Plant Circular RNA Database

Detail information of Os04g0304000_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os04g0304000_circ_g.1
					
						ID in PlantcircBase
						osa_circ_023352
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 13619223-13622965  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0304000						
					
						Parent gene annotation
						
							Similar to OSIGBa0092O07.4 protein. (Os04t0304000-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						1
					
						Tissues
						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  
						
							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
						Os04t0304000-01:2

General Information
CircRNA Name	Os04g0304000_circ_g.1
ID in PlantcircBase	osa_circ_023352
Alias	NA
Organism	Oryza sativa
Position	chr4: 13619223-13622965 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0304000
Parent gene annotation	Similar to OSIGBa0092O07.4 protein. (Os04t0304000-01)
Parent gene strand	-
Alternative splicing	NA
Support reads	1
Tissues	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	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	Os04t0304000-01:2

			
						 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  
						
							TGCCTTTTGGTTTGTTGAATGTCCAAATGCATTAGTGTCATCAATACTGCGTAGTTTTGCTTCC
AGAAGGTTGAGAGATGAGTCTAGTTTCACTATTTTCctgttgctccaaaagatccaacacagat
ggccatctttttccatgcttttcatgtcagctcccttatgtccttcagcaggtaggctattcct
cacgctgc

									
								

					

						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: 299
Transcript exons: 13619223-13619359,13622804-13622965
CTGTTGCTCCAAAAGATCCAACACAGATGGCCATCTTTTTCCATGCTTTTCATGTCAGCTCCCT
TATGTCCTTCAGCAGGTAGGCTATTCCTCACGCTGCCTGCCTTCCAGTGTAGCATAATCAAGCA
TCACCAGACCTAGAGGATTCACCCAATAAATTTGTAGGTTCAAATCTTCCATCTTGTGTGAATA
ATCCATGTGCCTTTTGGTTTGTTGAATGTCCAAATGCATTAGTGTCATCAATACTGCGTAGTTT
TGCTTCCAGAAGGTTGAGAGATGAGTCTAGTTTCACTATTTTC
						
					

						Genomic sequence
						
							CTGTTGCTCCAAAAGATCCAACACAGATGGCCATCTTTTTCCATGCTTTTCATGTCAGCTCCCT
TATGTCCTTCAGCAGGTAGGCTATTCCTCACGCTGCCTGCCTTCCAGTGTAGCATAATCAAGCA
TCACCAGACCTACATAATGCACACCATCATAACACAAAGCAATCAGTGTAACACGATTTTTTTT
CACGGTGAACATAATTCACAAAGCAATCAGTGTAACACGATTTTTTCATGGTGAACATTATTAA
GAACCGTTGACAGCAAAGCACATTATTTTACAAACAGTTTGCCAGGACTGATTCACAGAAATAG
CAAAAGTTCAAATCACTTGACAATCATCATCAACCCAGGGCAGACAAAGGCAAAGCTGATTAAA
TGGAGCACAAGGTGGAAAATAGAATGCCTGGAAAAATGTAATGAATGCACCCACATCACCCCAG
TACAGTCTCCTAAACATAACATAAGATCAATGCAAAGTTAAACAAAACATCATTCAGGATCTGG
TTCATGTTCAGAAGAAACAATGAAAGGTCAAGTGTTTCTTTCTGCTGTTTGAGGCCTTCTTTTA
AAGCAAAACGAAAAGGTAAAAATCTATAAAAGGAAGAAACAAGCAGCCTTTGGCATGTATTTCA
AGGAAAATGGTATATCATGTATTTCAAGTCACGATAGTATTTAAAAATAAATGGAAAATAAAAA
CTTGTGGTAACTTATGTCAGAAAACTCTATAGTTTACAATATTCAGAGTTGTTGGTCTAAGTGT
CAAATGTAAAAGTGAAACATGGAAACTTCACATTTTGATACAGATCTGATCAACTCCATGTCCT
CCGATAGACAAAAATGAGCAGTGACTGTGTTGCGTAAGTACATACTGCAGATAGTGCAAACCAC
ATCACACATATATGGTATTCTTTTAAGAGGAAAATATGGTAATTTGACACGCTCACGTATTTGA
GGAACTTACACTTGAAAAATCTCTACTACTTTAAAATTCCGTAGTGGTGGCGGTGACTCCAACC
CTGGAAGACACGCGGAACATGAGCTGTTGGATCGCCATATCCAACGCTCCCAGTTATCAGTTAT
CCCCATGTGCTTGTGCTTCCCCCCTCCGCCCGCAACCCAAACCCACGTCGCTCTCCCGATCCAA
CCGCCTCCGTCCAACCGCCGCCGCCGCCGCCGCTCCATCCCCTCGTCGCGCCTCGCCGTCGCAC
CACGATGCGCCGCCGCCGCTCCATCCCCTCCCGCTCCATCGCGCCGCAACGCCAGATTCATCGC
CGCTCCCCTCCCTCTCGACCGTTTCTCTCGGCGCCATCTCCGCACATCCCCGCCAGCGCCGGAT
CTCCCTTCTCGCCCTGTTTCCTTGCTGAAGCATTGTCGTGATATTCAGTTTGATCTGCTCGTCA
TATCGCTGCCGCACAACTCGCCGAATACCAAGGCTCGTAAACAAGCGCCGCCGCTGCCGCCAAA
TCCACCGAAACCAATCTACGCGGCCACCACACGATGGATGCATCACCGTCAATTCCGCCCTCGC
CGACTCCGCCACAGCCGCCTACTCCACCGCCACTACAGTTGTCAACGACTCCGCCGCCGCCACT
CCCGTCGTCGCCGGCTCCGCGACCGCCGTCCGTGCTGCCACCGCCCTTGCCGTCATCTTCGGCG
CCAAGCATTGTCAGCACAGATATCGATCCGGTAAGTTAAGCACCTAGCTTAATTAGTCCATGAA
AACTATCGATATATATGTGTGCGCTGTATTGCGATTTGGGTTACTTAGCTAGGTAATGTTAATG
CATGGTACTGTAGATTAATGCAAGGCACTGTACGTTAATTAATTATTAATTGAAGCACCTAGCT
AGCCATCCACTATTATATTATAAAATTATTACTTATAATATATCAATTGCATTAATATATACTC
CTACACTAGCTTGTGCGCAGTTCTCAGGCTTGCTTCTTTACTTATATGAGGAACTCATCTCTCG
CACTCGCAAAACTGAGGGACTCATTAACGCATGATTAATTAAATATTACTCCCTCCTTCCCAAA
TTGATAATCATGTAATAGAATCCAAAATTTCTCAAATTGATCATCATATTACTGCATGGACACA
GATTTCATCTAAATACAATTAATGCAGTATGAGAGAATGTGTGCATGCTATGATGTAATTGGCA
TAGGGTTTTAATCGATGCATGCATTGTGGGAGAATACGTGCATGGTGTCTTGATTGATGTGATT
TAAATTGTCCTTGGTCTTGGTACATAAACTTATATGATGATCAATTTGGGAAGGAGGGAGTAGT
TTTTAATTAGAACAAATAGATTTTTATGGTTTTATACAATAACTCTAACAACATAACTCAGCAT
AAAATCAACCTGGCCATCAGCTCATTTTACGAATATACAATACTCTGTGTGGCATGATTCACCA
AGAAAAAAAATAATTGATAGCTATGATCGAGCAAAATAAAGCATTGTACCAACTAATGCTACAC
TAATATTGACCTCCCTGCCGACGTGCTTTTTTCCAGTGTTATATATAATCTCCATGTGCAATAT
AGATATCCTTGCTTAATCTCATGTGGTACTCAGGTCAATCAAGACGCCATTCGTGCTGATATGA
TTACAACCTGACCCTCGAATAAAGCAAAAAATTCGGAATCCGAGGAGCATGGAAATTTTCAGTT
TGAAATAAGTAGCACAGCCTGAAATTTCTTTAACTGGGAAGACCATTTGTACAGGTTTGGTTTC
AATCGAAGCTACAGGTTTAATTTGGAAGATCATGCAGCCATGATGCTACAAATATTAATCTTGA
TGGTTTAAATTAACCTATTTCATCTATACAACTTGATTCAGCTTAATTTAGTTCCTACATTAGT
GCACAGTTATTCTTCATTTATTTGTGCGTACAGGATCTATGGAAGAGGGCCATTAGGTACTAAG
AGACCTATTGTGCCATTATATTCATGAATTTTTTGGCTGTTTGTAACCTGTGAAAACTTATAAG
GATGTGATGAAATTATTGTTCGTGCCATAATAAGGTTTTCATCATAATAAATTTAATTATTCAA
CATCATTTTACTGTGATTTTAAATTGGTGTATATTTTTTACCCGTTGCAACGCACGGGCACCTA
CCTAGTAAGGAATAAAAACAACATGGAATAGGGGAGCTGAACAATTACTTCATCAGATATTTAT
TGTTGTGGCATGATTAATTGTGAAATGCACTATTTGAATGAGAAATCCCCATCCATATACATCA
GGAAGCTAAACATCATTGAAAGACTATGACCGTGGATATACTATAAAAATTAAACAGAGGTCTA
TTTGTCAAAATTGAATGACAATTCCAAAGAGGAAATTATATCATTGACTATCAGAATAATATGA
CATGGCTAACTACATATTTGTAGTTTCCAAGGCCTCATGCTACTCACAATATTTAGCGTGCACT
ACTGTCACAAATGTAACAAAAAACAATTGAATAGGCACTATCAGGCCAATTAAAATATGCCAAT
ATGTGGCTATAGAATGATATATTACTGTATGAAACTATGAATAGCAATAAGACAGACTCACCTA
GAGGATTCACCCAATAAATTTGTAGGTTCAAATCTTCCATCTTGTGTGAATAATCCATGTGCCT
TTTGGTTTGTTGAATGTCCAAATGCATTAGTGTCATCAATACTGCGTAGTTTTGCTTCCAGAAG
GTTGAGAGATGAGTCTAGTTTCACTATTTTC
						
					

			
		

Sequences
Splice junction sequence	TGCCTTTTGGTTTGTTGAATGTCCAAATGCATTAGTGTCATCAATACTGCGTAGTTTTGCTTCC AGAAGGTTGAGAGATGAGTCTAGTTTCACTATTTTCctgttgctccaaaagatccaacacagat ggccatctttttccatgcttttcatgtcagctcccttatgtccttcagcaggtaggctattcct cacgctgc
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: 299 Transcript exons: 13619223-13619359,13622804-13622965 CTGTTGCTCCAAAAGATCCAACACAGATGGCCATCTTTTTCCATGCTTTTCATGTCAGCTCCCT TATGTCCTTCAGCAGGTAGGCTATTCCTCACGCTGCCTGCCTTCCAGTGTAGCATAATCAAGCA TCACCAGACCTAGAGGATTCACCCAATAAATTTGTAGGTTCAAATCTTCCATCTTGTGTGAATA ATCCATGTGCCTTTTGGTTTGTTGAATGTCCAAATGCATTAGTGTCATCAATACTGCGTAGTTT TGCTTCCAGAAGGTTGAGAGATGAGTCTAGTTTCACTATTTTC
Genomic sequence	CTGTTGCTCCAAAAGATCCAACACAGATGGCCATCTTTTTCCATGCTTTTCATGTCAGCTCCCT TATGTCCTTCAGCAGGTAGGCTATTCCTCACGCTGCCTGCCTTCCAGTGTAGCATAATCAAGCA TCACCAGACCTACATAATGCACACCATCATAACACAAAGCAATCAGTGTAACACGATTTTTTTT CACGGTGAACATAATTCACAAAGCAATCAGTGTAACACGATTTTTTCATGGTGAACATTATTAA GAACCGTTGACAGCAAAGCACATTATTTTACAAACAGTTTGCCAGGACTGATTCACAGAAATAG CAAAAGTTCAAATCACTTGACAATCATCATCAACCCAGGGCAGACAAAGGCAAAGCTGATTAAA TGGAGCACAAGGTGGAAAATAGAATGCCTGGAAAAATGTAATGAATGCACCCACATCACCCCAG TACAGTCTCCTAAACATAACATAAGATCAATGCAAAGTTAAACAAAACATCATTCAGGATCTGG TTCATGTTCAGAAGAAACAATGAAAGGTCAAGTGTTTCTTTCTGCTGTTTGAGGCCTTCTTTTA AAGCAAAACGAAAAGGTAAAAATCTATAAAAGGAAGAAACAAGCAGCCTTTGGCATGTATTTCA AGGAAAATGGTATATCATGTATTTCAAGTCACGATAGTATTTAAAAATAAATGGAAAATAAAAA CTTGTGGTAACTTATGTCAGAAAACTCTATAGTTTACAATATTCAGAGTTGTTGGTCTAAGTGT CAAATGTAAAAGTGAAACATGGAAACTTCACATTTTGATACAGATCTGATCAACTCCATGTCCT CCGATAGACAAAAATGAGCAGTGACTGTGTTGCGTAAGTACATACTGCAGATAGTGCAAACCAC ATCACACATATATGGTATTCTTTTAAGAGGAAAATATGGTAATTTGACACGCTCACGTATTTGA GGAACTTACACTTGAAAAATCTCTACTACTTTAAAATTCCGTAGTGGTGGCGGTGACTCCAACC CTGGAAGACACGCGGAACATGAGCTGTTGGATCGCCATATCCAACGCTCCCAGTTATCAGTTAT CCCCATGTGCTTGTGCTTCCCCCCTCCGCCCGCAACCCAAACCCACGTCGCTCTCCCGATCCAA CCGCCTCCGTCCAACCGCCGCCGCCGCCGCCGCTCCATCCCCTCGTCGCGCCTCGCCGTCGCAC CACGATGCGCCGCCGCCGCTCCATCCCCTCCCGCTCCATCGCGCCGCAACGCCAGATTCATCGC CGCTCCCCTCCCTCTCGACCGTTTCTCTCGGCGCCATCTCCGCACATCCCCGCCAGCGCCGGAT CTCCCTTCTCGCCCTGTTTCCTTGCTGAAGCATTGTCGTGATATTCAGTTTGATCTGCTCGTCA TATCGCTGCCGCACAACTCGCCGAATACCAAGGCTCGTAAACAAGCGCCGCCGCTGCCGCCAAA TCCACCGAAACCAATCTACGCGGCCACCACACGATGGATGCATCACCGTCAATTCCGCCCTCGC CGACTCCGCCACAGCCGCCTACTCCACCGCCACTACAGTTGTCAACGACTCCGCCGCCGCCACT CCCGTCGTCGCCGGCTCCGCGACCGCCGTCCGTGCTGCCACCGCCCTTGCCGTCATCTTCGGCG CCAAGCATTGTCAGCACAGATATCGATCCGGTAAGTTAAGCACCTAGCTTAATTAGTCCATGAA AACTATCGATATATATGTGTGCGCTGTATTGCGATTTGGGTTACTTAGCTAGGTAATGTTAATG CATGGTACTGTAGATTAATGCAAGGCACTGTACGTTAATTAATTATTAATTGAAGCACCTAGCT AGCCATCCACTATTATATTATAAAATTATTACTTATAATATATCAATTGCATTAATATATACTC CTACACTAGCTTGTGCGCAGTTCTCAGGCTTGCTTCTTTACTTATATGAGGAACTCATCTCTCG CACTCGCAAAACTGAGGGACTCATTAACGCATGATTAATTAAATATTACTCCCTCCTTCCCAAA TTGATAATCATGTAATAGAATCCAAAATTTCTCAAATTGATCATCATATTACTGCATGGACACA GATTTCATCTAAATACAATTAATGCAGTATGAGAGAATGTGTGCATGCTATGATGTAATTGGCA TAGGGTTTTAATCGATGCATGCATTGTGGGAGAATACGTGCATGGTGTCTTGATTGATGTGATT TAAATTGTCCTTGGTCTTGGTACATAAACTTATATGATGATCAATTTGGGAAGGAGGGAGTAGT TTTTAATTAGAACAAATAGATTTTTATGGTTTTATACAATAACTCTAACAACATAACTCAGCAT AAAATCAACCTGGCCATCAGCTCATTTTACGAATATACAATACTCTGTGTGGCATGATTCACCA AGAAAAAAAATAATTGATAGCTATGATCGAGCAAAATAAAGCATTGTACCAACTAATGCTACAC TAATATTGACCTCCCTGCCGACGTGCTTTTTTCCAGTGTTATATATAATCTCCATGTGCAATAT AGATATCCTTGCTTAATCTCATGTGGTACTCAGGTCAATCAAGACGCCATTCGTGCTGATATGA TTACAACCTGACCCTCGAATAAAGCAAAAAATTCGGAATCCGAGGAGCATGGAAATTTTCAGTT TGAAATAAGTAGCACAGCCTGAAATTTCTTTAACTGGGAAGACCATTTGTACAGGTTTGGTTTC AATCGAAGCTACAGGTTTAATTTGGAAGATCATGCAGCCATGATGCTACAAATATTAATCTTGA TGGTTTAAATTAACCTATTTCATCTATACAACTTGATTCAGCTTAATTTAGTTCCTACATTAGT GCACAGTTATTCTTCATTTATTTGTGCGTACAGGATCTATGGAAGAGGGCCATTAGGTACTAAG AGACCTATTGTGCCATTATATTCATGAATTTTTTGGCTGTTTGTAACCTGTGAAAACTTATAAG GATGTGATGAAATTATTGTTCGTGCCATAATAAGGTTTTCATCATAATAAATTTAATTATTCAA CATCATTTTACTGTGATTTTAAATTGGTGTATATTTTTTACCCGTTGCAACGCACGGGCACCTA CCTAGTAAGGAATAAAAACAACATGGAATAGGGGAGCTGAACAATTACTTCATCAGATATTTAT TGTTGTGGCATGATTAATTGTGAAATGCACTATTTGAATGAGAAATCCCCATCCATATACATCA GGAAGCTAAACATCATTGAAAGACTATGACCGTGGATATACTATAAAAATTAAACAGAGGTCTA TTTGTCAAAATTGAATGACAATTCCAAAGAGGAAATTATATCATTGACTATCAGAATAATATGA CATGGCTAACTACATATTTGTAGTTTCCAAGGCCTCATGCTACTCACAATATTTAGCGTGCACT ACTGTCACAAATGTAACAAAAAACAATTGAATAGGCACTATCAGGCCAATTAAAATATGCCAAT ATGTGGCTATAGAATGATATATTACTGTATGAAACTATGAATAGCAATAAGACAGACTCACCTA GAGGATTCACCCAATAAATTTGTAGGTTCAAATCTTCCATCTTGTGTGAATAATCCATGTGCCT TTTGGTTTGTTGAATGTCCAAATGCATTAGTGTCATCAATACTGCGTAGTTTTGCTTCCAGAAG GTTGAGAGATGAGTCTAGTTTCACTATTTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.195541228

Conservation Information
Conserved circRNAs	NA
PMCS	0.195541228

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13622944-13619340(+)
13619343-13619346(-)
						
						Potential amino acid sequence
						
							MSLVSLFSCCSKRSNTDGHLFPCFSCQLPYVLQQVGYSSRCLPSSVA*(+)
MLHWKAGSVRNSLPAEGHKGADMKSMEKDGHLCWIFWSNRKIVKLDSSLNLLEAKLRSIDDTNA
FGHSTNQKAHGLFTQDGRFEPTNLLGESSRSGDA*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13622944-13619340(+) 13619343-13619346(-)
Potential amino acid sequence	MSLVSLFSCCSKRSNTDGHLFPCFSCQLPYVLQQVGYSSRCLPSSVA(+) MLHWKAGSVRNSLPAEGHKGADMKSMEKDGHLCWIFWSNRKIVKLDSSLNLLEAKLRSIDDTNA FGHSTNQKAHGLFTQDGRFEPTNLLGESSRSGDA(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0304000_circ_g.1

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