Plant Circular RNA Database

Detail information of Os01g0175000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os01g0175000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_000488
					
						Alias
						Os01circ03506
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 3849155-3849551  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, SMALT, Segemehl
					
						Parent gene
						
							Os01g0175000						
					
						Parent gene annotation
						
							Similar to Biostress-resistance-related protein (Fragment). (Os0
1t0175000-01);Similar to Biostress-resistance-related protein (F
ragment). (Os01t0175000-02);Similar to Biostress-resistance-rela
ted protein (Fragment). (Os01t0175000-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						8/8
					
						Tissues
						leaf and panicle/shoot, root, anther
					
						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
						Os01t0175000-01:2
Os01t0175000-02:2
Os01t0175000-03:2

General Information
CircRNA Name	Os01g0175000_circ_g.1
ID in PlantcircBase	osa_circ_000488
Alias	Os01circ03506
Organism	Oryza sativa
Position	chr1: 3849155-3849551 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, SMALT, Segemehl
Parent gene	Os01g0175000
Parent gene annotation	Similar to Biostress-resistance-related protein (Fragment). (Os0 1t0175000-01);Similar to Biostress-resistance-related protein (F ragment). (Os01t0175000-02);Similar to Biostress-resistance-rela ted protein (Fragment). (Os01t0175000-03)
Parent gene strand	-
Alternative splicing	NA
Support reads	8/8
Tissues	leaf and panicle/shoot, root, anther
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	Os01t0175000-01:2 Os01t0175000-02:2 Os01t0175000-03:2

			
						 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  
						
							ACGGAGCTGGTGCCGCCGAAGCTGCTCATCCCGCGAACAATCGCCGCCGCCGCCGCCCCTCCGC
GTCCCCTCGCGGCCACGCTCGCTCCACCACCCAACTctggctccgttgtccccgaggccgtgga
gccagacgatggtggccttgtgcgcgcccttgggcctcacgacatgcgtccgcccgtactcgag
cctcttcc

						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: 3849155-3849255,3849484-3849551
CTGGCTCCGTTGTCCCCGAGGCCGTGGAGCCAGACGATGGTGGCCTTGTGCGCGCCCTTGGGCC
TCACGACATGCGTCCGCCCGTACTCGAGCCTCTTCCCGCGAACAATCGCCGCCGCCGCCGCCCC
TCCGCGTCCCCTCGCGGCCACGCTCGCTCCACCACCCAACT
Transcript length: 214
Transcript exons: 3849155-3849257,3849441-3849551
CTGGCTCCGTTGTCCCCGAGGCCGTGGAGCCAGACGATGGTGGCCTTGTGCGCGCCCTTGGGCC
TCACGACATGCGTCCGCCCGTACTCGAGCCTCTTCCCACCACCGGAGGCGACGGAGCTGGTGCC
GCCGAAGCTGCTCATCCCGCGAACAATCGCCGCCGCCGCCGCCCCTCCGCGTCCCCTCGCGGCC
ACGCTCGCTCCACCACCCAACT
						
						Genomic sequence
						
							CTGGCTCCGTTGTCCCCGAGGCCGTGGAGCCAGACGATGGTGGCCTTGTGCGCGCCCTTGGGCC
TCACGACATGCGTCCGCCCGTACTCGAGCCTCTTCCCACCTGCATCCAACCATCCAATCCCACC
CCCATTTTACGATTCGATCCCAAATCCCCCAACGCATTCGAATCAAAATCAGGAGCATCACGAA
CGCAATCAAATCACAGCATCAATCCCATCCCATTTCACGAATCAATCCCCCCCTCCTCAACGCA
TTCAACACCGATCAATGGAACGAAACGTACCACCGGAGGCGACGGAGCTGGTGCCGCCGAAGCT
GCTCATCCCGCGAACAATCGCCGCCGCCGCCGCCCCTCCGCGTCCCCTCGCGGCCACGCTCGCT
CCACCACCCAACT

Sequences
Splice junction sequence	ACGGAGCTGGTGCCGCCGAAGCTGCTCATCCCGCGAACAATCGCCGCCGCCGCCGCCCCTCCGC GTCCCCTCGCGGCCACGCTCGCTCCACCACCCAACTctggctccgttgtccccgaggccgtgga gccagacgatggtggccttgtgcgcgcccttgggcctcacgacatgcgtccgcccgtactcgag cctcttcc
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: 3849155-3849255,3849484-3849551 CTGGCTCCGTTGTCCCCGAGGCCGTGGAGCCAGACGATGGTGGCCTTGTGCGCGCCCTTGGGCC TCACGACATGCGTCCGCCCGTACTCGAGCCTCTTCCCGCGAACAATCGCCGCCGCCGCCGCCCC TCCGCGTCCCCTCGCGGCCACGCTCGCTCCACCACCCAACT Transcript length: 214 Transcript exons: 3849155-3849257,3849441-3849551 CTGGCTCCGTTGTCCCCGAGGCCGTGGAGCCAGACGATGGTGGCCTTGTGCGCGCCCTTGGGCC TCACGACATGCGTCCGCCCGTACTCGAGCCTCTTCCCACCACCGGAGGCGACGGAGCTGGTGCC GCCGAAGCTGCTCATCCCGCGAACAATCGCCGCCGCCGCCGCCCCTCCGCGTCCCCTCGCGGCC ACGCTCGCTCCACCACCCAACT
Genomic sequence	CTGGCTCCGTTGTCCCCGAGGCCGTGGAGCCAGACGATGGTGGCCTTGTGCGCGCCCTTGGGCC TCACGACATGCGTCCGCCCGTACTCGAGCCTCTTCCCACCTGCATCCAACCATCCAATCCCACC CCCATTTTACGATTCGATCCCAAATCCCCCAACGCATTCGAATCAAAATCAGGAGCATCACGAA CGCAATCAAATCACAGCATCAATCCCATCCCATTTCACGAATCAATCCCCCCCTCCTCAACGCA TTCAACACCGATCAATGGAACGAAACGTACCACCGGAGGCGACGGAGCTGGTGCCGCCGAAGCT GCTCATCCCGCGAACAATCGCCGCCGCCGCCGCCCCTCCGCGTCCCCTCGCGGCCACGCTCGCT CCACCACCCAACT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_001828* osi_circ_011090 						
					
						PMCS
						0.267144395

Conservation Information
Conserved circRNAs	osi_circ_001828* osi_circ_011090
PMCS	0.267144395

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3849192-3849548(+)
3849227-3849548(+)
3849482-3849479(-)
						
						Potential amino acid sequence
						
							MVALCAPLGLTTCVRPYSSLFPPPEATELVPPKLLIPRTIAAAAAPPRPLAATLAPPPNSGSVV
PEAVEPDDGGLVRALGPHDMRPPVLEPLPTTGGDGAGAAEAAHPANNRRRRRPSASPRGHARST
TQLWLRCPRGRGARRWWPCARPWASRHASARTRASSHHRRRRSWCRRSCSSREQSPPPPPLRVP
SRPRSLHHPTLAPLSPRPWSQTMVALCAPLGLTTCVRPYSSLFPPPEATELVPPKLLIPRTIAA
AAAPPRPLAATLAPPPN(+)
MRPPVLEPLPTTGGDGAGAAEAAHPANNRRRRRPSASPRGHARSTTQLWLRCPRGRGARRWWPC
ARPWASRHASARTRASSHHRRRRSWCRRSCSSREQSPPPPPLRVPSRPRSLHHPTLAPLSPRPW
SQTMVALCAPLGLTTCVRPYSSLFPPPEATELVPPKLLIPRTIAAAAAPPRPLAATLAPPPNSG
SVVPEAVEPDDGGLVRALGPHDMRPPVLEPLPTTGGDGAGAAEAAHPANNRRRRRPSASPRGHA
RSTTQ(+)
MSSFGGTSSVASGGGKRLEYGRTHVVRPKGAHKATIVWLHGLGDNGARVGWWSERGREGTRRGG
GGGDCSRDEQLRRHQLRRLRWWEEARVRADACREAQGRAQGHHRLAPRPRGQRSQSWVVERAWP
RGDAEGRRRRRLFAG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3849192-3849548(+) 3849227-3849548(+) 3849482-3849479(-)
Potential amino acid sequence	MVALCAPLGLTTCVRPYSSLFPPPEATELVPPKLLIPRTIAAAAAPPRPLAATLAPPPNSGSVV PEAVEPDDGGLVRALGPHDMRPPVLEPLPTTGGDGAGAAEAAHPANNRRRRRPSASPRGHARST TQLWLRCPRGRGARRWWPCARPWASRHASARTRASSHHRRRRSWCRRSCSSREQSPPPPPLRVP SRPRSLHHPTLAPLSPRPWSQTMVALCAPLGLTTCVRPYSSLFPPPEATELVPPKLLIPRTIAA AAAPPRPLAATLAPPPN(+) MRPPVLEPLPTTGGDGAGAAEAAHPANNRRRRRPSASPRGHARSTTQLWLRCPRGRGARRWWPC ARPWASRHASARTRASSHHRRRRSWCRRSCSSREQSPPPPPLRVPSRPRSLHHPTLAPLSPRPW SQTMVALCAPLGLTTCVRPYSSLFPPPEATELVPPKLLIPRTIAAAAAPPRPLAATLAPPPNSG SVVPEAVEPDDGGLVRALGPHDMRPPVLEPLPTTGGDGAGAAEAAHPANNRRRRRPSASPRGHA RSTTQ(+) MSSFGGTSSVASGGGKRLEYGRTHVVRPKGAHKATIVWLHGLGDNGARVGWWSERGREGTRRGG GGGDCSRDEQLRRHQLRRLRWWEEARVRADACREAQGRAQGHHRLAPRPRGQRSQSWVVERAWP RGDAEGRRRRRLFAG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os01g0175000_circ_g.1

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