Plant Circular RNA Database

Detail information of Os09g0114500_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os09g0114500_circ_g.4
					
						ID in PlantcircBase
						osa_circ_038404
					
						Alias
						Os_ciR520
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 1160334-1160819  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder, circseq_cup, find_circ
					
						Parent gene
						
							Os09g0114500						
					
						Parent gene annotation
						
							Kinesin-4 protein with transcription regulation activity, Cell c
ycle and wall modification, Cell elongation by regulating GA bio
synthesis pathway (Os09t0114500-01);Similar to Kinesin-like prot
ein. (Os09t0114500-02);Similar to FRA1 (FRAGILE FIBER 1); microt
ubule motor. (Os09t0114500-03);Hypothetical protein. (Os09t01145
00-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os09g0114500_circ_g.5 Os09g0114500_circ_g.6 Os09g0114500_circ_g.7 Os09g0114500_circ_g.8 Os09g0114500_circ_g.9 Os09g0114500_circ_g.10 Os09g0114500_circ_g.11 Os09g0114500_circ_g.12 Os09g0114500_circ_g.13 Os09g0114500_circ_g.14 						
					
						Support reads
						55/5/9
					
						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
						Os09t0114500-01:2
Os09t0114500-02:2

General Information
CircRNA Name	Os09g0114500_circ_g.4
ID in PlantcircBase	osa_circ_038404
Alias	Os_ciR520
Organism	Oryza sativa
Position	chr9: 1160334-1160819 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder, circseq_cup, find_circ
Parent gene	Os09g0114500
Parent gene annotation	Kinesin-4 protein with transcription regulation activity, Cell c ycle and wall modification, Cell elongation by regulating GA bio synthesis pathway (Os09t0114500-01);Similar to Kinesin-like prot ein. (Os09t0114500-02);Similar to FRA1 (FRAGILE FIBER 1); microt ubule motor. (Os09t0114500-03);Hypothetical protein. (Os09t01145 00-04)
Parent gene strand	+
Alternative splicing	Os09g0114500_circ_g.5 Os09g0114500_circ_g.6 Os09g0114500_circ_g.7 Os09g0114500_circ_g.8 Os09g0114500_circ_g.9 Os09g0114500_circ_g.10 Os09g0114500_circ_g.11 Os09g0114500_circ_g.12 Os09g0114500_circ_g.13 Os09g0114500_circ_g.14
Support reads	55/5/9
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	Os09t0114500-01:2 Os09t0114500-02:2

			
						 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  
						
							CCGAAGTGCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTCG
TGCAACTGGAAGTACCAACATGAACAACCAATCAAGactgggtcagggaagacctacaccatgg
ggacggcctgcaaggagggctcacacattgggattatcccgcgtgccatggccacgctgttcga
caagatcg

									
								

					

						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: 159
Transcript exons: 1160334-1160462,1160790-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA
GTGGAAGTACCAACATGAACAACCAATCAAG
Transcript length: 165
Transcript exons: 1160334-1160365,1160687-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACCGTCGAACGGGGTCATAACGTTAGCAGGATCG
ACCGAAGTGCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTC
GTGCAACTGGAAGTACCAACATGAACAACCAATCAAG
Transcript length: 206
Transcript exons: 1160334-1160480,1160761-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA
GCTGCGCGTTTCGTTTATTCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGAAGTACCAACATG
AACAACCAATCAAG
Transcript length: 229
Transcript exons: 1160334-1160470,1160728-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA
GCTGCGCGTCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTC
GTGCAACTGGAAGTACCAACATGAACAACCAATCAAG
Transcript length: 257
Transcript exons: 1160334-1160469,1160699-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA
GCTGCGCGTCATAACGTTAGCAGGATCGACCGAAGTGCATGTCACTACCCAGAAAGAAATGACG
GCATGCCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGAAGTACCAACATGAACAACCAATCAA
G
Transcript length: 272
Transcript exons: 1160334-1160416,1160631-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACTGGACATGCAACCAAGTTGTCGGTTCCAGGTAAACCCCCTGTTCA
GATCCGGGAGGCGTCGAACGGGGTCATAACGTTAGCAGGATCGACCGAAGTGCATGTCACTACC
CAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGAAGTACCAACA
TGAACAACCAATCAAG
Transcript length: 410
Transcript exons: 1160334-1160483,1160560-1160819
ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA
GCTGCGCGTTTCGTTTATTGAGATTCTGAAAGAAGAGGTGAGGGATTTGCTTGATCCTGCTACT
GCTGCTGTTGGCAAACTTGAGAATGGAAATGGACATGCAACCAAGTTGTCGGTTCCAGGTAAAC
CCCCTGTTCAGATCCGGGAGGCGTCGAACGGGGTCATAACGTTAGCAGGATCGACCGAAGTGCA
TGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGA
AGTACCAACATGAACAACCAATCAAG
						
					

						Genomic sequence
						
							ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA
TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA
GCTGCGCGTTTCGTTTATTGAGGTAAATTACCTGTTCCTGGATGAATCAAACATTTGTGGGATT
GTAGAGAATCCAATTGTGCTCGTTCTCTTGATAGATTCTGAAAGAAGAGGTGAGGGATTTGCTT
GATCCTGCTACTGCTGCTGTTGGCAAACTTGAGAATGGAAATGGACATGCAACCAAGTTGTCGG
TTCCAGGTAAACCCCCTGTTCAGATCCGGGAGGCGTCGAACGGGGTCATAACGTTAGCAGGATC
GACCGAAGTGCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGT
CGTGCAACTGGAAGTACCAACATGAACAACCAATCAAG
						
					

			
		

Sequences
Splice junction sequence	CCGAAGTGCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTCG TGCAACTGGAAGTACCAACATGAACAACCAATCAAGactgggtcagggaagacctacaccatgg ggacggcctgcaaggagggctcacacattgggattatcccgcgtgccatggccacgctgttcga caagatcg
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: 159 Transcript exons: 1160334-1160462,1160790-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA GTGGAAGTACCAACATGAACAACCAATCAAG Transcript length: 165 Transcript exons: 1160334-1160365,1160687-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACCGTCGAACGGGGTCATAACGTTAGCAGGATCG ACCGAAGTGCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTC GTGCAACTGGAAGTACCAACATGAACAACCAATCAAG Transcript length: 206 Transcript exons: 1160334-1160480,1160761-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA GCTGCGCGTTTCGTTTATTCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGAAGTACCAACATG AACAACCAATCAAG Transcript length: 229 Transcript exons: 1160334-1160470,1160728-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA GCTGCGCGTCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTC GTGCAACTGGAAGTACCAACATGAACAACCAATCAAG Transcript length: 257 Transcript exons: 1160334-1160469,1160699-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA GCTGCGCGTCATAACGTTAGCAGGATCGACCGAAGTGCATGTCACTACCCAGAAAGAAATGACG GCATGCCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGAAGTACCAACATGAACAACCAATCAA G Transcript length: 272 Transcript exons: 1160334-1160416,1160631-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACTGGACATGCAACCAAGTTGTCGGTTCCAGGTAAACCCCCTGTTCA GATCCGGGAGGCGTCGAACGGGGTCATAACGTTAGCAGGATCGACCGAAGTGCATGTCACTACC CAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGAAGTACCAACA TGAACAACCAATCAAG Transcript length: 410 Transcript exons: 1160334-1160483,1160560-1160819 ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA GCTGCGCGTTTCGTTTATTGAGATTCTGAAAGAAGAGGTGAGGGATTTGCTTGATCCTGCTACT GCTGCTGTTGGCAAACTTGAGAATGGAAATGGACATGCAACCAAGTTGTCGGTTCCAGGTAAAC CCCCTGTTCAGATCCGGGAGGCGTCGAACGGGGTCATAACGTTAGCAGGATCGACCGAAGTGCA TGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGTCGTGCAACTGGA AGTACCAACATGAACAACCAATCAAG
Genomic sequence	ACTGGGTCAGGGAAGACCTACACCATGGGGACGGCCTGCAAGGAGGGCTCACACATTGGGATTA TCCCGCGTGCCATGGCCACGCTGTTCGACAAGATCGACAAGCTCAAGAACCAAGTAGAGTTCCA GCTGCGCGTTTCGTTTATTGAGGTAAATTACCTGTTCCTGGATGAATCAAACATTTGTGGGATT GTAGAGAATCCAATTGTGCTCGTTCTCTTGATAGATTCTGAAAGAAGAGGTGAGGGATTTGCTT GATCCTGCTACTGCTGCTGTTGGCAAACTTGAGAATGGAAATGGACATGCAACCAAGTTGTCGG TTCCAGGTAAACCCCCTGTTCAGATCCGGGAGGCGTCGAACGGGGTCATAACGTTAGCAGGATC GACCGAAGTGCATGTCACTACCCAGAAAGAAATGACGGCATGCCTTGAGCAAGGATCTCTGAGT CGTGCAACTGGAAGTACCAACATGAACAACCAATCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_007935* osi_circ_018918 						
					
						PMCS
						0.694220542

Conservation Information
Conserved circRNAs	osi_circ_007935* osi_circ_018918
PMCS	0.694220542

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1160359-1160451(+)
						
						Potential amino acid sequence
						
							MGTACKEGSHIGIIPRAMATLFDKIDKLKNQVEFQLRVSFIEILKEEVRDLLDPATAAVGKLEN
GNGHATKLSVPGKPPVQIREASNGVITLAGSTEVHVTTQKEMTACLEQGSLSRATGSTNMNNQS
RLGQGRPTPWGRPARRAHTLGLSRVPWPRCSTRSTSSRTK*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1160359-1160451(+)
Potential amino acid sequence	MGTACKEGSHIGIIPRAMATLFDKIDKLKNQVEFQLRVSFIEILKEEVRDLLDPATAAVGKLEN GNGHATKLSVPGKPPVQIREASNGVITLAGSTEVHVTTQKEMTACLEQGSLSRATGSTNMNNQS RLGQGRPTPWGRPARRAHTLGLSRVPWPRCSTRSTSSRTK*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

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

circRNA

Detail information of Os09g0114500_circ_g.4

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