_ciR10787
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 6929234-6930114  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os06g0233400						
					
						Parent gene annotation
						
							Defective in cullin neddylation domain containing protein. (Os06
t0233400-01);Defective in cullin neddylation domain containing p
rotein. (Os06t0233400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os06g0233400_circ_g.1 Os06g0233400_circ_g.2 Os06g0233400_circ_g.4 Os06g0233400_circ_g.5 Os06g0233400_circ_g.6 Os06g0233400_circ_g.7 						
					
						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  
						
							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
						Os06t0233400-02:5
Os06t0233400-01:5

General Information
CircRNA Name	Os06g0233400_circ_g.3
ID in PlantcircBase	osa_circ_030312
Alias	Os_ciR10787
Organism	Oryza sativa
Position	chr6: 6929234-6930114 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os06g0233400
Parent gene annotation	Defective in cullin neddylation domain containing protein. (Os06 t0233400-01);Defective in cullin neddylation domain containing p rotein. (Os06t0233400-02)
Parent gene strand	-
Alternative splicing	Os06g0233400_circ_g.1 Os06g0233400_circ_g.2 Os06g0233400_circ_g.4 Os06g0233400_circ_g.5 Os06g0233400_circ_g.6 Os06g0233400_circ_g.7
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	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	Os06t0233400-02:5 Os06t0233400-01:5

			
						 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  
						
							TTGAAAATGGCACTCACCCAATTGACTGCAGTCCACCAATGAATTCCTGGCGAGTAAATTCACA
CATTGTGGCAGCTTTCATGTGCCATGATATGACAAGcttgacaaattccaacagttgagaccat
gtgtccctagaaatggctttattatgcctcacctgaaatttgaaggatttaaattagcaaagta
tcatctga

						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
						
							CTTGACAAATTCCAACAGTTGAGACCATGTGTCCCTAGAAATGGCTTTATTATGCCTCACCTGA
AATTTGAAGGATTTAAATTAGCAAAGTATCATCTGAAACCACTAAGTTTTTGAAATAGCAAGAT
GCTCTGAAAATGGAAGTACATGGAACCACCTTTGAGGCATACCTGTAAAAACTGGCACCAATGG
TCGATAAGGGGCCAGTGCCTTTCAGCAAAGAGCAACTGCCACATTCCAAGAGCAGTCTCCAGTG
CGAGAGATTTTTGACCCTGTAAGATCAAGAGCATATTTCAGGAAAATAAACATAGGGAACATCA
GGATCACAGGATGATGTTTATGAACAAAAAATGTTGTCCTGCTGCAAATAAAGACAAGGGTTCT
GAAACAAATATTCTTCAACTGAGGCTAACCTTTTCCCTAGCCCAAGCAAAAGCAAAGTTGTATA
TCTCACGGAATTTATCTGAGTGAGGAAAGAGTAACCACACAGATTAGATATCAAATAAAAGATG
GCATTGAATTCCTTCCATACACATTCTATTTCAGTTCCTTCATATTGGTCACAAATTGTAAACT
AAAATGTAGTGTTACTTCAACATAGAGAAAATCCAACTTCACACAAAGAAAACACATACGGTCA
TCTTTTATCTCAGCCCGTAAAGATGGCAATTTCTCACGGAGCTTTTCAATTGAATCCACCCTGC
AAATACCACCCGGGATATATGAAAAAACTATATCTAAGAAACACTCAATAGTTTGATCAATTAC
ATAGACACCATGATTGAAAATGGCACTCACCCAATTGACTGCAGTCCACCAATGAATTCCTGGC
GAGTAAATTCACACATTGTGGCAGCTTTCATGTGCCATGATATGACAAG

Sequences
Splice junction sequence	TTGAAAATGGCACTCACCCAATTGACTGCAGTCCACCAATGAATTCCTGGCGAGTAAATTCACA CATTGTGGCAGCTTTCATGTGCCATGATATGACAAGcttgacaaattccaacagttgagaccat gtgtccctagaaatggctttattatgcctcacctgaaatttgaaggatttaaattagcaaagta tcatctga
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	CTTGACAAATTCCAACAGTTGAGACCATGTGTCCCTAGAAATGGCTTTATTATGCCTCACCTGA AATTTGAAGGATTTAAATTAGCAAAGTATCATCTGAAACCACTAAGTTTTTGAAATAGCAAGAT GCTCTGAAAATGGAAGTACATGGAACCACCTTTGAGGCATACCTGTAAAAACTGGCACCAATGG TCGATAAGGGGCCAGTGCCTTTCAGCAAAGAGCAACTGCCACATTCCAAGAGCAGTCTCCAGTG CGAGAGATTTTTGACCCTGTAAGATCAAGAGCATATTTCAGGAAAATAAACATAGGGAACATCA GGATCACAGGATGATGTTTATGAACAAAAAATGTTGTCCTGCTGCAAATAAAGACAAGGGTTCT GAAACAAATATTCTTCAACTGAGGCTAACCTTTTCCCTAGCCCAAGCAAAAGCAAAGTTGTATA TCTCACGGAATTTATCTGAGTGAGGAAAGAGTAACCACACAGATTAGATATCAAATAAAAGATG GCATTGAATTCCTTCCATACACATTCTATTTCAGTTCCTTCATATTGGTCACAAATTGTAAACT AAAATGTAGTGTTACTTCAACATAGAGAAAATCCAACTTCACACAAAGAAAACACATACGGTCA TCTTTTATCTCAGCCCGTAAAGATGGCAATTTCTCACGGAGCTTTTCAATTGAATCCACCCTGC AAATACCACCCGGGATATATGAAAAAACTATATCTAAGAAACACTCAATAGTTTGATCAATTAC ATAGACACCATGATTGAAAATGGCACTCACCCAATTGACTGCAGTCCACCAATGAATTCCTGGC GAGTAAATTCACACATTGTGGCAGCTTTCATGTGCCATGATATGACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_016829 						
					
						PMCS
						0.144093672

Conservation Information
Conserved circRNAs	osi_circ_016829
PMCS	0.144093672

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							6930054-6929252(+)
6930098-6929236(-)
6929263-6930076(-)
						
						Potential amino acid sequence
						
							MNSWRVNSHIVAAFMCHDMTSLTNSNS*(+)
MKAATMCEFTRQEFIGGLQSIGVDSIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKS
LALETALGMWQLLFAERHWPLIDHWCQFLQVRHNKAISRDTWSQLLEFVKLVISWHMKAATMCE
FTRQEFIGGLQSIGVDSIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKSLALETALG
MWQLLFAERHWPLIDHWCQFLQVRHNKAISRDTWSQLLEFVKLVISWHMKAATMCEFTRQEFIG
GLQSIGVDSIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKSLALETALGMWQLLFAE
RHWPLIDHWCQFLQVRHNKAISRDTWSQLLEFVKLVISWHMKAATMCEFTRQEFIGGLQSIGVD
SIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKSLALETALGMWQLLFAERHWPLIDH
WCQFLQVRHNKAISRDTWSQLLEFVK(-)
MVSTVGICQACHIMAHESCHNV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	6930054-6929252(+) 6930098-6929236(-) 6929263-6930076(-)
Potential amino acid sequence	MNSWRVNSHIVAAFMCHDMTSLTNSNS(+) MKAATMCEFTRQEFIGGLQSIGVDSIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKS LALETALGMWQLLFAERHWPLIDHWCQFLQVRHNKAISRDTWSQLLEFVKLVISWHMKAATMCE FTRQEFIGGLQSIGVDSIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKSLALETALG MWQLLFAERHWPLIDHWCQFLQVRHNKAISRDTWSQLLEFVKLVISWHMKAATMCEFTRQEFIG GLQSIGVDSIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKSLALETALGMWQLLFAE RHWPLIDHWCQFLQVRHNKAISRDTWSQLLEFVKLVISWHMKAATMCEFTRQEFIGGLQSIGVD SIEKLREKLPSLRAEIKDDHKFREIYNFAFAWAREKGQKSLALETALGMWQLLFAERHWPLIDH WCQFLQVRHNKAISRDTWSQLLEFVK(-) MVSTVGICQACHIMAHESCHNV(-)
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 Os06g0233400_circ_g.3

Address

Any questions?

Supported by