Plant Circular RNA Database

Detail information of Os03g0849600_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os03g0849600_circ_g.2
					
						ID in PlantcircBase
						osa_circ_022714
					
						Alias
						Os_ciR1139
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 35736824-35737161  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os03g0849600						
					
						Parent gene annotation
						
							COG complex component, COG2 family protein. (Os03t0849600-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os03g0849600_circ_g.3 Os03g0849600_circ_g.4 Os03g0849600_circ_g.5 Os03g0849600_circ_g.6 Os03g0849600_circ_g.7 Os03g0849600_circ_g.8 Os03g0849600_circ_g.9 						
					
						Support reads
						25/2/4
					
						Tissues
						root/root/shoot, root, seed
					
						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
						Os03t0849600-01:2

General Information
CircRNA Name	Os03g0849600_circ_g.2
ID in PlantcircBase	osa_circ_022714
Alias	Os_ciR1139
Organism	Oryza sativa
Position	chr3: 35736824-35737161 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circseq_cup, find_circ
Parent gene	Os03g0849600
Parent gene annotation	COG complex component, COG2 family protein. (Os03t0849600-01)
Parent gene strand	-
Alternative splicing	Os03g0849600_circ_g.3 Os03g0849600_circ_g.4 Os03g0849600_circ_g.5 Os03g0849600_circ_g.6 Os03g0849600_circ_g.7 Os03g0849600_circ_g.8 Os03g0849600_circ_g.9
Support reads	25/2/4
Tissues	root/root/shoot, root, seed
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	Os03t0849600-01:2

			
						 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  
						
							TGTCATAATAAATTGAAGTGATCTTATCTGTCGATCCACGGCGCAGCTTTGCTTTATCATCTTC
TGATAAATAGTGAATACGGTCACCTTCAAGAAAAACctgaatgtcaagaaatagctgcatgcag
atcttgtcagtatcagaaatgatgttatccgaggtatcggtattagctcctactcgtctttgtg
caccttga

									
								

					

						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: 115
Transcript exons: 35736824-35736844,35737068-35737161
CTGAATGTCAAGAAATAGCTGAATAAATTGAAGTGATCTTATCTGTCGATCCACGGCGCAGCTT
TGCTTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAAAC
Transcript length: 174
Transcript exons: 35736824-35736935,35737100-35737161
CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA
TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCCGGCGCAGCTTTGCTT
TATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAAAC
Transcript length: 240
Transcript exons: 35736824-35736948,35737047-35737161
CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA
TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGCTA
CTTCAGACACCATGTCATAATAAATTGAAGTGATCTTATCTGTCGATCCACGGCGCAGCTTTGC
TTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAAAC
Transcript length: 258
Transcript exons: 35736824-35736958,35737039-35737161
CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA
TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGTTT
TCCTTGCCACAGTGACTACTTCAGACACCATGTCATAATAAATTGAAGTGATCTTATCTGTCGA
TCCACGGCGCAGCTTTGCTTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAA
AC
Transcript length: 258
Transcript exons: 35736824-35737161
CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA
TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGTTT
TCCTTGCCCCAGTGACTACTTCAGACACCATGTCATAATAAATTGAAGTGATCTTATCTGTCGA
TCCACGGCGCAGCTTTGCTTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAA
AC
						
					

						Genomic sequence
						
							CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA
TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGTTT
TCCTTGCCTTTATATTCAATAAAAATGGTTTAATTCACCAATAAGCAGATATGAGCTCTCATAA
GCAGTTAAGCATTCCTTACTTACCACAGTGACTACTTCAGACACCATGTCATAATAAATTGAAG
TGATCTTATCTGTCGATCCACGGCGCAGCTTTGCTTTATCATCTTCTGATAAATAGTGAATACG
GTCACCTTCAAGAAAAAC
						
					

			
		

Sequences
Splice junction sequence	TGTCATAATAAATTGAAGTGATCTTATCTGTCGATCCACGGCGCAGCTTTGCTTTATCATCTTC TGATAAATAGTGAATACGGTCACCTTCAAGAAAAACctgaatgtcaagaaatagctgcatgcag atcttgtcagtatcagaaatgatgttatccgaggtatcggtattagctcctactcgtctttgtg caccttga
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: 115 Transcript exons: 35736824-35736844,35737068-35737161 CTGAATGTCAAGAAATAGCTGAATAAATTGAAGTGATCTTATCTGTCGATCCACGGCGCAGCTT TGCTTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAAAC Transcript length: 174 Transcript exons: 35736824-35736935,35737100-35737161 CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCCGGCGCAGCTTTGCTT TATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAAAC Transcript length: 240 Transcript exons: 35736824-35736948,35737047-35737161 CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGCTA CTTCAGACACCATGTCATAATAAATTGAAGTGATCTTATCTGTCGATCCACGGCGCAGCTTTGC TTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAAAC Transcript length: 258 Transcript exons: 35736824-35736958,35737039-35737161 CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGTTT TCCTTGCCACAGTGACTACTTCAGACACCATGTCATAATAAATTGAAGTGATCTTATCTGTCGA TCCACGGCGCAGCTTTGCTTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAA AC Transcript length: 258 Transcript exons: 35736824-35737161 CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGTTT TCCTTGCCCCAGTGACTACTTCAGACACCATGTCATAATAAATTGAAGTGATCTTATCTGTCGA TCCACGGCGCAGCTTTGCTTTATCATCTTCTGATAAATAGTGAATACGGTCACCTTCAAGAAAA AC
Genomic sequence	CTGAATGTCAAGAAATAGCTGCATGCAGATCTTGTCAGTATCAGAAATGATGTTATCCGAGGTA TCGGTATTAGCTCCTACTCGTCTTTGTGCACCTTGACGTAGTCTTTGCAATGATGATTCAGTTT TCCTTGCCTTTATATTCAATAAAAATGGTTTAATTCACCAATAAGCAGATATGAGCTCTCATAA GCAGTTAAGCATTCCTTACTTACCACAGTGACTACTTCAGACACCATGTCATAATAAATTGAAG TGATCTTATCTGTCGATCCACGGCGCAGCTTTGCTTTATCATCTTCTGATAAATAGTGAATACG GTCACCTTCAAGAAAAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.486062549

Conservation Information
Conserved circRNAs	NA
PMCS	0.486062549

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							35737064-35736826(-)
						
						Potential amino acid sequence
						
							MVSEVVTVARKTESSLQRLRQGAQRRVGANTDTSDNIISDTDKICMQLFLDIQVFLEGDRIHYL
SEDDKAKLRRGSTDKITSIYYDMVSEVVTVARKTESSLQRLRQGAQRRVGANTDTSDNIISDTD
KICMQLFLDIQVFLEGDRIHYLSEDDKAKLRRGSTDKITSIYYDMVSEVVTVARKTESSLQRLR
QGAQRRVGANTDTSDNIISDTDKICMQLFLDIQVFLEGDRIHYLSEDDKAKLRRGSTDKITSIY
YDMVSEVVTVARKTESSLQRLRQGAQRRVGANTDTSDNIISDTDKICMQLFLDIQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	35737064-35736826(-)
Potential amino acid sequence	MVSEVVTVARKTESSLQRLRQGAQRRVGANTDTSDNIISDTDKICMQLFLDIQVFLEGDRIHYL SEDDKAKLRRGSTDKITSIYYDMVSEVVTVARKTESSLQRLRQGAQRRVGANTDTSDNIISDTD KICMQLFLDIQVFLEGDRIHYLSEDDKAKLRRGSTDKITSIYYDMVSEVVTVARKTESSLQRLR QGAQRRVGANTDTSDNIISDTDKICMQLFLDIQVFLEGDRIHYLSEDDKAKLRRGSTDKITSIY YDMVSEVVTVARKTESSLQRLRQGAQRRVGANTDTSDNIISDTDKICMQLFLDIQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Ye et al., 2016;Chu et al., 2017

circRNA

Detail information of Os03g0849600_circ_g.2

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