Plant Circular RNA Database

Detail information of Os03g0628800_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os03g0628800_circ_g.4
					
						ID in PlantcircBase
						osa_circ_020718
					
						Alias
						Os_ciR497
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 23994120-23994619  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os03g0628800						
					
						Parent gene annotation
						
							Similar to H1flk (Fragment). (Os03t0628800-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0628800_circ_g.1 Os03g0628800_circ_g.2 Os03g0628800_circ_g.3 						
					
						Support reads
						78/24/32
					
						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  
						
							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
						Os03t0628800-01:2

General Information
CircRNA Name	Os03g0628800_circ_g.4
ID in PlantcircBase	osa_circ_020718
Alias	Os_ciR497
Organism	Oryza sativa
Position	chr3: 23994120-23994619 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circseq_cup, find_circ
Parent gene	Os03g0628800
Parent gene annotation	Similar to H1flk (Fragment). (Os03t0628800-01)
Parent gene strand	+
Alternative splicing	Os03g0628800_circ_g.1 Os03g0628800_circ_g.2 Os03g0628800_circ_g.3
Support reads	78/24/32
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	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	Os03t0628800-01:2

			
						 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  
						
							GGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATG
GGCCACCACAACGACATGCTCCAGACTGCTGAGCTGgaagcagaggtttgagcgggtgacgagg
gacctgaaggtgacgagggtgttctcgacgctggtggaggagatgaaggcgatcggcgtcccga
cggcggcg

									
								

					

						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: 146
Transcript exons: 23994120-23994234,23994589-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCCCACAACGACATG
CTCCAGACTGCTGAGCTG
Transcript length: 146
Transcript exons: 23994120-23994237,23994592-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGCAACGACATG
CTCCAGACTGCTGAGCTG
Transcript length: 156
Transcript exons: 23994120-23994157,23994502-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGCAAGGACGAGGCGAATGCGGTGGTGG
TTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATGGGCCACCA
CAACGACATGCTCCAGACTGCTGAGCTG
Transcript length: 187
Transcript exons: 23994120-23994229,23994543-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGTCAAGGAGACGGACGTGA
TCTACCGTGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG
Transcript length: 190
Transcript exons: 23994120-23994190,23994501-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGACCAAGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACG
TGATCTACCGTGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG
Transcript length: 229
Transcript exons: 23994120-23994229,23994501-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGCCAAGGACGAGGCGAATG
CGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCAT
GGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG
Transcript length: 289
Transcript exons: 23994120-23994287,23994499-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGGAGGAGCCGC
ACTGCACCGACGTGATGGCGCCGGTGGCGCACGACGAGCGGTCCAAGGACGAGGCGAATGCGGT
GGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATGGGC
CACCACAACGACATGCTCCAGACTGCTGAGCTG
Transcript length: 373
Transcript exons: 23994120-23994362,23994490-23994619
GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGGAGGAGCCGC
ACTGCACCGACGTGATGGCGCCGGTGGCGCACGACGAGCGGAGCCCCGTGCTGCTGCTCATGGG
CGGTGGGATGGGCGCCGGCAAGAGCACCGTGCTCAAGGAGATTCTCCAGGAGCCACTGTGGTCC
AAGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACC
GTGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG
						
					

						Genomic sequence
						
							GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG
GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGGAGGAGCCGC
ACTGCACCGACGTGATGGCGCCGGTGGCGCACGACGAGCGGAGCCCCGTGCTGCTGCTCATGGG
CGGTGGGATGGGCGCCGGCAAGAGCACCGTGCTCAAGGAGATTCTCCAGGAGTAAGCAAATTAA
GCTAGCGAGAGAGCTCTGTTTTTTTAAAAAAAATTATTTGCACAGCATTTAAATTGCATAGGTT
ATAATTGAATAATTTGAAACGATTTTAAATATAAATTCTATAATGTTCAGGCCACTGTGGTCCA
AGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCG
TGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG
						
					

			
		

Sequences
Splice junction sequence	GGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATG GGCCACCACAACGACATGCTCCAGACTGCTGAGCTGgaagcagaggtttgagcgggtgacgagg gacctgaaggtgacgagggtgttctcgacgctggtggaggagatgaaggcgatcggcgtcccga cggcggcg
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: 146 Transcript exons: 23994120-23994234,23994589-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCCCACAACGACATG CTCCAGACTGCTGAGCTG Transcript length: 146 Transcript exons: 23994120-23994237,23994592-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGCAACGACATG CTCCAGACTGCTGAGCTG Transcript length: 156 Transcript exons: 23994120-23994157,23994502-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGCAAGGACGAGGCGAATGCGGTGGTGG TTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATGGGCCACCA CAACGACATGCTCCAGACTGCTGAGCTG Transcript length: 187 Transcript exons: 23994120-23994229,23994543-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGTCAAGGAGACGGACGTGA TCTACCGTGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG Transcript length: 190 Transcript exons: 23994120-23994190,23994501-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGACCAAGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACG TGATCTACCGTGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG Transcript length: 229 Transcript exons: 23994120-23994229,23994501-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGCCAAGGACGAGGCGAATG CGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCAT GGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG Transcript length: 289 Transcript exons: 23994120-23994287,23994499-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGGAGGAGCCGC ACTGCACCGACGTGATGGCGCCGGTGGCGCACGACGAGCGGTCCAAGGACGAGGCGAATGCGGT GGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCGTGCCATTAGCTCCATGGGC CACCACAACGACATGCTCCAGACTGCTGAGCTG Transcript length: 373 Transcript exons: 23994120-23994362,23994490-23994619 GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGGAGGAGCCGC ACTGCACCGACGTGATGGCGCCGGTGGCGCACGACGAGCGGAGCCCCGTGCTGCTGCTCATGGG CGGTGGGATGGGCGCCGGCAAGAGCACCGTGCTCAAGGAGATTCTCCAGGAGCCACTGTGGTCC AAGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACC GTGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG
Genomic sequence	GAAGCAGAGGTTTGAGCGGGTGACGAGGGACCTGAAGGTGACGAGGGTGTTCTCGACGCTGGTG GAGGAGATGAAGGCGATCGGCGTCCCGACGGCGGCGATGAACGGCGACGGCGAGGAGGAGCCGC ACTGCACCGACGTGATGGCGCCGGTGGCGCACGACGAGCGGAGCCCCGTGCTGCTGCTCATGGG CGGTGGGATGGGCGCCGGCAAGAGCACCGTGCTCAAGGAGATTCTCCAGGAGTAAGCAAATTAA GCTAGCGAGAGAGCTCTGTTTTTTTAAAAAAAATTATTTGCACAGCATTTAAATTGCATAGGTT ATAATTGAATAATTTGAAACGATTTTAAATATAAATTCTATAATGTTCAGGCCACTGTGGTCCA AGGACGAGGCGAATGCGGTGGTGGTTGAGGCGGATGCGTTCAAGGAGACGGACGTGATCTACCG TGCCATTAGCTCCATGGGCCACCACAACGACATGCTCCAGACTGCTGAGCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_004970* osi_circ_013341 						
					
						PMCS
						0.63112285

Conservation Information
Conserved circRNAs	osi_circ_004970* osi_circ_013341
PMCS	0.63112285

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							23994191-23994131(+)
23994310-23994575(-)
						
						Potential amino acid sequence
						
							MKAIGVPTAAMNGDGEEEPHCTDVMAPVAHDERSPVLLLMGGGMGAGKSTVLKEILQEPLWSKD
EANAVVVEADAFKETDVIYRAISSMGHHNDMLQTAELEAEV*(+)
MSSSTGLRSSCATGAITSVQCGSSSPSPFIAAVGTPIAFISSTSVENTLVTFRSLVTRSNLCFQ
LSSLEHVVVVAHGANGTVDHVRLLERIRLNHHRIRLVLGPQWLLENLLEHGALAGAHPTAHEQQ
HGAPLVVRHRRHHVGAVRLLLAVAVHRRRRDADRLHLLHQRREHPRHLQVPRHPLKPLLPAQQS
GACRCGGPWS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to Pi-starvation

Functional Information
Coding potential	Y
Potential coding position	23994191-23994131(+) 23994310-23994575(-)
Potential amino acid sequence	MKAIGVPTAAMNGDGEEEPHCTDVMAPVAHDERSPVLLLMGGGMGAGKSTVLKEILQEPLWSKD EANAVVVEADAFKETDVIYRAISSMGHHNDMLQTAELEAEV(+) MSSSTGLRSSCATGAITSVQCGSSSPSPFIAAVGTPIAFISSTSVENTLVTFRSLVTRSNLCFQ LSSLEHVVVVAHGANGTVDHVRLLERIRLNHHRIRLVLGPQWLLENLLEHGALAGAHPTAHEQQ HGAPLVVRHRRHHVGAVRLLLAVAVHRRRRDADRLHLLHQRREHPRHLQVPRHPLKPLLPAQQS GACRCGGPWS(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to Pi-starvation

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

circRNA

Detail information of Os03g0628800_circ_g.4

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