Plant Circular RNA Database

Detail information of Os01g0909500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os01g0909500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_005380
					
						Alias
						Os01circ30957/Os_ciR671
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 39620597-39623317  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os01g0909500						
					
						Parent gene annotation
						
							Hypothetical conserved gene. (Os01t0909500-02);Similar to cDNA c
lone:J013116D08, full insert sequence. (Os01t0909500-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os01g0909500_circ_g.1 Os01g0909500_circ_g.2 Os01g0909500_circ_g.4 Os01g0909500_circ_g.5 Os01g0909500_circ_g.6 Os01g0909500_circ_g.7 						
					
						Support reads
						10/44/4
					
						Tissues
						leaf and panicle/root/shoot, root
					
						Exon boundary  
						
							No-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
						Os01t0909500-02:6
Os01t0909500-03:6

General Information
CircRNA Name	Os01g0909500_circ_g.3
ID in PlantcircBase	osa_circ_005380
Alias	Os01circ30957/Os_ciR671
Organism	Oryza sativa
Position	chr1: 39620597-39623317 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os01g0909500
Parent gene annotation	Hypothetical conserved gene. (Os01t0909500-02);Similar to cDNA c lone:J013116D08, full insert sequence. (Os01t0909500-03)
Parent gene strand	-
Alternative splicing	Os01g0909500_circ_g.1 Os01g0909500_circ_g.2 Os01g0909500_circ_g.4 Os01g0909500_circ_g.5 Os01g0909500_circ_g.6 Os01g0909500_circ_g.7
Support reads	10/44/4
Tissues	leaf and panicle/root/shoot, root
Exon boundary	No-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	Os01t0909500-02:6 Os01t0909500-03:6

			
						 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  
						
							GTTATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCATTGCTGCT
TTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGCctttgcaggagtctcttcttcatcagaa
ctctcaccttcctttgcaggagtctctttttcatcagtactctcaccttcctttgcagtagtct
cttcttca

									
								

					

						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: 184
Transcript exons: 39620597-39620720,39623258-39623317
CTTTGCAGGAGTCTCTTCTTCATCAGAACTCTCACCTTCCTTTGCAGGAGTCTCTTTTTCATCA
GTACTCTCACCTTCCTTTGCAGTAGTCTCTTCTTCATCAGAACTCTTACCTTCATAATCACAAA
AATCGACGTCCATTGCTGCTTTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGC
						
					

						Genomic sequence
						
							CTTTGCAGGAGTCTCTTCTTCATCAGAACTCTCACCTTCCTTTGCAGGAGTCTCTTTTTCATCA
GTACTCTCACCTTCCTTTGCAGTAGTCTCTTCTTCATCAGAACTCTTACCTTCATAATCAGCAT
CATCACTTGAATCCTATTTGTCAATCATATCATACAAATGTATCGCAGGATTATAATATATCCA
ACACAATTCATGACTGCTCATTTTTAATAATGTCACTGTTACGTACCTCATTACCAGTAGATTC
ACCAACTACTGAAATATCACGGTATCGTTCATTGTTGTCATCATCAGCTTTTGATTTCTCATAG
TGCTCTATTTCCTTTACAAAAGCCTTTTGCATGGCGGATGCAACTGTAGCAGACTTTGCAGGAA
GTTTACTTTTCTGTGCTTCTTTGATCATATTATCTGAAAGTTTAACATAAAAAAATATATCATT
CGAAGATTCGCTTACCGGCTCACATTAGCATGTCTAGCAGATTCTATCATAAAATGTAACATGG
ACGAAGCACTTCAAACTACACAAGCATACTGATGTGACCATGGTTACCATAGATACAACCATAG
TTCACATCATAGCTCAACTAGAAGACATCGCCGTAGAAGTTCTAAAATCCAATTCGGTCACCTG
CAACAGTGCTGATTTCAAATGGCCGCCAAATGTGCATACAAGCTCCGTTTTTGGCCCATGAGTA
CTTGATGGAAAGCTCTTGGAGTCTTATTTCCAACTAATCTAGTCTCATCTCCAAATTCCATCTC
GGTCGACCGCAATCACAGAAACTAGGTGTTGCGTCATCTATAATGGACGTATAGGCTTGTAACT
TCATTTAGGGCCTCGACCCAAGTGGGATGTGCCCAACCTGGTGGAGCACGACTCTAGAGACCCC
ATGGTCGTCCTCCCACCTCTTTAAATAACTAGGTACCTCTTCAGGGTTTTTCAGGTTTTGTTTA
GATTAAAGTTTAGCTTTGCTACTTTGCCATATAATCTCGTGACTTGTTAGATCGTTACGGAATT
CTAACTTGTTATTTGTATTCAATTCTTATTTGCAATTTACATTGCTTTTTATCTCGCTCTTGCT
TGTTTCTTCGATTTGCTTGCGGGAACAAGGTTGATCTACACCCGTACGATATGGGAGAAACGTT
TACGACCTGACTACAACCGTACGAGACGTTGTTGTGTTACGCCTTAACGATCGATACACCTTTT
CGTGGGTTGTTGATCTTGCCGGTATAGATTAACCTTATTCCTGCAAGCAAATAAAAAAAAAACA
AGCAAGAACAAAATAAAACCAATCTAAATTACAAATAGCAATTGAATATAAATGATAATTTGGG
ATTCCGTAACGAGCAAACAGACGATCTAACAAATCACGGGATTACACGGCAAAGTAGAAAAGCT
AAACTTTAATCTAAACAAAACCCGAAAAAACCTGAAGGGGTACCTAGCTATTTAAGGAGGTGGG
AGGATGACCATGGGGTCCCTAAAGTCATGTTCCATCAAGTTGGGGCGCACCCCACATGGGCCCT
ACTTGGACCGGGGTCCCAGACGAAGTTATAAACCCATAGGCCCATTATAGGTGATGCAACACCT
AGTTTCTGTGATTGCGACCGACTGAGATGGAATTTGGAGATGAGACTAGTTCCGTTGGGAAGAA
GACTCGAAGAGCTTTCCATCGAGTACTCACGGGCTAAAAACGGAGCTCGTATACACACATTGGG
AATCAGCACTGTTGTAGGTGACCGAATTGGAATCCAGAACTTCTGCGACTTGATCGCGATGTCT
TCCAGTTGAGCTAATGTGAACTATGGTTGTATCTATGGTAGCCATGGTCACGCCACATACACTT
TATGGAAGTTGAATTAGCGTAGTATTCTATAAAAAAGGTAAGCGTTCTTAAGGCTTATAAAGTA
ATTATTATGATTAGCAAAGCATATACCATCTAACTTGGGGTATAGACGAATACCTGGTGGAACC
TCCTCATCAGATTCATCACCTGAAACATCACATCTCAAGAATTGTGATTATCATGAAGCCAAGT
GTAGGGGAAACATTAGAGATGACCAATTTACCTTCAGAATCAGTGAATTTTCCCAAATTCTTTA
CTTGATAGCCACAAAAGGCAACTTTGCTGATTAGTGAGGTGTGGAATAGTTGAAAGTTCTTCTT
GAAACAGAAGTCAACCTTGATATGCGGATGCCTTTTGGAGGAAAGCGTCCCAATCGCAAACTTC
TCATCATTAACTTCGACAAATACTTTCACATTGGAGTCTTTTAGCCCGTAAGCCTCATCAAGGG
CTACCTGCGATTTAAGTTATAACAGTAAGATGAGACATCACTATAAATAATGAGACCTGGTAAG
AAAATTGATAATATGAGAGATAACAAGTACTCCCTCTGTCTCCATCCTAGAATATAGCAACCTA
GAACCCAACTTATTACAATCCTAGGTTGCTATATTCTGAGATGGAGGGAGTAGAACATACCGAT
GTTAGATGATACAGGGTATCCTCAGGACAAAAGATCTCCTTCTTATTGCACGGCTCAATTACCA
CTCCTAATAAACAATAACATTAATCACAAAGTTGTTTTTTTTTAATCTTAATGAGACAGTTGTT
ATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCATTGCTGCTTTT
GTTATTTTCTTCCCGAGCTTTTAGAGATTTGGC
						
					

			
		

Sequences
Splice junction sequence	GTTATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCATTGCTGCT TTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGCctttgcaggagtctcttcttcatcagaa ctctcaccttcctttgcaggagtctctttttcatcagtactctcaccttcctttgcagtagtct cttcttca
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: 184 Transcript exons: 39620597-39620720,39623258-39623317 CTTTGCAGGAGTCTCTTCTTCATCAGAACTCTCACCTTCCTTTGCAGGAGTCTCTTTTTCATCA GTACTCTCACCTTCCTTTGCAGTAGTCTCTTCTTCATCAGAACTCTTACCTTCATAATCACAAA AATCGACGTCCATTGCTGCTTTTGTTATTTTCTTCCCGAGCTTTTAGAGATTTGGC
Genomic sequence	CTTTGCAGGAGTCTCTTCTTCATCAGAACTCTCACCTTCCTTTGCAGGAGTCTCTTTTTCATCA GTACTCTCACCTTCCTTTGCAGTAGTCTCTTCTTCATCAGAACTCTTACCTTCATAATCAGCAT CATCACTTGAATCCTATTTGTCAATCATATCATACAAATGTATCGCAGGATTATAATATATCCA ACACAATTCATGACTGCTCATTTTTAATAATGTCACTGTTACGTACCTCATTACCAGTAGATTC ACCAACTACTGAAATATCACGGTATCGTTCATTGTTGTCATCATCAGCTTTTGATTTCTCATAG TGCTCTATTTCCTTTACAAAAGCCTTTTGCATGGCGGATGCAACTGTAGCAGACTTTGCAGGAA GTTTACTTTTCTGTGCTTCTTTGATCATATTATCTGAAAGTTTAACATAAAAAAATATATCATT CGAAGATTCGCTTACCGGCTCACATTAGCATGTCTAGCAGATTCTATCATAAAATGTAACATGG ACGAAGCACTTCAAACTACACAAGCATACTGATGTGACCATGGTTACCATAGATACAACCATAG TTCACATCATAGCTCAACTAGAAGACATCGCCGTAGAAGTTCTAAAATCCAATTCGGTCACCTG CAACAGTGCTGATTTCAAATGGCCGCCAAATGTGCATACAAGCTCCGTTTTTGGCCCATGAGTA CTTGATGGAAAGCTCTTGGAGTCTTATTTCCAACTAATCTAGTCTCATCTCCAAATTCCATCTC GGTCGACCGCAATCACAGAAACTAGGTGTTGCGTCATCTATAATGGACGTATAGGCTTGTAACT TCATTTAGGGCCTCGACCCAAGTGGGATGTGCCCAACCTGGTGGAGCACGACTCTAGAGACCCC ATGGTCGTCCTCCCACCTCTTTAAATAACTAGGTACCTCTTCAGGGTTTTTCAGGTTTTGTTTA GATTAAAGTTTAGCTTTGCTACTTTGCCATATAATCTCGTGACTTGTTAGATCGTTACGGAATT CTAACTTGTTATTTGTATTCAATTCTTATTTGCAATTTACATTGCTTTTTATCTCGCTCTTGCT TGTTTCTTCGATTTGCTTGCGGGAACAAGGTTGATCTACACCCGTACGATATGGGAGAAACGTT TACGACCTGACTACAACCGTACGAGACGTTGTTGTGTTACGCCTTAACGATCGATACACCTTTT CGTGGGTTGTTGATCTTGCCGGTATAGATTAACCTTATTCCTGCAAGCAAATAAAAAAAAAACA AGCAAGAACAAAATAAAACCAATCTAAATTACAAATAGCAATTGAATATAAATGATAATTTGGG ATTCCGTAACGAGCAAACAGACGATCTAACAAATCACGGGATTACACGGCAAAGTAGAAAAGCT AAACTTTAATCTAAACAAAACCCGAAAAAACCTGAAGGGGTACCTAGCTATTTAAGGAGGTGGG AGGATGACCATGGGGTCCCTAAAGTCATGTTCCATCAAGTTGGGGCGCACCCCACATGGGCCCT ACTTGGACCGGGGTCCCAGACGAAGTTATAAACCCATAGGCCCATTATAGGTGATGCAACACCT AGTTTCTGTGATTGCGACCGACTGAGATGGAATTTGGAGATGAGACTAGTTCCGTTGGGAAGAA GACTCGAAGAGCTTTCCATCGAGTACTCACGGGCTAAAAACGGAGCTCGTATACACACATTGGG AATCAGCACTGTTGTAGGTGACCGAATTGGAATCCAGAACTTCTGCGACTTGATCGCGATGTCT TCCAGTTGAGCTAATGTGAACTATGGTTGTATCTATGGTAGCCATGGTCACGCCACATACACTT TATGGAAGTTGAATTAGCGTAGTATTCTATAAAAAAGGTAAGCGTTCTTAAGGCTTATAAAGTA ATTATTATGATTAGCAAAGCATATACCATCTAACTTGGGGTATAGACGAATACCTGGTGGAACC TCCTCATCAGATTCATCACCTGAAACATCACATCTCAAGAATTGTGATTATCATGAAGCCAAGT GTAGGGGAAACATTAGAGATGACCAATTTACCTTCAGAATCAGTGAATTTTCCCAAATTCTTTA CTTGATAGCCACAAAAGGCAACTTTGCTGATTAGTGAGGTGTGGAATAGTTGAAAGTTCTTCTT GAAACAGAAGTCAACCTTGATATGCGGATGCCTTTTGGAGGAAAGCGTCCCAATCGCAAACTTC TCATCATTAACTTCGACAAATACTTTCACATTGGAGTCTTTTAGCCCGTAAGCCTCATCAAGGG CTACCTGCGATTTAAGTTATAACAGTAAGATGAGACATCACTATAAATAATGAGACCTGGTAAG AAAATTGATAATATGAGAGATAACAAGTACTCCCTCTGTCTCCATCCTAGAATATAGCAACCTA GAACCCAACTTATTACAATCCTAGGTTGCTATATTCTGAGATGGAGGGAGTAGAACATACCGAT GTTAGATGATACAGGGTATCCTCAGGACAAAAGATCTCCTTCTTATTGCACGGCTCAATTACCA CTCCTAATAAACAATAACATTAATCACAAAGTTGTTTTTTTTTAATCTTAATGAGACAGTTGTT ATTTAAATACACTAAATTGGAAAGAGGAAACAAACCCCAAAAATCGACGTCCATTGCTGCTTTT GTTATTTTCTTCCCGAGCTTTTAGAGATTTGGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002601* osi_circ_011092 						
					
						PMCS
						0.446155876

Conservation Information
Conserved circRNAs	osi_circ_002601* osi_circ_011092
PMCS	0.446155876

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0909500_circ_g.3

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