Plant Circular RNA Database

Detail information of Os03g0352500_circ_g.2

			
						 General Information
					
						CircRNA Name
						Os03g0352500_circ_g.2
					
						ID in PlantcircBase
						osa_circ_019850
					
						Alias
						Os_ciR8510
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr3: 13245242-13246446  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
					
						Parent gene
						
							Os03g0352500						
					
						Parent gene annotation
						
							Similar to AGR379Wp. (Os03t0352500-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os03g0352500_circ_igg.1 Os03g0352450_circ_ig.2 Os03g0352500_circ_g.1 						
					
						Support reads
						2/9
					
						Tissues
						root/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
						Os03t0352500-01:2

General Information
CircRNA Name	Os03g0352500_circ_g.2
ID in PlantcircBase	osa_circ_019850
Alias	Os_ciR8510
Organism	Oryza sativa
Position	chr3: 13245242-13246446 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, KNIFE, PcircRNA_finder, find_circ
Parent gene	Os03g0352500
Parent gene annotation	Similar to AGR379Wp. (Os03t0352500-01)
Parent gene strand	+
Alternative splicing	Os03g0352500_circ_igg.1 Os03g0352450_circ_ig.2 Os03g0352500_circ_g.1
Support reads	2/9
Tissues	root/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	Os03t0352500-01:2

			
						 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  
						
							AAAGGGCATCAAGGTTGACAAAGAAGGAGATTTGATGCTTGAAGACTTGGATGATCAAACTTCA
GGGGCTGCAGAACATGATAACACATCAAGCAAAAAGgtaacggtgtatagacttatatgcaaag
atacaatagaagagaagatattgcagagggcaaagcagaaaaatgcagtgcaagagttggtcat
gaaaggaa

									
								

					

						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: 330
Transcript exons: 13245242-13245442,13246318-13246446
GTAACGGTGTATAGACTTATATGCAAAGATACAATAGAAGAGAAGATATTGCAGAGGGCAAAGC
AGAAAAATGCAGTGCAAGAGTTGGTCATGAAAGGAAAACATGTCCAGGATGATCATCTGATGAG
ACAAGAGGATGTTGTTTCATTACTTATTGATGACACACAGATATCGCACAAATTAAAAGAAATA
TCAATGCAGGCAAAGGACCGACTAAAAAAGAGGCGTACAAAGGGCATCAAGGTTGACAAAGAAG
GAGATTTGATGCTTGAAGACTTGGATGATCAAACTTCAGGGGCTGCAGAACATGATAACACATC
AAGCAAAAAG
						
					

						Genomic sequence
						
							GTAACGGTGTATAGACTTATATGCAAAGATACAATAGAAGAGAAGATATTGCAGAGGGCAAAGC
AGAAAAATGCAGTGCAAGAGTTGGTCATGAAAGGAAAACATGTCCAGGATGATCATCTGATGAG
ACAAGAGGATGTTGTTTCATTACTTATTGATGACACACAGATATCGCACAAATTAAAAGAAATA
TCAATGCAGGTATTTTTTATACTACTTCCATCTTTTATTTGGCACATCGCATTGTTTTCATCTA
GTCCACCCATATACTTGAAACGTTGACAGCATACATGGATGACCTAGATTTGAGATGTAAGAAC
TAGATTTATAATCGAACTAATCTCCCTTTGCCTACCAATCAGTGGCATGCTTTTGTTCATTTTT
TCCCCATTTAGTAACACCTGTTTGGCATATGCTATTCAAACTCTTTGAATAGTTGCAAATCACC
GTGTTATTAATGTTCTCAAGATGATTGGGAAAATCTATCCCCATTGGGACAATAAACCAACCAT
AGGGCCCACCCCTTATTAGATTCAGTGCAAAAACCTTACTACTTTTATTGAGTTAAGACTTGAT
TCATGATTGGTTGATTTCTGGTTCTGCCAATTATCAAGGAGTTTATGTAGTGTATTATTGAAAA
ACTTAAGAAAACAACCTCAAAAAAGTACGAAGCTTATTTCTCCTGTTTGTTTTTGAGATTTTGC
CTAGTTCATTTTATGGTTTGCATTAGAAAACGTATCATCATGAAAGCATTTGGAAACCTTTCAT
TGGTTTATGGAAGAGTTTGGCGACCAACTTTTTTTCTTGTTGGTATTGTACTATAACAATTGTT
ACACATGTCATCTTATTACATGTTATTAGGTTTTACATGCTGTAGAACAACAAACCTTGAATTA
AAATTGCTGCAGTAATATGGCAAAAGATGAGGTTGTTTGAATTGGTTTCTTAATAGAATGTCCG
TTGAGTTTTCGTTATAATGAAATATTGAGTATGGCATGGAATGTCAACATGTTTTATTTAATTT
CAATGGAAAAAAGTCGGGTGACAATGTTTTTCATTTCTATTTACCCTTTTAGGCAAAGGACCGA
CTAAAAAAGAGGCGTACAAAGGGCATCAAGGTTGACAAAGAAGGAGATTTGATGCTTGAAGACT
TGGATGATCAAACTTCAGGGGCTGCAGAACATGATAACACATCAAGCAAAAAG
						
					

			
		

Sequences
Splice junction sequence	AAAGGGCATCAAGGTTGACAAAGAAGGAGATTTGATGCTTGAAGACTTGGATGATCAAACTTCA GGGGCTGCAGAACATGATAACACATCAAGCAAAAAGgtaacggtgtatagacttatatgcaaag atacaatagaagagaagatattgcagagggcaaagcagaaaaatgcagtgcaagagttggtcat gaaaggaa
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: 330 Transcript exons: 13245242-13245442,13246318-13246446 GTAACGGTGTATAGACTTATATGCAAAGATACAATAGAAGAGAAGATATTGCAGAGGGCAAAGC AGAAAAATGCAGTGCAAGAGTTGGTCATGAAAGGAAAACATGTCCAGGATGATCATCTGATGAG ACAAGAGGATGTTGTTTCATTACTTATTGATGACACACAGATATCGCACAAATTAAAAGAAATA TCAATGCAGGCAAAGGACCGACTAAAAAAGAGGCGTACAAAGGGCATCAAGGTTGACAAAGAAG GAGATTTGATGCTTGAAGACTTGGATGATCAAACTTCAGGGGCTGCAGAACATGATAACACATC AAGCAAAAAG
Genomic sequence	GTAACGGTGTATAGACTTATATGCAAAGATACAATAGAAGAGAAGATATTGCAGAGGGCAAAGC AGAAAAATGCAGTGCAAGAGTTGGTCATGAAAGGAAAACATGTCCAGGATGATCATCTGATGAG ACAAGAGGATGTTGTTTCATTACTTATTGATGACACACAGATATCGCACAAATTAAAAGAAATA TCAATGCAGGTATTTTTTATACTACTTCCATCTTTTATTTGGCACATCGCATTGTTTTCATCTA GTCCACCCATATACTTGAAACGTTGACAGCATACATGGATGACCTAGATTTGAGATGTAAGAAC TAGATTTATAATCGAACTAATCTCCCTTTGCCTACCAATCAGTGGCATGCTTTTGTTCATTTTT TCCCCATTTAGTAACACCTGTTTGGCATATGCTATTCAAACTCTTTGAATAGTTGCAAATCACC GTGTTATTAATGTTCTCAAGATGATTGGGAAAATCTATCCCCATTGGGACAATAAACCAACCAT AGGGCCCACCCCTTATTAGATTCAGTGCAAAAACCTTACTACTTTTATTGAGTTAAGACTTGAT TCATGATTGGTTGATTTCTGGTTCTGCCAATTATCAAGGAGTTTATGTAGTGTATTATTGAAAA ACTTAAGAAAACAACCTCAAAAAAGTACGAAGCTTATTTCTCCTGTTTGTTTTTGAGATTTTGC CTAGTTCATTTTATGGTTTGCATTAGAAAACGTATCATCATGAAAGCATTTGGAAACCTTTCAT TGGTTTATGGAAGAGTTTGGCGACCAACTTTTTTTCTTGTTGGTATTGTACTATAACAATTGTT ACACATGTCATCTTATTACATGTTATTAGGTTTTACATGCTGTAGAACAACAAACCTTGAATTA AAATTGCTGCAGTAATATGGCAAAAGATGAGGTTGTTTGAATTGGTTTCTTAATAGAATGTCCG TTGAGTTTTCGTTATAATGAAATATTGAGTATGGCATGGAATGTCAACATGTTTTATTTAATTT CAATGGAAAAAAGTCGGGTGACAATGTTTTTCATTTCTATTTACCCTTTTAGGCAAAGGACCGA CTAAAAAAGAGGCGTACAAAGGGCATCAAGGTTGACAAAGAAGGAGATTTGATGCTTGAAGACT TGGATGATCAAACTTCAGGGGCTGCAGAACATGATAACACATCAAGCAAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_013027 						
					
						PMCS
						0.242633233

Conservation Information
Conserved circRNAs	osi_circ_013027
PMCS	0.242633233

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							13245333-13246443(+)
13245363-13246437(-)
13245335-13246403(-)
						
						Potential amino acid sequence
						
							MKGKHVQDDHLMRQEDVVSLLIDDTQISHKLKEISMQAKDRLKKRRTKGIKVDKEGDLMLEDLD
DQTSGAAEHDNTSSKKVTVYRLICKDTIEEKILQRAKQKNAVQELVMKGKHVQDDHLMRQEDVV
SLLIDDTQISHKLKEISMQAKDRLKKRRTKGIKVDKEGDLMLEDLDDQTSGAAEHDNTSSKKVT
VYRLICKDTIEEKILQRAKQKNAVQELVMKGKHVQDDHLMRQEDVVSLLIDDTQISHKLKEISM
QAKDRLKKRRTKGIKVDKEGDLMLEDLDDQTSGAAEHDNTSSKKVTVYRLICKDTIEEKILQRA
KQKNAVQELVMKGKHVQDDHLMRQEDVVSLLIDDTQISHKLKEISMQAKDRLKKRRTKGIKVDK
EGDLMLEDLDDQTSGAAEHDNTSSKK(+)
MIILDMFSFHDQLLHCIFLLCPLQYLLFYCIFAYKSIHRYLFA*(-)
MTNSCTAFFCFALCNIFSSIVSLHISLYTVTFLLDVLSCSAAPEV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	13245333-13246443(+) 13245363-13246437(-) 13245335-13246403(-)
Potential amino acid sequence	MKGKHVQDDHLMRQEDVVSLLIDDTQISHKLKEISMQAKDRLKKRRTKGIKVDKEGDLMLEDLD DQTSGAAEHDNTSSKKVTVYRLICKDTIEEKILQRAKQKNAVQELVMKGKHVQDDHLMRQEDVV SLLIDDTQISHKLKEISMQAKDRLKKRRTKGIKVDKEGDLMLEDLDDQTSGAAEHDNTSSKKVT VYRLICKDTIEEKILQRAKQKNAVQELVMKGKHVQDDHLMRQEDVVSLLIDDTQISHKLKEISM QAKDRLKKRRTKGIKVDKEGDLMLEDLDDQTSGAAEHDNTSSKKVTVYRLICKDTIEEKILQRA KQKNAVQELVMKGKHVQDDHLMRQEDVVSLLIDDTQISHKLKEISMQAKDRLKKRRTKGIKVDK EGDLMLEDLDDQTSGAAEHDNTSSKK(+) MIILDMFSFHDQLLHCIFLLCPLQYLLFYCIFAYKSIHRYLFA(-) MTNSCTAFFCFALCNIFSSIVSLHISLYTVTFLLDVLSCSAAPEV(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os03g0352500_circ_g.2

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