Plant Circular RNA Database

Detail information of Os04g0492300_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os04g0492300_circ_g.2
					
						ID in PlantcircBase
						osa_circ_024358
					
						Alias
						Os04circ08232/Os_ciR3022
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24597384-24598667  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, SMALT, Segemehl, find_circ
					
						Parent gene
						
							Os04g0492300						
					
						Parent gene annotation
						
							Similar to DNA-directed RNA polymerase II largest chain. (Os04t0
492300-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0492300_circ_g.3 						
					
						Support reads
						2/4/1
					
						Tissues
						panicle/root/root
					
						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
						Os04t0492300-01:3

General Information
CircRNA Name	Os04g0492300_circ_g.2
ID in PlantcircBase	osa_circ_024358
Alias	Os04circ08232/Os_ciR3022
Organism	Oryza sativa
Position	chr4: 24597384-24598667 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, SMALT, Segemehl, find_circ
Parent gene	Os04g0492300
Parent gene annotation	Similar to DNA-directed RNA polymerase II largest chain. (Os04t0 492300-01)
Parent gene strand	+
Alternative splicing	Os04g0492300_circ_g.3
Support reads	2/4/1
Tissues	panicle/root/root
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	Os04t0492300-01:3

			
						 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  
						
							CAAAGGTGCACTCCGTTTGCAGCCCGGTTGCAACGCAGCCCAAACATTGGAGCAAAGTATAACT
CGTGTACTGAATGAAATCAGAGAAGAAGCTGGAAAAcctattgagctttggactggtaaacaac
tcttcagtgtgttagtacgtcctaacgcatgtacaaaggtgtttctgaatcttactgttaaaga
gaaaattt

									
								

					

						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: 543
Transcript exons: 24597384-24597597,24597960-24598053,24598433-24598667
CCTATTGAGCTTTGGACTGGTAAACAACTCTTCAGTGTGTTAGTACGTCCTAACGCATGTACAA
AGGTGTTTCTGAATCTTACTGTTAAAGAGAAAATTTATAAGACTCCTAAGGGTTCAACTCTGGA
ACCTGAAGCAATGTGTCCCAATGATGGTTTTGTCTACTTCCGAAACAGTGAACTTCTATCTGGG
CAAGTTGGGAAGGCCACTTTAGGTAATGGGAATAAGGATGGCATGTTCTCCACTCTTGTAAGAG
ATTATAATTCTCATGCTGCGGCAAGCTGTATGAACCGCTTGGCAAAATTTAGTGCAAGATTTAT
AGGGAACCATGGTTTCTCAATTGGTGTGGACGATGTCCAACCGGGAGAACATTTAAACCAAGAG
AAGAAAATGAAAATAGATGGAGGGTACAAAGATTGCCATGATCTTATTGCTTCCTATTCCAAAG
GTGCACTCCGTTTGCAGCCCGGTTGCAACGCAGCCCAAACATTGGAGCAAAGTATAACTCGTGT
ACTGAATGAAATCAGAGAAGAAGCTGGAAAA
						
					

						Genomic sequence
						
							CCTATTGAGCTTTGGACTGGTAAACAACTCTTCAGTGTGTTAGTACGTCCTAACGCATGTACAA
AGGTGTTTCTGAATCTTACTGTTAAAGAGAAAATTTATAAGACTCCTAAGGGTTCAACTCTGGA
ACCTGAAGCAATGTGTCCCAATGATGGTTTTGTCTACTTCCGAAACAGTGAACTTCTATCTGGG
CAAGTTGGGAAGGCCACTTTAGGTGAGAATCCCACCCAGTACTGATTCATAGCTAAAACGACTG
CCAACCTGATAATCCTAAGTACTCACTCTGTCCCAAAAATATAGGTACCTCTCTAATCTGAGCT
AGAAAGGCAGCTATATTTTGGGATGGAGGAGTATGCTATATTCTCTTTAGGAGAACATTAGTTT
ATAGGCATGGACTATAAACAATAGTCCTGGCATGGTTTACCCTCTTATGAATCACCACATACAA
TAAATGTTCCTTTAATCAGGTTTGGAAAATGTATTGTTCACTTGTGCTAGTTAGTTGTCCTTGT
TATTTTCATCCTGCTTGTTAAATTTGGAAGCAAACCAAAACAATCTTTAATCTTTTGTTTCCAG
GTAATGGGAATAAGGATGGCATGTTCTCCACTCTTGTAAGAGATTATAATTCTCATGCTGCGGC
AAGCTGTATGAACCGCTTGGCAAAATTTAGGTGAGCTACAAAATTGCGTAATGGACCCATTCTT
TCCTAAATATTAACTAACAAATGCTATGCAATTATTTTTTTGTTCTGTCTTTGTTCCATTAAAG
AATGCGAGAGGGTTAATAGAAATCACTAATAAGTCAAACACTCTGCCTTCTTTTTATTTTATTT
TACGTGAATCTGCCATCTTTTTTATTTGTACGCAAACCACTTTGCCATTTGACACTAATTAAGT
CAGGGAGCTTAGTTGGTGTACACTCGTTCAATTTTATCTCTCTATTATTACCATTTTGCTGAGT
TTCTCATTTGTATTGTTGGTGTTAGATTGTTACATAATTTAGTGCACATTTTTTTTTCTGATTT
GAATTGCATTCATCTTTTCCTGCAGTGCAAGATTTATAGGGAACCATGGTTTCTCAATTGGTGT
GGACGATGTCCAACCGGGAGAACATTTAAACCAAGAGAAGAAAATGAAAATAGATGGAGGGTAC
AAAGATTGCCATGATCTTATTGCTTCCTATTCCAAAGGTGCACTCCGTTTGCAGCCCGGTTGCA
ACGCAGCCCAAACATTGGAGCAAAGTATAACTCGTGTACTGAATGAAATCAGAGAAGAAGCTGG
AAAA
						
					

			
		

Sequences
Splice junction sequence	CAAAGGTGCACTCCGTTTGCAGCCCGGTTGCAACGCAGCCCAAACATTGGAGCAAAGTATAACT CGTGTACTGAATGAAATCAGAGAAGAAGCTGGAAAAcctattgagctttggactggtaaacaac tcttcagtgtgttagtacgtcctaacgcatgtacaaaggtgtttctgaatcttactgttaaaga gaaaattt
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: 543 Transcript exons: 24597384-24597597,24597960-24598053,24598433-24598667 CCTATTGAGCTTTGGACTGGTAAACAACTCTTCAGTGTGTTAGTACGTCCTAACGCATGTACAA AGGTGTTTCTGAATCTTACTGTTAAAGAGAAAATTTATAAGACTCCTAAGGGTTCAACTCTGGA ACCTGAAGCAATGTGTCCCAATGATGGTTTTGTCTACTTCCGAAACAGTGAACTTCTATCTGGG CAAGTTGGGAAGGCCACTTTAGGTAATGGGAATAAGGATGGCATGTTCTCCACTCTTGTAAGAG ATTATAATTCTCATGCTGCGGCAAGCTGTATGAACCGCTTGGCAAAATTTAGTGCAAGATTTAT AGGGAACCATGGTTTCTCAATTGGTGTGGACGATGTCCAACCGGGAGAACATTTAAACCAAGAG AAGAAAATGAAAATAGATGGAGGGTACAAAGATTGCCATGATCTTATTGCTTCCTATTCCAAAG GTGCACTCCGTTTGCAGCCCGGTTGCAACGCAGCCCAAACATTGGAGCAAAGTATAACTCGTGT ACTGAATGAAATCAGAGAAGAAGCTGGAAAA
Genomic sequence	CCTATTGAGCTTTGGACTGGTAAACAACTCTTCAGTGTGTTAGTACGTCCTAACGCATGTACAA AGGTGTTTCTGAATCTTACTGTTAAAGAGAAAATTTATAAGACTCCTAAGGGTTCAACTCTGGA ACCTGAAGCAATGTGTCCCAATGATGGTTTTGTCTACTTCCGAAACAGTGAACTTCTATCTGGG CAAGTTGGGAAGGCCACTTTAGGTGAGAATCCCACCCAGTACTGATTCATAGCTAAAACGACTG CCAACCTGATAATCCTAAGTACTCACTCTGTCCCAAAAATATAGGTACCTCTCTAATCTGAGCT AGAAAGGCAGCTATATTTTGGGATGGAGGAGTATGCTATATTCTCTTTAGGAGAACATTAGTTT ATAGGCATGGACTATAAACAATAGTCCTGGCATGGTTTACCCTCTTATGAATCACCACATACAA TAAATGTTCCTTTAATCAGGTTTGGAAAATGTATTGTTCACTTGTGCTAGTTAGTTGTCCTTGT TATTTTCATCCTGCTTGTTAAATTTGGAAGCAAACCAAAACAATCTTTAATCTTTTGTTTCCAG GTAATGGGAATAAGGATGGCATGTTCTCCACTCTTGTAAGAGATTATAATTCTCATGCTGCGGC AAGCTGTATGAACCGCTTGGCAAAATTTAGGTGAGCTACAAAATTGCGTAATGGACCCATTCTT TCCTAAATATTAACTAACAAATGCTATGCAATTATTTTTTTGTTCTGTCTTTGTTCCATTAAAG AATGCGAGAGGGTTAATAGAAATCACTAATAAGTCAAACACTCTGCCTTCTTTTTATTTTATTT TACGTGAATCTGCCATCTTTTTTATTTGTACGCAAACCACTTTGCCATTTGACACTAATTAAGT CAGGGAGCTTAGTTGGTGTACACTCGTTCAATTTTATCTCTCTATTATTACCATTTTGCTGAGT TTCTCATTTGTATTGTTGGTGTTAGATTGTTACATAATTTAGTGCACATTTTTTTTTCTGATTT GAATTGCATTCATCTTTTCCTGCAGTGCAAGATTTATAGGGAACCATGGTTTCTCAATTGGTGT GGACGATGTCCAACCGGGAGAACATTTAAACCAAGAGAAGAAAATGAAAATAGATGGAGGGTAC AAAGATTGCCATGATCTTATTGCTTCCTATTCCAAAGGTGCACTCCGTTTGCAGCCCGGTTGCA ACGCAGCCCAAACATTGGAGCAAAGTATAACTCGTGTACTGAATGAAATCAGAGAAGAAGCTGG AAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_005577* osi_circ_014490 						
					
						PMCS
						0.244328998

Conservation Information
Conserved circRNAs	osi_circ_005577* osi_circ_014490
PMCS	0.244328998

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24597523-24598664(+)
24598643-24597423(+)
						
						Potential amino acid sequence
						
							MCPNDGFVYFRNSELLSGQVGKATLGNGNKDGMFSTLVRDYNSHAAASCMNRLAKFSARFIGNH
GFSIGVDDVQPGEHLNQEKKMKIDGGYKDCHDLIASYSKGALRLQPGCNAAQTLEQSITRVLNE
IREEAGKPIELWTGKQLFSVLVRPNACTKVFLNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFR
NSELLSGQVGKATLGNGNKDGMFSTLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQP
GEHLNQEKKMKIDGGYKDCHDLIASYSKGALRLQPGCNAAQTLEQSITRVLNEIREEAGKPIEL
WTGKQLFSVLVRPNACTKVFLNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFRNSELLSGQVGK
ATLGNGNKDGMFSTLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGEHLNQEKKMK
IDGGYKDCHDLIASYSKGALRLQPGCNAAQTLEQSITRVLNEIREEAGKPIELWTGKQLFSVLV
RPNACTKVFLNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFRNSELLSGQVGKATLGNGNKDGM
FSTLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGEHLNQEKKMKIDGGYKDCHDL
IASYSKGALRLQPGCNAAQTLEQSITRVLNEIREEAGK(+)
MKSEKKLENLLSFGLVNNSSVC*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24597523-24598664(+) 24598643-24597423(+)
Potential amino acid sequence	MCPNDGFVYFRNSELLSGQVGKATLGNGNKDGMFSTLVRDYNSHAAASCMNRLAKFSARFIGNH GFSIGVDDVQPGEHLNQEKKMKIDGGYKDCHDLIASYSKGALRLQPGCNAAQTLEQSITRVLNE IREEAGKPIELWTGKQLFSVLVRPNACTKVFLNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFR NSELLSGQVGKATLGNGNKDGMFSTLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQP GEHLNQEKKMKIDGGYKDCHDLIASYSKGALRLQPGCNAAQTLEQSITRVLNEIREEAGKPIEL WTGKQLFSVLVRPNACTKVFLNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFRNSELLSGQVGK ATLGNGNKDGMFSTLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGEHLNQEKKMK IDGGYKDCHDLIASYSKGALRLQPGCNAAQTLEQSITRVLNEIREEAGKPIELWTGKQLFSVLV RPNACTKVFLNLTVKEKIYKTPKGSTLEPEAMCPNDGFVYFRNSELLSGQVGKATLGNGNKDGM FSTLVRDYNSHAAASCMNRLAKFSARFIGNHGFSIGVDDVQPGEHLNQEKKMKIDGGYKDCHDL IASYSKGALRLQPGCNAAQTLEQSITRVLNEIREEAGK(+) MKSEKKLENLLSFGLVNNSSVC*(+)
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 Os04g0492300_circ_g.2

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