Plant Circular RNA Database

Detail information of Os01g0838100_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os01g0838100_circ_g.2
					
						ID in PlantcircBase
						osa_circ_004781
					
						Alias
						Os_ciR6258
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 35940335-35941522  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						circseq_cup, find_circ
					
						Parent gene
						
							Os01g0838100						
					
						Parent gene annotation
						
							Conserved hypothetical protein. (Os01t0838100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0838100_circ_g.1 Os01g0838100_circ_g.3 						
					
						Support reads
						2/14
					
						Tissues
						root/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  
						
							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
						Os01t0838100-01:7

General Information
CircRNA Name	Os01g0838100_circ_g.2
ID in PlantcircBase	osa_circ_004781
Alias	Os_ciR6258
Organism	Oryza sativa
Position	chr1: 35940335-35941522 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	circseq_cup, find_circ
Parent gene	Os01g0838100
Parent gene annotation	Conserved hypothetical protein. (Os01t0838100-01)
Parent gene strand	+
Alternative splicing	Os01g0838100_circ_g.1 Os01g0838100_circ_g.3
Support reads	2/14
Tissues	root/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	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	Os01t0838100-01:7

			
						 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  
						
							CGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTA
CCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAGgtgcttattgtcgcggtcaggtccgtgc
gatacgttcgttactgttgtgctgctgttccctttaccatcagctcctgttcaggtgagctttg
tttctttg

									
								

					

						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: 169
Transcript exons: 35940335-35940394,35941414-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCCCTG
AGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGC
TATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 174
Transcript exons: 35940335-35940389,35941404-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTATGGCCC
TCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGAT
TCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 180
Transcript exons: 35940335-35940397,35941406-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA
TGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAG
AAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 183
Transcript exons: 35940335-35940394,35941400-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCGTGA
TTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGC
AAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 190
Transcript exons: 35940335-35940393,35941392-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCGGATA
GGTGTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGA
ACGGTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 192
Transcript exons: 35940335-35940410,35941407-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA
CCATCAGCTCCTTGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAG
GAACGGTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 194
Transcript exons: 35940335-35940394,35941389-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCAAAG
GATAGGTGTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACC
AGGAACGGTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAA
AG
Transcript length: 202
Transcript exons: 35940335-35940410,35941388-35941488,35941498-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA
CCATCAGCTCCTCAAAGGATAGGTGTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGC
TGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTACCGTCTGTTACAACCTT
TGTTGCAAAG
Transcript length: 291
Transcript exons: 35940335-35940511,35941409-35941522
GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA
CCATCAGCTCCTGTTCAGGTGAGCTTTGTTTCTTTGCTATTTCTTTGGGGCTGACATCCTTTTT
GTTTTGTAGTTTATTTGTGCCTTGTGGTTTGGTGTATGTTCTTTCTTTTGCCCTCCTGAGTATC
GCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTAC
CAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
Transcript length: 581
Transcript exons: 35940335-35941522
CTTAGATCATCTTCCTCTAATTCAGCTGCCAGCGAATATGTTTGGGAGACTGTTGCTCCACCCC
GTCAGGACGATGGATTTTTCCCTATCTACCCTGCATGGTATTCTTCAAAAAGACGGCAAATGCG
TTCAAAAAAATTGGCCATGAAACGATTGGTGGCTGCAGGCAAAAAACCTTGCCGTATTGCTCCT
GTCTCTTGCAACAAGTTTGACAGTGATTATGCCAAGTTTTTGAGAGAGACTTCAAAGGATAGGT
GTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACG
GTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAGGTGCT
TATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTACCATC
AGCTCCTGTTCAGGTTGCGGACCACATCTTCTGTGCCCGTACATGTCGGCTAAGTTCCTATATG
GAAGGGGGTTGTGTGGTTAGGCCTGCTCGTCGACGGGATCGCCGATTGCTAGAGCGTAGCAGCG
CTTCT
						
					

						Genomic sequence
						
							GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA
CCATCAGCTCCTGTTCAGGTGAGCTTTGTTTCTTTGCTATTTCTTTGGGGCTGACATCCTTTTT
GTTTTGTAGTTTATTTGTGCCTTGTGGTTTGGTGTATGTTCTTTCTTTTATCTGATATCCAGCT
TAAATTACATTCTTATTCCCTGCAGGTTGCGGACCACATCTTCTGTGCCCGTACATGTCGGCTA
AGGTATAACAATTGGCCTCTGTTGCTTCAGCTATCTATACATTATTCGAGCTGCGCTTTTCCTT
GTGGGTTATATGTTCTATATGTGTGCACGACATTTCTGTTTTTCTGTGCGTTTAGTTCCTATAT
GGAAGGGGGTTGTGTGGTTAGGCCTGCTCGTCGACGGGATCGCCGATTGCTAGAGCGTAGCAGC
GCTTCTCTTAGATGTATGGTTTGTTGCGGTTTGTTTTTTTAGACGCTTTAGATTTTATATCTTT
TCCTGGGTGGAAAGATTAAATCGTCTGTTGCTTGTTTAGCATCTTCCTCTAATTCAGCTGCCAG
CGAATATGTTTGGGAGACTGTTGCTCCACCCCGTCAGGGTATGTGATTTACTGATCTGTGTGCG
ACTGTTGTTGTGGCTTGTTTATATTTATGTAGTCGTTGCTCATATATTTTTCTCGCTTTGGTAG
ACGATGGATTTTTCCCTATCTACCCTGCATGGTATTCTTCAAAAAGACGGCAAATGCGTTCAAA
AAAATTGGCCATGAAACGATTGGTGGCTGCAGGTTTTTCCATTGGATCTTTGGTTTTCTGCATA
TGTTCTTGCTGACATGGCTTACATGGACGTTATGTCTCCTTCCCTATAGGCAAAAAACCTTGCC
GTATTGCTCCTGTCTCTTGCAACAAGTTTGACAGTGATTATGCCAAGTTTTTGAGAGGTTGCTT
TCATCTCTGATTCGTTTCCATTCCCTTGTTTGCAATGCCAGCATGCTGGGTTTAAACATAAATT
TCTTTTTTTGAATGCTTGCACAGAGACTTCAAAGGATAGGTGTGATTATGGCCCTCCTGAGTAT
CGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTA
CCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG
						
					

			
		

Sequences
Splice junction sequence	CGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTA CCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAGgtgcttattgtcgcggtcaggtccgtgc gatacgttcgttactgttgtgctgctgttccctttaccatcagctcctgttcaggtgagctttg tttctttg
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: 169 Transcript exons: 35940335-35940394,35941414-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCCCTG AGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGC TATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 174 Transcript exons: 35940335-35940389,35941404-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTATGGCCC TCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGAT TCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 180 Transcript exons: 35940335-35940397,35941406-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA TGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAG AAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 183 Transcript exons: 35940335-35940394,35941400-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCGTGA TTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGC AAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 190 Transcript exons: 35940335-35940393,35941392-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCGGATA GGTGTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGA ACGGTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 192 Transcript exons: 35940335-35940410,35941407-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA CCATCAGCTCCTTGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAG GAACGGTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 194 Transcript exons: 35940335-35940394,35941389-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCAAAG GATAGGTGTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACC AGGAACGGTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAA AG Transcript length: 202 Transcript exons: 35940335-35940410,35941388-35941488,35941498-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA CCATCAGCTCCTCAAAGGATAGGTGTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGC TGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTACCGTCTGTTACAACCTT TGTTGCAAAG Transcript length: 291 Transcript exons: 35940335-35940511,35941409-35941522 GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA CCATCAGCTCCTGTTCAGGTGAGCTTTGTTTCTTTGCTATTTCTTTGGGGCTGACATCCTTTTT GTTTTGTAGTTTATTTGTGCCTTGTGGTTTGGTGTATGTTCTTTCTTTTGCCCTCCTGAGTATC GCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTAC CAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG Transcript length: 581 Transcript exons: 35940335-35941522 CTTAGATCATCTTCCTCTAATTCAGCTGCCAGCGAATATGTTTGGGAGACTGTTGCTCCACCCC GTCAGGACGATGGATTTTTCCCTATCTACCCTGCATGGTATTCTTCAAAAAGACGGCAAATGCG TTCAAAAAAATTGGCCATGAAACGATTGGTGGCTGCAGGCAAAAAACCTTGCCGTATTGCTCCT GTCTCTTGCAACAAGTTTGACAGTGATTATGCCAAGTTTTTGAGAGAGACTTCAAAGGATAGGT GTGATTATGGCCCTCCTGAGTATCGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACG GTGCAAGAAAGATTCTGCTATTACCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAGGTGCT TATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTACCATC AGCTCCTGTTCAGGTTGCGGACCACATCTTCTGTGCCCGTACATGTCGGCTAAGTTCCTATATG GAAGGGGGTTGTGTGGTTAGGCCTGCTCGTCGACGGGATCGCCGATTGCTAGAGCGTAGCAGCG CTTCT
Genomic sequence	GTGCTTATTGTCGCGGTCAGGTCCGTGCGATACGTTCGTTACTGTTGTGCTGCTGTTCCCTTTA CCATCAGCTCCTGTTCAGGTGAGCTTTGTTTCTTTGCTATTTCTTTGGGGCTGACATCCTTTTT GTTTTGTAGTTTATTTGTGCCTTGTGGTTTGGTGTATGTTCTTTCTTTTATCTGATATCCAGCT TAAATTACATTCTTATTCCCTGCAGGTTGCGGACCACATCTTCTGTGCCCGTACATGTCGGCTA AGGTATAACAATTGGCCTCTGTTGCTTCAGCTATCTATACATTATTCGAGCTGCGCTTTTCCTT GTGGGTTATATGTTCTATATGTGTGCACGACATTTCTGTTTTTCTGTGCGTTTAGTTCCTATAT GGAAGGGGGTTGTGTGGTTAGGCCTGCTCGTCGACGGGATCGCCGATTGCTAGAGCGTAGCAGC GCTTCTCTTAGATGTATGGTTTGTTGCGGTTTGTTTTTTTAGACGCTTTAGATTTTATATCTTT TCCTGGGTGGAAAGATTAAATCGTCTGTTGCTTGTTTAGCATCTTCCTCTAATTCAGCTGCCAG CGAATATGTTTGGGAGACTGTTGCTCCACCCCGTCAGGGTATGTGATTTACTGATCTGTGTGCG ACTGTTGTTGTGGCTTGTTTATATTTATGTAGTCGTTGCTCATATATTTTTCTCGCTTTGGTAG ACGATGGATTTTTCCCTATCTACCCTGCATGGTATTCTTCAAAAAGACGGCAAATGCGTTCAAA AAAATTGGCCATGAAACGATTGGTGGCTGCAGGTTTTTCCATTGGATCTTTGGTTTTCTGCATA TGTTCTTGCTGACATGGCTTACATGGACGTTATGTCTCCTTCCCTATAGGCAAAAAACCTTGCC GTATTGCTCCTGTCTCTTGCAACAAGTTTGACAGTGATTATGCCAAGTTTTTGAGAGGTTGCTT TCATCTCTGATTCGTTTCCATTCCCTTGTTTGCAATGCCAGCATGCTGGGTTTAAACATAAATT TCTTTTTTTGAATGCTTGCACAGAGACTTCAAAGGATAGGTGTGATTATGGCCCTCCTGAGTAT CGCTGCCGTTTGTGCGCTGCTCAGTTCTGGTACCAGGAACGGTGCAAGAAAGATTCTGCTATTA CCAAGCGCCGTGTCTGTTACAACCTTTGTTGCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.613857456

Conservation Information
Conserved circRNAs	NA
PMCS	0.613857456

			
						 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
						Ye et al., 2015;Ye et al., 2016

circRNA

Detail information of Os01g0838100_circ_g.2

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