Plant Circular RNA Database

Detail information of Os04g0606400_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0606400_circ_g.1
					
						ID in PlantcircBase
						osa_circ_025120
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 30622456-30625115  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0606400						
					
						Parent gene annotation
						
							Similar to Mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.
2.1.113). (Os04t0606400-01);Similar to OSIGBa0113I13.2 protein. 
(Os04t0606400-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0606400_circ_g.2 Os04g0606400_circ_g.3 						
					
						Support reads
						1
					
						Tissues
						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
						Os04t0606400-02:6
Os04t0606400-01:6

General Information
CircRNA Name	Os04g0606400_circ_g.1
ID in PlantcircBase	osa_circ_025120
Alias	NA
Organism	Oryza sativa
Position	chr4: 30622456-30625115 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0606400
Parent gene annotation	Similar to Mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3. 2.1.113). (Os04t0606400-01);Similar to OSIGBa0113I13.2 protein. (Os04t0606400-02)
Parent gene strand	-
Alternative splicing	Os04g0606400_circ_g.2 Os04g0606400_circ_g.3
Support reads	1
Tissues	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	Os04t0606400-02:6 Os04t0606400-01:6

			
						 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  
						
							ATCCCAAGCAGGTAGTAGACGGTCAGTAATATCTTTGGCCTTCTCAAGAAATACTTTGTCACCA
GATAGATCATATGCACTGAGGAGGCCTCCAACAACTctctttcgcaagattcataatttcttca
gccttttcagtctcctcatagccagaggcccccagtgccagcataccaggggcaaaacatgcaa
gctcatcc

									
								

					

						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
						
							CTCTTTCGCAAGATTCATAATTTCTTCAGCCTTTTCAGTCTCCTCATAGCCAGAGGCCCCCAGT
GCCAGCATACCAGGGGCAAAACATGCAAGCTCATCCATCTGTGCTAGTCACAAGCCGAACCAGT
GAGAACTCCCGAGAGAGAATGAAAGTTAAGTCCAAATGATCCTCTTGTTGATTACAGCCAACCA
AATGGGATTATTTACCTTGTCAGACAATGAACCACCATTCTTCTCGCAAATGTAGTAGTAATTA
GAGGGTGTAGTTTTTTTGGTCAAGCTTAGTAGGCCTTCCATTGATGTCTCCCACATTTGTCTAG
TCAAAAATCATATAAACAGTTATCAACATGCTAAATGAAACTGTATGGAATTTCCAGTAAAAGA
AATCAGTGAAGGGAATATGAAAAGGTGAAAAGTGAGGCTTATAGGCTCAAACCTGTAATGCTTT
ACATGCTCAGTTTTATTCCCCTGGACCCAAACCTTGAGCAAGTACTCGTAGAAGCTGAACCACA
AATGTAGTTAGCTCCATTTTTCAATCATTCTACACTCACTAAAATTAGGGTATGCAACAGAAAA
TTTATGAACAATCCAATAGAGCAAGTTGCTTAAAGGTTTGCACAAATTAACATGGAAAGTACTA
ATGTTAATCACAGAAGGACCACTATGTTTTCAGGAAGGAAATAGCTTGTTTGAATAAGTGAGAA
TAGAAGTATAACCTATCTCCCATTGCACCAAATGTAATTGTTGAGTACGACGCAGTTCCTGAAT
GAGGGTTTATGTATATAGGGAGTAAGCCATCGCTTGGGTATATCTTCTGAAGCTGTCTGATGAC
ATTCTCTGCCTAAAATTGTATTGTATCAGGCCAAACTGTGAGTTCAATATTAAGAAAGCCAAAA
AGAGATTTTCAGGCAGGATTTAAATTTATATAAATTATATACGGGCAGATGCCATTTTTTGTAG
GGCTTTGCTTACGCACACTGGTTAGCAAAATATTATAAACATTAAAAGAAAAGGCAGTAATAAA
TAAGTACGGGCCAACATAAACCAATGATGTAGGATACAAATTTACATTAGGGATCAAAGTTTTT
GATGGAACTCATACCAATTGATTTGATCCATGCAATAGCATGTCAAATAAATAGGATAAGGAAC
AAGGTTATTTAGGATCTATAAGTAGGACCAATATAATCAAATTGATTATGATTTGGATATATTT
TCTATTTCCAACTTATAACAGCCTTTTCTTTGAGACACTATTTTATTCTTGAAAGGAGATCTAA
AGCAAACCTGGCGTCATCTGATAGAGAGAAGTCAGTATATATACTTAACCCACAATACTGGGGT
CAAGCTAAATTCAAGAACTTTTCAGGGGAAGAACATTTGTATATGAAGAAGGCTATGATTTTGA
AGGCCATCCAGAAAATAAAACACTTTAAATATGACTTATGAACTATCACAAAAAATCATTTATT
CCCGCAGTCATGATTTGAGTACTTATGTGTGTCACAAAAGGAGGCATCAAGGAGATTTGGTTCC
AGTGGTTATGACCATAGCATCAAGTGAAAAAGGGATGCATGCATGCACATCAACAACAAAGGGA
ACAATCAAAGTATTATATATGATTACAAGGTCCTTTTTGCTTGCTCAAGAGTCAAGAGCCAGGT
GGTTAGTCTCACGTCGTGGTTTGGTTTGTGGGTCGTGGTCATTTTATCTGTTTGTGTTTGTGGT
CGGGTTTGTGACACGCATGGTTCCTAGAACTCAGTGTGTGCGTGTTTGGTTTTGCACGCGTGTT
CTACCCCCTCTTCTTCTTATTCGAGGAAGGAAATAGAAGCCATGTTTTGCACACAACTGGTTGC
ACTTAATTTACCAAGATAATTGCATAAAACTGGCAGGATGTATGAAATATGAGTAATCTGTAGA
ACCTTTTGTTGATACTTGGGATCACCAGTCCTCTGTGACAAAGCTATAAATTCAAGTTGCTCCG
TGCCAGAATCAGCAAGGATACTATCACCCTGCAGAAACACACAATGTACATGGTTCACCATCCA
AAGAGAGAGAAAATAGTTTCAGGTCAAATGCATTTATAAACAATCCATTGAGCAATTATTGATG
TGTTTTTATAAAGATTATGCAGCTCTCTTGACTATTCGAGAAAAAAGTGTTTTTACAAAGATAT
TGGTAAATATCACATTAAACTTCTAATTTGATCAGTTTTTTTAAAAAAACTTCTAATTTGATCA
CTGTGGAGATAAGGGGCTGAAACAAATTATAAACATGATGAATTAATCATAAAGATGTATGTGA
TGACATGTGATTCAATCCCTCGAATGAAAACAGAGCTCTAAAGGAACAACAAAGTTTGCATCAT
TATGAAGAAAAATGGGATGCTGTGAACATGGTTAAAACAGTTAGCTGTAAGCTTCAGTGTGCTT
AGAAGGAACACTCCATGTAATTGACTACCACTAGCAAAATAGAATCTATTACTCACATTGGTCC
ATCCAGGATTATGGGCTCGTCCATGAGCTAGGTTGATTCTATTATAAGGGATACCAGATGGTGT
ATCCCAAGCAGGTAGTAGACGGTCAGTAATATCTTTGGCCTTCTCAAGAAATACTTTGTCACCA
GATAGATCATATGCACTGAGGAGGCCTCCAACAACT
						
					

			
		

Sequences
Splice junction sequence	ATCCCAAGCAGGTAGTAGACGGTCAGTAATATCTTTGGCCTTCTCAAGAAATACTTTGTCACCA GATAGATCATATGCACTGAGGAGGCCTCCAACAACTctctttcgcaagattcataatttcttca gccttttcagtctcctcatagccagaggcccccagtgccagcataccaggggcaaaacatgcaa gctcatcc
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	CTCTTTCGCAAGATTCATAATTTCTTCAGCCTTTTCAGTCTCCTCATAGCCAGAGGCCCCCAGT GCCAGCATACCAGGGGCAAAACATGCAAGCTCATCCATCTGTGCTAGTCACAAGCCGAACCAGT GAGAACTCCCGAGAGAGAATGAAAGTTAAGTCCAAATGATCCTCTTGTTGATTACAGCCAACCA AATGGGATTATTTACCTTGTCAGACAATGAACCACCATTCTTCTCGCAAATGTAGTAGTAATTA GAGGGTGTAGTTTTTTTGGTCAAGCTTAGTAGGCCTTCCATTGATGTCTCCCACATTTGTCTAG TCAAAAATCATATAAACAGTTATCAACATGCTAAATGAAACTGTATGGAATTTCCAGTAAAAGA AATCAGTGAAGGGAATATGAAAAGGTGAAAAGTGAGGCTTATAGGCTCAAACCTGTAATGCTTT ACATGCTCAGTTTTATTCCCCTGGACCCAAACCTTGAGCAAGTACTCGTAGAAGCTGAACCACA AATGTAGTTAGCTCCATTTTTCAATCATTCTACACTCACTAAAATTAGGGTATGCAACAGAAAA TTTATGAACAATCCAATAGAGCAAGTTGCTTAAAGGTTTGCACAAATTAACATGGAAAGTACTA ATGTTAATCACAGAAGGACCACTATGTTTTCAGGAAGGAAATAGCTTGTTTGAATAAGTGAGAA TAGAAGTATAACCTATCTCCCATTGCACCAAATGTAATTGTTGAGTACGACGCAGTTCCTGAAT GAGGGTTTATGTATATAGGGAGTAAGCCATCGCTTGGGTATATCTTCTGAAGCTGTCTGATGAC ATTCTCTGCCTAAAATTGTATTGTATCAGGCCAAACTGTGAGTTCAATATTAAGAAAGCCAAAA AGAGATTTTCAGGCAGGATTTAAATTTATATAAATTATATACGGGCAGATGCCATTTTTTGTAG GGCTTTGCTTACGCACACTGGTTAGCAAAATATTATAAACATTAAAAGAAAAGGCAGTAATAAA TAAGTACGGGCCAACATAAACCAATGATGTAGGATACAAATTTACATTAGGGATCAAAGTTTTT GATGGAACTCATACCAATTGATTTGATCCATGCAATAGCATGTCAAATAAATAGGATAAGGAAC AAGGTTATTTAGGATCTATAAGTAGGACCAATATAATCAAATTGATTATGATTTGGATATATTT TCTATTTCCAACTTATAACAGCCTTTTCTTTGAGACACTATTTTATTCTTGAAAGGAGATCTAA AGCAAACCTGGCGTCATCTGATAGAGAGAAGTCAGTATATATACTTAACCCACAATACTGGGGT CAAGCTAAATTCAAGAACTTTTCAGGGGAAGAACATTTGTATATGAAGAAGGCTATGATTTTGA AGGCCATCCAGAAAATAAAACACTTTAAATATGACTTATGAACTATCACAAAAAATCATTTATT CCCGCAGTCATGATTTGAGTACTTATGTGTGTCACAAAAGGAGGCATCAAGGAGATTTGGTTCC AGTGGTTATGACCATAGCATCAAGTGAAAAAGGGATGCATGCATGCACATCAACAACAAAGGGA ACAATCAAAGTATTATATATGATTACAAGGTCCTTTTTGCTTGCTCAAGAGTCAAGAGCCAGGT GGTTAGTCTCACGTCGTGGTTTGGTTTGTGGGTCGTGGTCATTTTATCTGTTTGTGTTTGTGGT CGGGTTTGTGACACGCATGGTTCCTAGAACTCAGTGTGTGCGTGTTTGGTTTTGCACGCGTGTT CTACCCCCTCTTCTTCTTATTCGAGGAAGGAAATAGAAGCCATGTTTTGCACACAACTGGTTGC ACTTAATTTACCAAGATAATTGCATAAAACTGGCAGGATGTATGAAATATGAGTAATCTGTAGA ACCTTTTGTTGATACTTGGGATCACCAGTCCTCTGTGACAAAGCTATAAATTCAAGTTGCTCCG TGCCAGAATCAGCAAGGATACTATCACCCTGCAGAAACACACAATGTACATGGTTCACCATCCA AAGAGAGAGAAAATAGTTTCAGGTCAAATGCATTTATAAACAATCCATTGAGCAATTATTGATG TGTTTTTATAAAGATTATGCAGCTCTCTTGACTATTCGAGAAAAAAGTGTTTTTACAAAGATAT TGGTAAATATCACATTAAACTTCTAATTTGATCAGTTTTTTTAAAAAAACTTCTAATTTGATCA CTGTGGAGATAAGGGGCTGAAACAAATTATAAACATGATGAATTAATCATAAAGATGTATGTGA TGACATGTGATTCAATCCCTCGAATGAAAACAGAGCTCTAAAGGAACAACAAAGTTTGCATCAT TATGAAGAAAAATGGGATGCTGTGAACATGGTTAAAACAGTTAGCTGTAAGCTTCAGTGTGCTT AGAAGGAACACTCCATGTAATTGACTACCACTAGCAAAATAGAATCTATTACTCACATTGGTCC ATCCAGGATTATGGGCTCGTCCATGAGCTAGGTTGATTCTATTATAAGGGATACCAGATGGTGT ATCCCAAGCAGGTAGTAGACGGTCAGTAATATCTTTGGCCTTCTCAAGAAATACTTTGTCACCA GATAGATCATATGCACTGAGGAGGCCTCCAACAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.117140602

Conservation Information
Conserved circRNAs	NA
PMCS	0.117140602

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							30623184-30625088(-)
						
						Potential amino acid sequence
						
							MGDSFYEYLLKVWVQGNKTEHVKHYRQMWETSMEGLLSLTKKTTPSNYYYICEKNGGSLSDKMD
ELACFAPGMLALGASGYEETEKAEEIMNLAKESCWRPPQCI*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	30623184-30625088(-)
Potential amino acid sequence	MGDSFYEYLLKVWVQGNKTEHVKHYRQMWETSMEGLLSLTKKTTPSNYYYICEKNGGSLSDKMD ELACFAPGMLALGASGYEETEKAEEIMNLAKESCWRPPQCI*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0606400_circ_g.1

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