Plant Circular RNA Database

Detail information of Os04g0509300_circ_g.9

			
						 General Information
					
						CircRNA Name
						Os04g0509300_circ_g.9
					
						ID in PlantcircBase
						osa_circ_024541
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 25484643-25487940  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0509300						
					
						Parent gene annotation
						
							Rnase III family protein, Shoot apical meristem (SAM) formation 
and maintenance (Os04t0509300-01);Rnase III family protein, Tran
s-acting siRNA3 (ta-siRNA)(TAS3) biogenesis (Os04t0509300-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0509300_circ_g.7 Os04g0509300_circ_g.8 Os04g0509300_circ_g.10 						
					
						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
						Os04t0509300-01:7
Os04t0509300-02:8

General Information
CircRNA Name	Os04g0509300_circ_g.9
ID in PlantcircBase	osa_circ_024541
Alias	NA
Organism	Oryza sativa
Position	chr4: 25484643-25487940 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0509300
Parent gene annotation	Rnase III family protein, Shoot apical meristem (SAM) formation and maintenance (Os04t0509300-01);Rnase III family protein, Tran s-acting siRNA3 (ta-siRNA)(TAS3) biogenesis (Os04t0509300-02)
Parent gene strand	-
Alternative splicing	Os04g0509300_circ_g.7 Os04g0509300_circ_g.8 Os04g0509300_circ_g.10
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	Os04t0509300-01:7 Os04t0509300-02:8

			
						 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  
						
							ATAAATCAGCAGCACGGCAATGTGCGTCTTACCGCATCCTGTCCCAAGGTACACTATGATGTTC
TCCTCCACAGCCCTCTTGCAGAGATCCAATTGATACttgcagagctccgaaagaaccaagttct
tgcaaacagaaaataatattttcatgcaacctccataaggacttcagtttcttctgagaatcct
tgaaatcg

									
								

					

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					

						Genomic sequence
						
							TTGCAGAGCTCCGAAAGAACCAAGTTCTTGCAAACAGAAAATAATATTTTCATGCAACCTCCAT
AAGGACTTCAGTTTCTTCTGAGAATCCTTGAAATCGCATAGGCTCGCTCTTAGCATGCGCTCGC
TCTGTATTAAGCCCAATAAAAATAATGAGAAGGGAAAAAAGGAAACAGAACACATAAGGTTTTG
TCAATTGGAGTAATGACAATTTCAGCATAATGGTGGAACAAAACTTTACCTGAAGCTTTAAGCT
ATCAAGCTCTTTGATGCATATTGTGGTAAGGTTAGAGTGATTAACTGGGCCATAAAAGTACACC
TCCATATCAGGAGATGCAACCACACTTTCAAGTTCTTCATTATCAACTGAACAAACCTATCCAA
CATGAGAGTGAAAAGTTTTACAGAGAAGAATATCACTGAGTAATTTCCCCCAATCCCTAGAAAT
CTTGCCATGAGCACCAGCAATATGTACCTTTGCATGAAGTAATTCCTCAAGACTGTTGATACAT
TTCGTGTAGTTAAGTTTATTAGACCCACCTGCCATATAAAACATATGTACATTAATCGACCAGA
CATGCTTAATATAAAAGATAATCGAAGCAACCAAAAATAATTTTAGGGTAAGACTACTTCTATT
CTTAGCGGTCCAAAAGGCAAGGCTGAAAAAGAGAAAAACCCCAAAATTAACTCTAAAATTAAGT
TCTAAAAGGAATTCAACGGGCCAACCTAATTTATTAAGATTGGAGCAGAAGAAAACTCAAAGGT
GCTCAACAACAGGGTTGTTGAAGGTACATATGCTACAATTACAACCGCAGGCAGGCGACCACAC
ATTTAGCACTAGGTAGCCACAGAACAACAGAAAGCTCTACACTCCAGCATCAGGAGGGTCAAGG
AACTTCTAGAATTCAAATGCTGGCTGAGGCTTATAAACCAACGCGCAGCTAATATTTCAAAGTG
TTACATAAGTTACTCCAGCAAACATTTTTTTGAGCCCTGACCATAACATTTTAGCATTAAATTT
CAAAAGATATCTCAGGTAATCATGTTTTAACTTATAATGTACTAATGGTGTAAATCACAAACAT
TTGTTCATAACTCATCCAGCTTTGACCTTTTGGAAGAAAAAATATTAGAGGCTGACAAGGAGAC
CTTCCTCCTTTTTCTGTAAAGCTGTGTGAAGGCATGACACCTGGGATGGTGAAGATGGTTACAG
AAGCACCCACGCAAACATGACATGCACATGAGTTGAATACTCAATATATGCAGAATTTCAATGC
GTAAAGCAAAACTTCAGTGCGTCAAGAATTTATTTTATGTGTTTTTGGTCCAATTTTCCTCTTT
GCTTTGGTACTATGAGGCTTCAAGTGCAATTTCTGACCAACTGTAGTGGAGCAGAGACATTTTA
TATTTGAGCACATTTCCGTTCGGTTTTTAGAACTAGGAGTTGATATAATGATAAATACTCTTTG
ATCCCAATTTCTTGTTCAATTATGAGTTTCAGAAAACCTTTGGTGTTTCTCTTCCAATGGATCA
TATTTTTTTTCAACCACTGACAACATAAAGATTTAAGGATTTAAAATGATCCCAAAAAATTTAG
TGGCATTTACCCTGTGTTGTAAATTTAAAAGCATACCAAGAAATAGAATAGTATCCAAGAATTG
ATTGTATGTAATGAGGCAAGGTTATGTCCTAACTCTTAGATAAATAAAGAAGATAATATACGTC
AGGAGCATATTGACTGTACAAAATGCATTACAGAAGAAAAGTGGTATGCAGTACTGGTAGAAAG
AATCATTACCTTTCCCAATAATTGGTGAAGCAGTCATGCCAAAAACCCGAGGGAATTTCTCAAC
ACTGTTACTATTATAGAATTCCTGAAACATTGTCATAAATATTTTTAATCCAGAAAAATTGCAG
TTCATTGAATTAACTACAGGTACTATTTAATATAAGAAGCTGTCCTACAATCCTATAGGTTTAC
TTATGTATGAACAATTTGCTCACCTATTGATACAACAGGAGCAACAAGCAACTGGACCCAAAAG
CCTACTCCTACCATGTGGATATAGTTTATAAGAAACAATTTAAATGAAAAGAGTATCAATGATG
TACTGCAGCATGAGGTTTAATGGGTTAAAAACTAAACAACTAAGTATTCCAATAGATGTAGATT
ACCAAGAATTCAAAAGTTGTAATAAAGCAAGAAAATCATGAACTTGCCTTCATAATTTGCGCAT
ATGGATGCCGTTTTTGCGGTTGTGCATGATGGCACTCATCAAGTATCAGAAGTGCAATTGAGTT
CATCTTGATGAAGCAATGACGCAAACTTTGCAATAATATTTGGGGAGTCATTACAAGGACCTGA
CGTGGCAGAGGAAGTACAAAAGTTACGCAAAGAACTAATGTACAGAGTAGAAGAAAAGATGAAT
TCAAATGGATTATATTTGAAAAAAATGAATACAATAATGATATATGTGCTGTCTACATGTTCTC
GGAGTCAGACCTCTAGTTTCAGAATAAATTAGGCAGGATTAAGCAGGACCTTTTAGCTGAAGAT
TCTTCTCCATCGTGTGCATCTTAAATTAGTTTATGATAAGTCAACTAGTTATCTACAAAGCTTC
TCTTTCGTTTACAAATACTTTTCATGCTGGAATAATAATTTGACTGGTCTGCAGAGGTAATGTA
CTGCAAAGTGTACCTCAAACTCCCTCATGTCGTTCTCCCATTCCTGATGATCTCTCGAGTTTTT
ACCATTCCCATAATAACATTGAACTTTGAAATCGGTGGAACTTGCGATCACCACAGCTTGCTGT
ATAATATAATAAAGAATACTTACTTTTTTAGTGAGCAAGAGCACAGATTAACCATGGTTTTTCT
TTTTTGATAATACACTGATTAACCATGTAAAGTTTTATTTGATTCTGAAAGGTGGAGCTATAAC
CATTCATAAGCAAATTGAGATGCACACTTCTAGTGAGAAATTAAGAACCCATGTTCCCAATTCA
AATCGGTTACCCTGACATATTGCAAATTGGAAACTTAATGGTAACAAATGATTGGGAGCAGCTG
CAAGTTGATGTAAACCTACAGTGCGGACCAGGAAAGGAGGATATCTACCTGGCGTACAAGGGGG
ATGGTTGGGGCAAGGAAGATGCAGACCTCGCGGCTTGGCTTGCGGATGAGATGACCAAGCTCAT
AAATCAGCAGCACGGCAATGTGCGTCTTACCGCATCCTGTCCCAAGGTACACTATGATGTTCTC
CTCCACAGCCCTCTTGCAGAGATCCAATTGATAC
						
					

			
		

Sequences
Splice junction sequence	ATAAATCAGCAGCACGGCAATGTGCGTCTTACCGCATCCTGTCCCAAGGTACACTATGATGTTC TCCTCCACAGCCCTCTTGCAGAGATCCAATTGATACttgcagagctccgaaagaaccaagttct tgcaaacagaaaataatattttcatgcaacctccataaggacttcagtttcttctgagaatcct tgaaatcg
Assembled circRNA sequence	NA 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	NA
Genomic sequence	TTGCAGAGCTCCGAAAGAACCAAGTTCTTGCAAACAGAAAATAATATTTTCATGCAACCTCCAT AAGGACTTCAGTTTCTTCTGAGAATCCTTGAAATCGCATAGGCTCGCTCTTAGCATGCGCTCGC TCTGTATTAAGCCCAATAAAAATAATGAGAAGGGAAAAAAGGAAACAGAACACATAAGGTTTTG TCAATTGGAGTAATGACAATTTCAGCATAATGGTGGAACAAAACTTTACCTGAAGCTTTAAGCT ATCAAGCTCTTTGATGCATATTGTGGTAAGGTTAGAGTGATTAACTGGGCCATAAAAGTACACC TCCATATCAGGAGATGCAACCACACTTTCAAGTTCTTCATTATCAACTGAACAAACCTATCCAA CATGAGAGTGAAAAGTTTTACAGAGAAGAATATCACTGAGTAATTTCCCCCAATCCCTAGAAAT CTTGCCATGAGCACCAGCAATATGTACCTTTGCATGAAGTAATTCCTCAAGACTGTTGATACAT TTCGTGTAGTTAAGTTTATTAGACCCACCTGCCATATAAAACATATGTACATTAATCGACCAGA CATGCTTAATATAAAAGATAATCGAAGCAACCAAAAATAATTTTAGGGTAAGACTACTTCTATT CTTAGCGGTCCAAAAGGCAAGGCTGAAAAAGAGAAAAACCCCAAAATTAACTCTAAAATTAAGT TCTAAAAGGAATTCAACGGGCCAACCTAATTTATTAAGATTGGAGCAGAAGAAAACTCAAAGGT GCTCAACAACAGGGTTGTTGAAGGTACATATGCTACAATTACAACCGCAGGCAGGCGACCACAC ATTTAGCACTAGGTAGCCACAGAACAACAGAAAGCTCTACACTCCAGCATCAGGAGGGTCAAGG AACTTCTAGAATTCAAATGCTGGCTGAGGCTTATAAACCAACGCGCAGCTAATATTTCAAAGTG TTACATAAGTTACTCCAGCAAACATTTTTTTGAGCCCTGACCATAACATTTTAGCATTAAATTT CAAAAGATATCTCAGGTAATCATGTTTTAACTTATAATGTACTAATGGTGTAAATCACAAACAT TTGTTCATAACTCATCCAGCTTTGACCTTTTGGAAGAAAAAATATTAGAGGCTGACAAGGAGAC CTTCCTCCTTTTTCTGTAAAGCTGTGTGAAGGCATGACACCTGGGATGGTGAAGATGGTTACAG AAGCACCCACGCAAACATGACATGCACATGAGTTGAATACTCAATATATGCAGAATTTCAATGC GTAAAGCAAAACTTCAGTGCGTCAAGAATTTATTTTATGTGTTTTTGGTCCAATTTTCCTCTTT GCTTTGGTACTATGAGGCTTCAAGTGCAATTTCTGACCAACTGTAGTGGAGCAGAGACATTTTA TATTTGAGCACATTTCCGTTCGGTTTTTAGAACTAGGAGTTGATATAATGATAAATACTCTTTG ATCCCAATTTCTTGTTCAATTATGAGTTTCAGAAAACCTTTGGTGTTTCTCTTCCAATGGATCA TATTTTTTTTCAACCACTGACAACATAAAGATTTAAGGATTTAAAATGATCCCAAAAAATTTAG TGGCATTTACCCTGTGTTGTAAATTTAAAAGCATACCAAGAAATAGAATAGTATCCAAGAATTG ATTGTATGTAATGAGGCAAGGTTATGTCCTAACTCTTAGATAAATAAAGAAGATAATATACGTC AGGAGCATATTGACTGTACAAAATGCATTACAGAAGAAAAGTGGTATGCAGTACTGGTAGAAAG AATCATTACCTTTCCCAATAATTGGTGAAGCAGTCATGCCAAAAACCCGAGGGAATTTCTCAAC ACTGTTACTATTATAGAATTCCTGAAACATTGTCATAAATATTTTTAATCCAGAAAAATTGCAG TTCATTGAATTAACTACAGGTACTATTTAATATAAGAAGCTGTCCTACAATCCTATAGGTTTAC TTATGTATGAACAATTTGCTCACCTATTGATACAACAGGAGCAACAAGCAACTGGACCCAAAAG CCTACTCCTACCATGTGGATATAGTTTATAAGAAACAATTTAAATGAAAAGAGTATCAATGATG TACTGCAGCATGAGGTTTAATGGGTTAAAAACTAAACAACTAAGTATTCCAATAGATGTAGATT ACCAAGAATTCAAAAGTTGTAATAAAGCAAGAAAATCATGAACTTGCCTTCATAATTTGCGCAT ATGGATGCCGTTTTTGCGGTTGTGCATGATGGCACTCATCAAGTATCAGAAGTGCAATTGAGTT CATCTTGATGAAGCAATGACGCAAACTTTGCAATAATATTTGGGGAGTCATTACAAGGACCTGA CGTGGCAGAGGAAGTACAAAAGTTACGCAAAGAACTAATGTACAGAGTAGAAGAAAAGATGAAT TCAAATGGATTATATTTGAAAAAAATGAATACAATAATGATATATGTGCTGTCTACATGTTCTC GGAGTCAGACCTCTAGTTTCAGAATAAATTAGGCAGGATTAAGCAGGACCTTTTAGCTGAAGAT TCTTCTCCATCGTGTGCATCTTAAATTAGTTTATGATAAGTCAACTAGTTATCTACAAAGCTTC TCTTTCGTTTACAAATACTTTTCATGCTGGAATAATAATTTGACTGGTCTGCAGAGGTAATGTA CTGCAAAGTGTACCTCAAACTCCCTCATGTCGTTCTCCCATTCCTGATGATCTCTCGAGTTTTT ACCATTCCCATAATAACATTGAACTTTGAAATCGGTGGAACTTGCGATCACCACAGCTTGCTGT ATAATATAATAAAGAATACTTACTTTTTTAGTGAGCAAGAGCACAGATTAACCATGGTTTTTCT TTTTTGATAATACACTGATTAACCATGTAAAGTTTTATTTGATTCTGAAAGGTGGAGCTATAAC CATTCATAAGCAAATTGAGATGCACACTTCTAGTGAGAAATTAAGAACCCATGTTCCCAATTCA AATCGGTTACCCTGACATATTGCAAATTGGAAACTTAATGGTAACAAATGATTGGGAGCAGCTG CAAGTTGATGTAAACCTACAGTGCGGACCAGGAAAGGAGGATATCTACCTGGCGTACAAGGGGG ATGGTTGGGGCAAGGAAGATGCAGACCTCGCGGCTTGGCTTGCGGATGAGATGACCAAGCTCAT AAATCAGCAGCACGGCAATGTGCGTCTTACCGCATCCTGTCCCAAGGTACACTATGATGTTCTC CTCCACAGCCCTCTTGCAGAGATCCAATTGATAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.102776832

Conservation Information
Conserved circRNAs	NA
PMCS	0.102776832

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							25487378-25484683(+)
25487360-25487871(-)
25484697-25487871(-)
						
						Potential amino acid sequence
						
							MISRVFTIPIITLNFEIGGTCDHHSLLAYKGDGWGKEDADLAAWLADEMTKLINQQHGNVRLTA
SCPKVHYDVLLHSPLAEIQLILAELRKNQVLANRK*(+)
MREFEVLVMTPQILLQSLRHCFIKMNSIALLILDECHHAQPQKRHPYAQIMKEFYNSNSVEKFP
RVFGMTASPIIGKGGSNKLNYTKCINSLEELLHAKVCSVDNEELESVVASPDMEVYFYGPVNHS
NLTTICIKELDSLKLQSERMLRASLCDFKDSQKKLKSLWRLHENIIFCLQELGSFGALQVSIGS
LQEGCGGEHHSVPWDRMR*(-)
MKILFSVCKNLVLSELCKYQLDLCKRAVEENIIVYLGTGCGKTHIAVLLIYELGHLIRKPSREV
CIFLAPTIPLVRQQAVVIASSTDFKVQCYYGNGKNSRDHQEWENDMREFEVLVMTPQILLQSLR
HCFIKMNSIALLILDECHHAQPQKRHPYAQIMKEFYNSNSVEKFPRVFGMTASPIIGKGGSNKL
NYTKCINSLEELLHAKVCSVDNEELESVVASPDMEVYFYGPVNHSNLTTICIKELDSLKLQSER
MLRASLCDFKDSQKKLKSLWRLHENIIFCLQELGSFGALQVSIGSLQEGCGGEHHSVPWDRMR*
(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	25487378-25484683(+) 25487360-25487871(-) 25484697-25487871(-)
Potential amino acid sequence	MISRVFTIPIITLNFEIGGTCDHHSLLAYKGDGWGKEDADLAAWLADEMTKLINQQHGNVRLTA SCPKVHYDVLLHSPLAEIQLILAELRKNQVLANRK(+) MREFEVLVMTPQILLQSLRHCFIKMNSIALLILDECHHAQPQKRHPYAQIMKEFYNSNSVEKFP RVFGMTASPIIGKGGSNKLNYTKCINSLEELLHAKVCSVDNEELESVVASPDMEVYFYGPVNHS NLTTICIKELDSLKLQSERMLRASLCDFKDSQKKLKSLWRLHENIIFCLQELGSFGALQVSIGS LQEGCGGEHHSVPWDRMR(-) MKILFSVCKNLVLSELCKYQLDLCKRAVEENIIVYLGTGCGKTHIAVLLIYELGHLIRKPSREV CIFLAPTIPLVRQQAVVIASSTDFKVQCYYGNGKNSRDHQEWENDMREFEVLVMTPQILLQSLR HCFIKMNSIALLILDECHHAQPQKRHPYAQIMKEFYNSNSVEKFPRVFGMTASPIIGKGGSNKL NYTKCINSLEELLHAKVCSVDNEELESVVASPDMEVYFYGPVNHSNLTTICIKELDSLKLQSER MLRASLCDFKDSQKKLKSLWRLHENIIFCLQELGSFGALQVSIGSLQEGCGGEHHSVPWDRMR* (-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0509300_circ_g.9

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