Plant Circular RNA Database

Detail information of Os11g0175900_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os11g0175900_circ_g.1
					
						ID in PlantcircBase
						osa_circ_008681
					
						Alias
						Os_ciR4604
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr11: 3784872-3786246  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os11g0175900						
					
						Parent gene annotation
						
							Similar to TPLATE; binding. (Os11t0175900-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os11g0175900_circ_g.2 Os11g0175900_circ_g.3 						
					
						Support reads
						4/2
					
						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
						Os11t0175900-01:3

General Information
CircRNA Name	Os11g0175900_circ_g.1
ID in PlantcircBase	osa_circ_008681
Alias	Os_ciR4604
Organism	Oryza sativa
Position	chr11: 3784872-3786246 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os11g0175900
Parent gene annotation	Similar to TPLATE; binding. (Os11t0175900-01)
Parent gene strand	-
Alternative splicing	Os11g0175900_circ_g.2 Os11g0175900_circ_g.3
Support reads	4/2
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	Os11t0175900-01:3

			
						 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  
						
							GATCCTCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGC
CCATATCAACCGTGATGATATTCTTGGGGTATGGACctgggaaacaagattacggaggtgtcga
acggtgcgggaaaatccatccatgtaatacagtgctccagagagtccaactcggatatcaaccc
tgttgagc

									
								

					

						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: 786
Transcript exons: 3784872-3784994,3785424-3785724,3785885-3786246
CTGGGAAACAAGATTACGGAGGTGTCGAACGGTGCGGGAAAATCCATCCATGTAATACAGTGCT
CCAGAGAGTCCAACTCGGATATCAACCCTGTTGAGCTCCGGCTCAGTCAAATTCAAGATCTTTA
GATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCATGGATC
ACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTTTTGTC
TGTAGCAGACTCAACTGTGTGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTACTAACC
CCTCCAATTTCCTGTCTTGAGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGGTGGCT
AAATGGATAATCCCCTGTGGCATCACCTACGCCCACCCACCTGTTATCTGGATGGCTTGTCACA
TATTTTATTATCTGCAAGACATAACGTGACTGATGTTTGGTGACAAAATCAGCTGAAGTACTTG
CTCTATATTCTTCCAATTCTTTACTGAGGAGCTGGCCAGCTCTTGCATTTCTTGTTCCCAAACG
TTGGGCACATATGAGGACAGACTGCATATCTTGTATCCTATTCGATGTAGTGGTAGAGGATTCG
GTGTTGAATAAAATCTTGTGCATGTTAGATATGATAATATTCAGTGGATCCTCTGGGTCATCAG
CTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGCCCATATCAACCGTGATGA
TATTCTTGGGGTATGGAC
						
					

						Genomic sequence
						
							CTGGGAAACAAGATTACGGAGGTGTCGAACGGTGCGGGAAAATCCATCCATGTAATACAGTGCT
CCAGAGAGTCCAACTCGGATATCAACCCTGTTGAGCTCCGGCTCAGTCAAATTCAAGATCTGCA
ACAACACAAACTAGTCAAAAAACATGGTAATAATAAACAAGCAATAACAGATCTTAGAGCAAGC
AATATATGCAGTTATTTTAACTTCAAACCAATCCAGTAATCTACCAAGATGGATAAGTGTTCTA
ACATGTCCCCACAAATTAGAATATATTGGCAGACTTCCAGTAGTATGTCTGCTTGCATAAGCAT
AAGAACGCCACTCCATAACTTGGATAATAAAAAAACAGTTGTACGGTTGGCAGAAAACCACAAC
AAATTTACAACAAAAAAAAACTATTGCCATGCTGGGGTCAAATATTAGTGTATTTTAAGTTCAG
AAATTATCATGACAGAACCAGCATTTAACAGTGACCATGACAGAAACATTAATTCAATAAAAAG
TATGAAATCAAATAGAGAAAAGAAGTCCATCAGGCCTTACCTTTAGATGCAGTGTGATTCTGCC
ATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCATGGATCACTGCTGCCGGTCAAAGTA
TACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTTTTGTCTGTAGCAGACTCAACTGTG
TGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTACTAACCCCTCCAATTTCCTGTCTTG
AGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGGTGGCTAAATGGATAATCCCCTGTG
GCATCACCTACGCCCACCCACCTGAATGACATATCAGAAAAGTAGACAATTATTATATTTATTT
CATAATGCATGTTCTAGTAGACAACTTTCTTTCAGGTATAATATTTTCGTTCTTTATCTATGTG
AACACTTCAACCTCCGCGGAGAATTTGTTACTCAAGTTCCAAAATACACTCACCTGTTATCTGG
ATGGCTTGTCACATATTTTATTATCTGCAAGACATAACGTGACTGATGTTTGGTGACAAAATCA
GCTGAAGTACTTGCTCTATATTCTTCCAATTCTTTACTGAGGAGCTGGCCAGCTCTTGCATTTC
TTGTTCCCAAACGTTGGGCACATATGAGGACAGACTGCATATCTTGTATCCTATTCGATGTAGT
GGTAGAGGATTCGGTGTTGAATAAAATCTTGTGCATGTTAGATATGATAATATTCAGTGGATCC
TCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGCCCATA
TCAACCGTGATGATATTCTTGGGGTATGGAC
						
					

			
		

Sequences
Splice junction sequence	GATCCTCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGC CCATATCAACCGTGATGATATTCTTGGGGTATGGACctgggaaacaagattacggaggtgtcga acggtgcgggaaaatccatccatgtaatacagtgctccagagagtccaactcggatatcaaccc tgttgagc
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: 786 Transcript exons: 3784872-3784994,3785424-3785724,3785885-3786246 CTGGGAAACAAGATTACGGAGGTGTCGAACGGTGCGGGAAAATCCATCCATGTAATACAGTGCT CCAGAGAGTCCAACTCGGATATCAACCCTGTTGAGCTCCGGCTCAGTCAAATTCAAGATCTTTA GATGCAGTGTGATTCTGCCATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCATGGATC ACTGCTGCCGGTCAAAGTATACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTTTTGTC TGTAGCAGACTCAACTGTGTGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTACTAACC CCTCCAATTTCCTGTCTTGAGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGGTGGCT AAATGGATAATCCCCTGTGGCATCACCTACGCCCACCCACCTGTTATCTGGATGGCTTGTCACA TATTTTATTATCTGCAAGACATAACGTGACTGATGTTTGGTGACAAAATCAGCTGAAGTACTTG CTCTATATTCTTCCAATTCTTTACTGAGGAGCTGGCCAGCTCTTGCATTTCTTGTTCCCAAACG TTGGGCACATATGAGGACAGACTGCATATCTTGTATCCTATTCGATGTAGTGGTAGAGGATTCG GTGTTGAATAAAATCTTGTGCATGTTAGATATGATAATATTCAGTGGATCCTCTGGGTCATCAG CTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGCCCATATCAACCGTGATGA TATTCTTGGGGTATGGAC
Genomic sequence	CTGGGAAACAAGATTACGGAGGTGTCGAACGGTGCGGGAAAATCCATCCATGTAATACAGTGCT CCAGAGAGTCCAACTCGGATATCAACCCTGTTGAGCTCCGGCTCAGTCAAATTCAAGATCTGCA ACAACACAAACTAGTCAAAAAACATGGTAATAATAAACAAGCAATAACAGATCTTAGAGCAAGC AATATATGCAGTTATTTTAACTTCAAACCAATCCAGTAATCTACCAAGATGGATAAGTGTTCTA ACATGTCCCCACAAATTAGAATATATTGGCAGACTTCCAGTAGTATGTCTGCTTGCATAAGCAT AAGAACGCCACTCCATAACTTGGATAATAAAAAAACAGTTGTACGGTTGGCAGAAAACCACAAC AAATTTACAACAAAAAAAAACTATTGCCATGCTGGGGTCAAATATTAGTGTATTTTAAGTTCAG AAATTATCATGACAGAACCAGCATTTAACAGTGACCATGACAGAAACATTAATTCAATAAAAAG TATGAAATCAAATAGAGAAAAGAAGTCCATCAGGCCTTACCTTTAGATGCAGTGTGATTCTGCC ATCAGTTGGATCTGCCAAATGATACGCTTCAATATAGCATGGATCACTGCTGCCGGTCAAAGTA TACGCTTTTGGGAGCTCTTTATGCAAAGTACCAATCCCTTTTGTCTGTAGCAGACTCAACTGTG TGGGACTTGGCCTCCAGAGCTCCAGAATAGCTTTATGTACTAACCCCTCCAATTTCCTGTCTTG AGCAGCAGACGCCTCTGAAAACTGGACGGTGAGTTTGTGGTGGCTAAATGGATAATCCCCTGTG GCATCACCTACGCCCACCCACCTGAATGACATATCAGAAAAGTAGACAATTATTATATTTATTT CATAATGCATGTTCTAGTAGACAACTTTCTTTCAGGTATAATATTTTCGTTCTTTATCTATGTG AACACTTCAACCTCCGCGGAGAATTTGTTACTCAAGTTCCAAAATACACTCACCTGTTATCTGG ATGGCTTGTCACATATTTTATTATCTGCAAGACATAACGTGACTGATGTTTGGTGACAAAATCA GCTGAAGTACTTGCTCTATATTCTTCCAATTCTTTACTGAGGAGCTGGCCAGCTCTTGCATTTC TTGTTCCCAAACGTTGGGCACATATGAGGACAGACTGCATATCTTGTATCCTATTCGATGTAGT GGTAGAGGATTCGGTGTTGAATAAAATCTTGTGCATGTTAGATATGATAATATTCAGTGGATCC TCTGGGTCATCAGCTAAGAGAGGATCCAGACCTTCAAGATCGAAGTGTTCAGAAATCGCCCATA TCAACCGTGATGATATTCTTGGGGTATGGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.286421479

Conservation Information
Conserved circRNAs	NA
PMCS	0.286421479

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							3786242-3785426(+)
3786048-3784923(+)
3786226-3784966(+)
3786125-3784874(-)
3784920-3786218(-)
						
					

						Potential amino acid sequence
						
							MDLGNKITEVSNGAGKSIHVIQCSRESNSDINPVELRLSQIQDL*(+)
MRTDCISCILFDVVVEDSVLNKILCMLDMIIFSGSSGSSAKRGSRPSRSKCSEIAHINRDDILG
VWTWETRLRRCRTVRENPSM*(+)
MIFLGYGPGKQDYGGVERCGKIHPCNTVLQRVQLGYQPC*(+)
MHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFVTKHQSR
YVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAILELWRPS
PTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKILNLTEPELNRV
DIRVGLSGALYYMDGFSRTVRHLRNLVSQVHTPRISSRLIWAISEHFDLEGLDPLLADDPEDPL
NIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFV
TKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAIL
ELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKILNLTE
PELNRVDIRVGLSGALYYMDGFSRTVRHLRNLVSQVHTPRISSRLIWAISEHFDLEGLDPLLAD
DPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRAS
TSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGL
VHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLK
ILNLTEPELNRVDIRVGLSGALYYMDGFSRTVRHLRNLVSQVHTPRISSRLIWAISEHFDLEGL
DPLLADDPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKEL
EEYRASTSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQD
RKLEGLVHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGR
ITLHLKILNLTEPELNRVDIRVGLSGALYYMDGFSRTVRHLRNLVSQ(-)
MDFPAPFDTSVILFPRSIPQEYHHG*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	3786242-3785426(+) 3786048-3784923(+) 3786226-3784966(+) 3786125-3784874(-) 3784920-3786218(-)
Potential amino acid sequence	MDLGNKITEVSNGAGKSIHVIQCSRESNSDINPVELRLSQIQDL(+) MRTDCISCILFDVVVEDSVLNKILCMLDMIIFSGSSGSSAKRGSRPSRSKCSEIAHINRDDILG VWTWETRLRRCRTVRENPSM(+) MIFLGYGPGKQDYGGVERCGKIHPCNTVLQRVQLGYQPC(+) MHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFVTKHQSR YVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAILELWRPS PTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKILNLTEPELNRV DIRVGLSGALYYMDGFSRTVRHLRNLVSQVHTPRISSRLIWAISEHFDLEGLDPLLADDPEDPL NIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRASTSADFV TKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGLVHKAIL ELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLKILNLTE PELNRVDIRVGLSGALYYMDGFSRTVRHLRNLVSQVHTPRISSRLIWAISEHFDLEGLDPLLAD DPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKELEEYRAS TSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQDRKLEGL VHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGRITLHLK ILNLTEPELNRVDIRVGLSGALYYMDGFSRTVRHLRNLVSQVHTPRISSRLIWAISEHFDLEGL DPLLADDPEDPLNIIISNMHKILFNTESSTTTSNRIQDMQSVLICAQRLGTRNARAGQLLSKEL EEYRASTSADFVTKHQSRYVLQIIKYVTSHPDNRWVGVGDATGDYPFSHHKLTVQFSEASAAQD RKLEGLVHKAILELWRPSPTQLSLLQTKGIGTLHKELPKAYTLTGSSDPCYIEAYHLADPTDGR ITLHLKILNLTEPELNRVDIRVGLSGALYYMDGFSRTVRHLRNLVSQ(-) MDFPAPFDTSVILFPRSIPQEYHHG(-)
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 Os11g0175900_circ_g.1

Address

Any questions?

Supported by