Plant Circular RNA Database

Detail information of Os09g0109800_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0109800_circ_g.3
					
						ID in PlantcircBase
						osa_circ_038398
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 885461-887410  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0109800						
					
						Parent gene annotation
						
							Similar to Na+/H+ antiporter, probable CP0838. (Os09t0109800-01)
;Similar to Na+/H+ antiporter, probable CP0838. (Os09t0109800-02
);Divalent ion symporter domain containing protein. (Os09t010980
0-03);Similar to Na+/H+ antiporter, probable CP0838. (Os09t01098
00-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0109800_circ_g.2 						
					
						Support reads
						1
					
						Tissues
						shoot, 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
						Os09t0109800-04:3
Os09t0109800-02:3
Os09t0109800-03:3
Os09t0109800-01:3

General Information
CircRNA Name	Os09g0109800_circ_g.3
ID in PlantcircBase	osa_circ_038398
Alias	NA
Organism	Oryza sativa
Position	chr9: 885461-887410 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0109800
Parent gene annotation	Similar to Na+/H+ antiporter, probable CP0838. (Os09t0109800-01) ;Similar to Na+/H+ antiporter, probable CP0838. (Os09t0109800-02 );Divalent ion symporter domain containing protein. (Os09t010980 0-03);Similar to Na+/H+ antiporter, probable CP0838. (Os09t01098 00-04)
Parent gene strand	+
Alternative splicing	Os09g0109800_circ_g.2
Support reads	1
Tissues	shoot, 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	Os09t0109800-04:3 Os09t0109800-02:3 Os09t0109800-03:3 Os09t0109800-01:3

			
						 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  
						
							GGGACTCTGGAAGGCAGAGATTGAAAGTTCCACAAGCGCTGTCACGGATTGATACACAAGGAGT
TCTATTTTTCTTAGGAATTCTTATGTCAGTTGGCAGattgttaggcgctgttgttgtgatatct
gcaaatgctgggggtgcatggacaccaattggtgatgtgacgaccactatgttgtggattcatg
gtcagatt

									
								

					

						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: 486
Transcript exons: 885461-885581,886958-887019,887108-887410
ATTGTTAGGCGCTGTTGTTGTGATATCTGCAAATGCTGGGGGTGCATGGACACCAATTGGTGAT
GTGACGACCACTATGTTGTGGATTCATGGTCAGATTACAACGTTGAACACAATGCAGGGCTTGT
TTCTTCCCTCAGTTGTTTCATTGGCAGTTCCACTGGCTCTGATGTCCCTCACGAGTGAAGCAAA
TGGATCTTCTCAGAAATCTTCCAGCTTGCTGTCATCAGAGCAGATGGCTCCTCGAGGACAACTT
GTATTTGCTGTTGGCCTTGGAGCCTTAGTGTTTGTTCCAGTGTTTAAAGCTCTCACTGGGCTGC
CACCTTTCATGGGCATGATGCTTGGTCTTGCAATTCTTTGGATCCTGACAGATGCGATACATTA
TGGGGACTCTGGAAGGCAGAGATTGAAAGTTCCACAAGCGCTGTCACGGATTGATACACAAGGA
GTTCTATTTTTCTTAGGAATTCTTATGTCAGTTGGCAG
						
					

						Genomic sequence
						
							ATTGTTAGGCGCTGTTGTTGTGATATCTGCAAATGCTGGGGGTGCATGGACACCAATTGGTGAT
GTGACGACCACTATGTTGTGGATTCATGGTCAGATTACAACGTTGAACACAATGCAGGTCAGCT
TTATAGTGTTTTATTATGTGTTTATATAATTGTTTCATGGCTGTGAGGCCTCTAAAACATACGT
CAAGTTTTTTGGATTATAATGTTGCATTATTCCCCTTAATTGGTACTGGATGTATCAACTAAGA
TTTGAGTACTCACATCTATGATTGATTTTATAAACATCCTACATATATGCATGTCCTTTTTTAT
TGGAAATGCATGACTTCCGCTACATTGAACTTTTTAATCTGGATGGCTAGAGGGCTGGACTTGT
GCGTTGCCTCTTAGGTGATGAGTGTATGTGTGTGTGTGTGTGTTCTATGGGGATGACAGTTTTG
ATCCTCTCGTTTATATTTTTTTTCCTCCTTCTTTCTTTTTAATGAAATGAAGTTTAGTCCTGTG
TTTTCAAGGAAAAAAACTACATTGAATTTTTTTATTGTATTATTTTGCAAATGCTATATATTAA
GTAAAACTACATAAAAATTCCTTAAAATTATTTTTGTTCAAATTGTGTATCATTAGTCAAATTA
TCAAAGAACACATTTTGGTTCACACTGCACCTTATCAGCTAAATTACCGAACAAATGCAGCTCA
AGTGTGATATTTTAGCAGTATTTCTCATGGTTCTAGCTATTTTTGTTGTTTTAATATTTGAGAA
CTTGTTTTGAACATTTGAATAATCCTTTCAGAAAGCTAAGGAATTTGGTAATCCCAGTACACAT
TTTTTTGTGAATATTTTAAAAAAATAGACAAACTGTGTGTGGCAGGTATTAAAAATTAAAATTC
ACCCAAATAATTATAATGCATGTTGAGATGATGGTTTCAAATGCTTGTTTAAGTAATCTGTATT
GCCAACCTCTTTTACATATTCTGTTCTTTTTATAATATACTCCGTCTGTATAAAAATGTACGGG
TTATTTCTTCAAGGCTTCTGTAAAAGGAATGTAGGGCGCACACATTTTTCAAAGCACCTTTTAT
GTGTTGTTACCCTTAATACCCCTATTTTTTTATAGGCTATAAATGCATGCAACTAGAGTAGTAC
TACATTAGTTATGGGTATTTTAGTAAAAACAAACAGGTTTCCTTGGTGTAAGAGCCTGCAAACT
ATATGCCTTTATATACATTTTTAAATGGAGGAAGTATATATATCACGCAGTAGGCCTGTAGGAG
TATCTCCTGCTGACTTTTGTAAAAAAAAAAGTGAGGTAGCTTAAATAAGTATTGAAATCAAGTA
CCATGAGAATTGTGGCAAATTAGGTCATTGGGTCTGTATTTGCACGGTAACTTATTGGTAATTT
TTGTTTTTCATCCTGTTTCTGCCTACCACGTCATCAAAACACTACTTATTTGGATCGTGAAATG
AATTGGTTGGGTTATGATCTGGCAGGGCTTGTTTCTTCCCTCAGTTGTTTCATTGGCAGTTCCA
CTGGCTCTGATGTCCCTCACGAGGTTGTTAACCAATCACTACTAATAGATAGCATGAAAAGAGT
ATTTCTGTTGCCTCATCTAACATTTACTTTATATATGTTGGAATCAGTGAAGCAAATGGATCTT
CTCAGAAATCTTCCAGCTTGCTGTCATCAGAGCAGATGGCTCCTCGAGGACAACTTGTATTTGC
TGTTGGCCTTGGAGCCTTAGTGTTTGTTCCAGTGTTTAAAGCTCTCACTGGGCTGCCACCTTTC
ATGGGCATGATGCTTGGTCTTGCAATTCTTTGGATCCTGACAGATGCGATACATTATGGGGACT
CTGGAAGGCAGAGATTGAAAGTTCCACAAGCGCTGTCACGGATTGATACACAAGGAGTTCTATT
TTTCTTAGGAATTCTTATGTCAGTTGGCAG
						
					

			
		

Sequences
Splice junction sequence	GGGACTCTGGAAGGCAGAGATTGAAAGTTCCACAAGCGCTGTCACGGATTGATACACAAGGAGT TCTATTTTTCTTAGGAATTCTTATGTCAGTTGGCAGattgttaggcgctgttgttgtgatatct gcaaatgctgggggtgcatggacaccaattggtgatgtgacgaccactatgttgtggattcatg gtcagatt
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: 486 Transcript exons: 885461-885581,886958-887019,887108-887410 ATTGTTAGGCGCTGTTGTTGTGATATCTGCAAATGCTGGGGGTGCATGGACACCAATTGGTGAT GTGACGACCACTATGTTGTGGATTCATGGTCAGATTACAACGTTGAACACAATGCAGGGCTTGT TTCTTCCCTCAGTTGTTTCATTGGCAGTTCCACTGGCTCTGATGTCCCTCACGAGTGAAGCAAA TGGATCTTCTCAGAAATCTTCCAGCTTGCTGTCATCAGAGCAGATGGCTCCTCGAGGACAACTT GTATTTGCTGTTGGCCTTGGAGCCTTAGTGTTTGTTCCAGTGTTTAAAGCTCTCACTGGGCTGC CACCTTTCATGGGCATGATGCTTGGTCTTGCAATTCTTTGGATCCTGACAGATGCGATACATTA TGGGGACTCTGGAAGGCAGAGATTGAAAGTTCCACAAGCGCTGTCACGGATTGATACACAAGGA GTTCTATTTTTCTTAGGAATTCTTATGTCAGTTGGCAG
Genomic sequence	ATTGTTAGGCGCTGTTGTTGTGATATCTGCAAATGCTGGGGGTGCATGGACACCAATTGGTGAT GTGACGACCACTATGTTGTGGATTCATGGTCAGATTACAACGTTGAACACAATGCAGGTCAGCT TTATAGTGTTTTATTATGTGTTTATATAATTGTTTCATGGCTGTGAGGCCTCTAAAACATACGT CAAGTTTTTTGGATTATAATGTTGCATTATTCCCCTTAATTGGTACTGGATGTATCAACTAAGA TTTGAGTACTCACATCTATGATTGATTTTATAAACATCCTACATATATGCATGTCCTTTTTTAT TGGAAATGCATGACTTCCGCTACATTGAACTTTTTAATCTGGATGGCTAGAGGGCTGGACTTGT GCGTTGCCTCTTAGGTGATGAGTGTATGTGTGTGTGTGTGTGTTCTATGGGGATGACAGTTTTG ATCCTCTCGTTTATATTTTTTTTCCTCCTTCTTTCTTTTTAATGAAATGAAGTTTAGTCCTGTG TTTTCAAGGAAAAAAACTACATTGAATTTTTTTATTGTATTATTTTGCAAATGCTATATATTAA GTAAAACTACATAAAAATTCCTTAAAATTATTTTTGTTCAAATTGTGTATCATTAGTCAAATTA TCAAAGAACACATTTTGGTTCACACTGCACCTTATCAGCTAAATTACCGAACAAATGCAGCTCA AGTGTGATATTTTAGCAGTATTTCTCATGGTTCTAGCTATTTTTGTTGTTTTAATATTTGAGAA CTTGTTTTGAACATTTGAATAATCCTTTCAGAAAGCTAAGGAATTTGGTAATCCCAGTACACAT TTTTTTGTGAATATTTTAAAAAAATAGACAAACTGTGTGTGGCAGGTATTAAAAATTAAAATTC ACCCAAATAATTATAATGCATGTTGAGATGATGGTTTCAAATGCTTGTTTAAGTAATCTGTATT GCCAACCTCTTTTACATATTCTGTTCTTTTTATAATATACTCCGTCTGTATAAAAATGTACGGG TTATTTCTTCAAGGCTTCTGTAAAAGGAATGTAGGGCGCACACATTTTTCAAAGCACCTTTTAT GTGTTGTTACCCTTAATACCCCTATTTTTTTATAGGCTATAAATGCATGCAACTAGAGTAGTAC TACATTAGTTATGGGTATTTTAGTAAAAACAAACAGGTTTCCTTGGTGTAAGAGCCTGCAAACT ATATGCCTTTATATACATTTTTAAATGGAGGAAGTATATATATCACGCAGTAGGCCTGTAGGAG TATCTCCTGCTGACTTTTGTAAAAAAAAAAGTGAGGTAGCTTAAATAAGTATTGAAATCAAGTA CCATGAGAATTGTGGCAAATTAGGTCATTGGGTCTGTATTTGCACGGTAACTTATTGGTAATTT TTGTTTTTCATCCTGTTTCTGCCTACCACGTCATCAAAACACTACTTATTTGGATCGTGAAATG AATTGGTTGGGTTATGATCTGGCAGGGCTTGTTTCTTCCCTCAGTTGTTTCATTGGCAGTTCCA CTGGCTCTGATGTCCCTCACGAGGTTGTTAACCAATCACTACTAATAGATAGCATGAAAAGAGT ATTTCTGTTGCCTCATCTAACATTTACTTTATATATGTTGGAATCAGTGAAGCAAATGGATCTT CTCAGAAATCTTCCAGCTTGCTGTCATCAGAGCAGATGGCTCCTCGAGGACAACTTGTATTTGC TGTTGGCCTTGGAGCCTTAGTGTTTGTTCCAGTGTTTAAAGCTCTCACTGGGCTGCCACCTTTC ATGGGCATGATGCTTGGTCTTGCAATTCTTTGGATCCTGACAGATGCGATACATTATGGGGACT CTGGAAGGCAGAGATTGAAAGTTCCACAAGCGCTGTCACGGATTGATACACAAGGAGTTCTATT TTTCTTAGGAATTCTTATGTCAGTTGGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_018883 						
					
						PMCS
						0.281233859

Conservation Information
Conserved circRNAs	osi_circ_018883
PMCS	0.281233859

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							885538-887407(+)
885509-887397(-)
						
						Potential amino acid sequence
						
							MLWIHGQITTLNTMQGLFLPSVVSLAVPLALMSLTSEANGSSQKSSSLLSSEQMAPRGQLVFAV
GLGALVFVPVFKALTGLPPFMGMMLGLAILWILTDAIHYGDSGRQRLKVPQALSRIDTQGVLFF
LGILMSVGRLLGAVVVISANAGGAWTPIGDVTTTMLWIHGQITTLNTMQGLFLPSVVSLAVPLA
LMSLTSEANGSSQKSSSLLSSEQMAPRGQLVFAVGLGALVFVPVFKALTGLPPFMGMMLGLAIL
WILTDAIHYGDSGRQRLKVPQALSRIDTQGVLFFLGILMSVGRLLGAVVVISANAGGAWTPIGD
VTTTMLWIHGQITTLNTMQGLFLPSVVSLAVPLALMSLTSEANGSSQKSSSLLSSEQMAPRGQL
VFAVGLGALVFVPVFKALTGLPPFMGMMLGLAILWILTDAIHYGDSGRQRLKVPQALSRIDTQG
VLFFLGILMSVGRLLGAVVVISANAGGAWTPIGDVTTTMLWIHGQITTLNTMQGLFLPSVVSLA
VPLALMSLTSEANGSSQKSSSLLSSEQMAPRGQLVFAVGLGALVFVPVFKALTGLPPFMGMMLG
LAILWILTDAIHYGDSGRQRLKVPQALSRIDTQGVLFFLGILMSVG(+)
MHPQHLQISQQQRLTICQLT*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	885538-887407(+) 885509-887397(-)
Potential amino acid sequence	MLWIHGQITTLNTMQGLFLPSVVSLAVPLALMSLTSEANGSSQKSSSLLSSEQMAPRGQLVFAV GLGALVFVPVFKALTGLPPFMGMMLGLAILWILTDAIHYGDSGRQRLKVPQALSRIDTQGVLFF LGILMSVGRLLGAVVVISANAGGAWTPIGDVTTTMLWIHGQITTLNTMQGLFLPSVVSLAVPLA LMSLTSEANGSSQKSSSLLSSEQMAPRGQLVFAVGLGALVFVPVFKALTGLPPFMGMMLGLAIL WILTDAIHYGDSGRQRLKVPQALSRIDTQGVLFFLGILMSVGRLLGAVVVISANAGGAWTPIGD VTTTMLWIHGQITTLNTMQGLFLPSVVSLAVPLALMSLTSEANGSSQKSSSLLSSEQMAPRGQL VFAVGLGALVFVPVFKALTGLPPFMGMMLGLAILWILTDAIHYGDSGRQRLKVPQALSRIDTQG VLFFLGILMSVGRLLGAVVVISANAGGAWTPIGDVTTTMLWIHGQITTLNTMQGLFLPSVVSLA VPLALMSLTSEANGSSQKSSSLLSSEQMAPRGQLVFAVGLGALVFVPVFKALTGLPPFMGMMLG LAILWILTDAIHYGDSGRQRLKVPQALSRIDTQGVLFFLGILMSVG(+) MHPQHLQISQQQRLTICQLT*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0109800_circ_g.3

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