Plant Circular RNA Database

Detail information of Os01g0691600_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0691600_circ_g.4
					
						ID in PlantcircBase
						osa_circ_003433
					
						Alias
						Os_ciR1843
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 28547584-28547947  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os01g0691600						
					
						Parent gene annotation
						
							Similar to DNA repair helicase XPB2 (EC 3.6.1.-) (XPB homolog 2)
 (ERCC3 homolog 2) (RAD25 homolog 2) (AtXPB2). (Os01t0691600-01)
;Similar to XPB1 (ARABIDOPSIS HOMOLOG OF XERODERMA PIGMENTOSUM C
OMPLEMENTATION GROUP B 1); ATP-dependent helicase. (Os01t0691600
-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0691600_circ_g.5 Os01g0691600_circ_g.6 						
					
						Support reads
						6/3
					
						Tissues
						root/shoot, root, seed, pistil
					
						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  
						
							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
						Os01t0691600-01:2

General Information
CircRNA Name	Os01g0691600_circ_g.4
ID in PlantcircBase	osa_circ_003433
Alias	Os_ciR1843
Organism	Oryza sativa
Position	chr1: 28547584-28547947 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, find_circ
Parent gene	Os01g0691600
Parent gene annotation	Similar to DNA repair helicase XPB2 (EC 3.6.1.-) (XPB homolog 2) (ERCC3 homolog 2) (RAD25 homolog 2) (AtXPB2). (Os01t0691600-01) ;Similar to XPB1 (ARABIDOPSIS HOMOLOG OF XERODERMA PIGMENTOSUM C OMPLEMENTATION GROUP B 1); ATP-dependent helicase. (Os01t0691600 -02)
Parent gene strand	+
Alternative splicing	Os01g0691600_circ_g.5 Os01g0691600_circ_g.6
Support reads	6/3
Tissues	root/shoot, root, seed, pistil
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	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	Os01t0691600-01:2

			
						 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  
						
							CTATTATTTTCTATTTATGTGAGCTGCGATATCTCATCTCCAGGTTTTGAAGACGCTTCTGAAA
GATGATATCATTTGCAGAGCACGGATATCTCCTGAGgccagaatccatgcacgagtacaatcta
acaccccactcactatatgctgcggtctcagttgggcttgagactagcactataatcagtgtca
tgagcaag

						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: 280
Transcript exons: 28547584-28547806,28547891-28547947
GCCAGAATCCATGCACGAGTACAATCTAACACCCCACTCACTATATGCTGCGGTCTCAGTTGGG
CTTGAGACTAGCACTATAATCAGTGTCATGAGCAAGCTCTCCAAGACTAAACTGCCTCGTGAAA
TAATTGATTTTATCCATGCATCAACTGCCAATTATGGTAAAGTGAAGCTTGTTCTGAAGAAGAA
TCGATATTTTGTGGAGTCTCCATTCCCTGAGGTTTTGAAGACGCTTCTGAAAGATGATATCATT
TGCAGAGCACGGATATCTCCTGAG
						
						Genomic sequence
						
							GCCAGAATCCATGCACGAGTACAATCTAACACCCCACTCACTATATGCTGCGGTCTCAGTTGGG
CTTGAGACTAGCACTATAATCAGTGTCATGAGCAAGCTCTCCAAGACTAAACTGCCTCGTGAAA
TAATTGATTTTATCCATGCATCAACTGCCAATTATGGTAAAGTGAAGCTTGTTCTGAAGAAGAA
TCGATATTTTGTGGAGTCTCCATTCCCTGAGGTCATACCATACTTCCGTGATTAAAAAATATTC
TTTTTTGTCTATTATTTTCTATTTATGTGAGCTGCGATATCTCATCTCCAGGTTTTGAAGACGC
TTCTGAAAGATGATATCATTTGCAGAGCACGGATATCTCCTGAG

Sequences
Splice junction sequence	CTATTATTTTCTATTTATGTGAGCTGCGATATCTCATCTCCAGGTTTTGAAGACGCTTCTGAAA GATGATATCATTTGCAGAGCACGGATATCTCCTGAGgccagaatccatgcacgagtacaatcta acaccccactcactatatgctgcggtctcagttgggcttgagactagcactataatcagtgtca tgagcaag
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: 280 Transcript exons: 28547584-28547806,28547891-28547947 GCCAGAATCCATGCACGAGTACAATCTAACACCCCACTCACTATATGCTGCGGTCTCAGTTGGG CTTGAGACTAGCACTATAATCAGTGTCATGAGCAAGCTCTCCAAGACTAAACTGCCTCGTGAAA TAATTGATTTTATCCATGCATCAACTGCCAATTATGGTAAAGTGAAGCTTGTTCTGAAGAAGAA TCGATATTTTGTGGAGTCTCCATTCCCTGAGGTTTTGAAGACGCTTCTGAAAGATGATATCATT TGCAGAGCACGGATATCTCCTGAG
Genomic sequence	GCCAGAATCCATGCACGAGTACAATCTAACACCCCACTCACTATATGCTGCGGTCTCAGTTGGG CTTGAGACTAGCACTATAATCAGTGTCATGAGCAAGCTCTCCAAGACTAAACTGCCTCGTGAAA TAATTGATTTTATCCATGCATCAACTGCCAATTATGGTAAAGTGAAGCTTGTTCTGAAGAAGAA TCGATATTTTGTGGAGTCTCCATTCCCTGAGGTCATACCATACTTCCGTGATTAAAAAATATTC TTTTTTGTCTATTATTTTCTATTTATGTGAGCTGCGATATCTCATCTCCAGGTTTTGAAGACGC TTCTGAAAGATGATATCATTTGCAGAGCACGGATATCTCCTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_010581 						
					
						PMCS
						0.34231337

Conservation Information
Conserved circRNAs	osi_circ_010581
PMCS	0.34231337

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							28547595-28547649(+)
28547914-28547649(+)
28547678-28547734(-)
						
						Potential amino acid sequence
						
							MHEYNLTPHSLYAAVSVGLETSTIISVMSKLSKTKLPREIIDFIHASTANYGKVKLVLKKNRYF
VESPFPEVLKTLLKDDIICRARISPEARIHARVQSNTPLTICCGLSWA*(+)
MISFAEHGYLLRPESMHEYNLTPHSLYAAVSVGLETSTIISVMSKLSKTKLPREIIDFIHASTA
NYGKVKLVLKKNRYFVESPFPEVLKTLLKDDIICRARISPEARIHARVQSNTPLTICCGLSWA*
(+)
MTLIIVLVSSPTETAAYSEWGVRLYSCMDSGLRRYPCSANDIIFQKRLQNLREWRLHKISILLQ
NKLHFTIIGS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	28547595-28547649(+) 28547914-28547649(+) 28547678-28547734(-)
Potential amino acid sequence	MHEYNLTPHSLYAAVSVGLETSTIISVMSKLSKTKLPREIIDFIHASTANYGKVKLVLKKNRYF VESPFPEVLKTLLKDDIICRARISPEARIHARVQSNTPLTICCGLSWA(+) MISFAEHGYLLRPESMHEYNLTPHSLYAAVSVGLETSTIISVMSKLSKTKLPREIIDFIHASTA NYGKVKLVLKKNRYFVESPFPEVLKTLLKDDIICRARISPEARIHARVQSNTPLTICCGLSWA (+) MTLIIVLVSSPTETAAYSEWGVRLYSCMDSGLRRYPCSANDIIFQKRLQNLREWRLHKISILLQ NKLHFTIIGS*(-)
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 Os01g0691600_circ_g.4

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