Plant Circular RNA Database

Detail information of Os06g0239000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os06g0239000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_030345
					
						Alias
						Os_ciR4052
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr6: 7223162-7223973  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os06g0239000						
					
						Parent gene annotation
						
							Similar to Glucose-inhibited division protein B-like protein. (O
s06t0239000-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os06g0235900_circ_ag.1 Os06g0235900_circ_ag.2 Os06g0235900_circ_ag.3 Os06g0236300_circ_g.1 Os06g0236900_circ_g.1 Os06g0237200_circ_g.1 Os06g0237300_circ_g.1 Os06g0237300_circ_g.2 Os06g0237300_circ_g.3 Os06g0237300_circ_g.4 Os06g0237300_circ_g.5 Os06g0237502_circ_g.1 Os06g0237502_circ_g.2 Os06g0237502_circ_g.3 EPlOSAG00000042224_circ_ig.1 Os06g0238300_circ_g.1 Os06g0238300_circ_g.2 Os06g0239000_circ_g.1 Os06g0239000_circ_g.2 Os06g0239500_circ_g.1 Os06g0242700_circ_igg.1 Os06g0243801_circ_ag.1 Os06g0244000_circ_g.1 Os06g0244000_circ_g.2 Os06g0244000_circ_g.3 Os06g0244000_circ_g.4 Os06g0244000_circ_g.5 Os06g0244000_circ_g.6 Os06g0244000_circ_g.7 Os06g0244200_circ_g.1 						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os06t0239000-01:3

General Information
CircRNA Name	Os06g0239000_circ_g.3
ID in PlantcircBase	osa_circ_030345
Alias	Os_ciR4052
Organism	Oryza sativa
Position	chr6: 7223162-7223973 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os06g0239000
Parent gene annotation	Similar to Glucose-inhibited division protein B-like protein. (O s06t0239000-01)
Parent gene strand	+
Alternative splicing	Os06g0235900_circ_ag.1 Os06g0235900_circ_ag.2 Os06g0235900_circ_ag.3 Os06g0236300_circ_g.1 Os06g0236900_circ_g.1 Os06g0237200_circ_g.1 Os06g0237300_circ_g.1 Os06g0237300_circ_g.2 Os06g0237300_circ_g.3 Os06g0237300_circ_g.4 Os06g0237300_circ_g.5 Os06g0237502_circ_g.1 Os06g0237502_circ_g.2 Os06g0237502_circ_g.3 EPlOSAG00000042224_circ_ig.1 Os06g0238300_circ_g.1 Os06g0238300_circ_g.2 Os06g0239000_circ_g.1 Os06g0239000_circ_g.2 Os06g0239500_circ_g.1 Os06g0242700_circ_igg.1 Os06g0243801_circ_ag.1 Os06g0244000_circ_g.1 Os06g0244000_circ_g.2 Os06g0244000_circ_g.3 Os06g0244000_circ_g.4 Os06g0244000_circ_g.5 Os06g0244000_circ_g.6 Os06g0244000_circ_g.7 Os06g0244200_circ_g.1
Support reads	2/1
Tissues	root/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	Os06t0239000-01:3

			
						 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  
						
							TATCCATTCACAGTTGAATCTATGGGACCTCATGGTCAACGGACGGCTGTTGTGTACATAAAGG
AGTGCATTACTCCAAAGAAATACCCGCGGCATCCAGccgagtactgcctcccgttagtccgaat
tgatggtttatttatagctgcgaaaggacacaatccccatgtaagtcttttgggcattagccta
ttgtgcat

						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
						
							CCGAGTACTGCCTCCCGTTAGTCCGAATTGATGGTTTATTTATAGCTGCGAAAGGACACAATCC
CCATGTAAGTCTTTTGGGCATTAGCCTATTGTGCATTTGAATAAAATTAACTTGTGCTAATATA
ATTTCCTATTTTGTTGTGACAGGAAGAAATAAAAAATGCTAAAAGTGCAGTACATAAGTTGGGT
GCCTCCATGTTAGAAATATGTGATGGTATGCTATTCTATCTGCTTATGAAGATTGTGAAATTCT
ATAGCACATTTTTTATTCTATTTGTTATTTGCACCCTACATGGTATTTCAACTAGTGACTCAAA
ATAGGGAGAAAATGCTACTCCCTCCGTCCCAAAATACAAGGGATTTCAGGTGGATGGGATGTAT
CCTAGTACTACGAACCTGGATATGCTCCTGTCCAGATTCAAAGTACTAGAATACGTCACATCCA
ACCAAAATCCCTTATATTTAGGGACGGAGGGAGTAGTGTGTATGAAACAAAAGAAATTTCCATG
GTATCAAAAGAAATGTGGAATGCAATATCTATGTTGGAGAGCTGACGCAATTGTTGACTTGACC
CATTTACTAATCAATGGATAGTAACATATATATATATATATCCATGTTGATTGAAGAGTAGATG
ATGTTTTTGACCTGGTCGCTTTACTAATTCATGAGTATGTCATAATCATATACTCCCAACAACT
TAACCCTCTATCCATTCACAGTTGAATCTATGGGACCTCATGGTCAACGGACGGCTGTTGTGTA
CATAAAGGAGTGCATTACTCCAAAGAAATACCCGCGGCATCCAG

Sequences
Splice junction sequence	TATCCATTCACAGTTGAATCTATGGGACCTCATGGTCAACGGACGGCTGTTGTGTACATAAAGG AGTGCATTACTCCAAAGAAATACCCGCGGCATCCAGccgagtactgcctcccgttagtccgaat tgatggtttatttatagctgcgaaaggacacaatccccatgtaagtcttttgggcattagccta ttgtgcat
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	CCGAGTACTGCCTCCCGTTAGTCCGAATTGATGGTTTATTTATAGCTGCGAAAGGACACAATCC CCATGTAAGTCTTTTGGGCATTAGCCTATTGTGCATTTGAATAAAATTAACTTGTGCTAATATA ATTTCCTATTTTGTTGTGACAGGAAGAAATAAAAAATGCTAAAAGTGCAGTACATAAGTTGGGT GCCTCCATGTTAGAAATATGTGATGGTATGCTATTCTATCTGCTTATGAAGATTGTGAAATTCT ATAGCACATTTTTTATTCTATTTGTTATTTGCACCCTACATGGTATTTCAACTAGTGACTCAAA ATAGGGAGAAAATGCTACTCCCTCCGTCCCAAAATACAAGGGATTTCAGGTGGATGGGATGTAT CCTAGTACTACGAACCTGGATATGCTCCTGTCCAGATTCAAAGTACTAGAATACGTCACATCCA ACCAAAATCCCTTATATTTAGGGACGGAGGGAGTAGTGTGTATGAAACAAAAGAAATTTCCATG GTATCAAAAGAAATGTGGAATGCAATATCTATGTTGGAGAGCTGACGCAATTGTTGACTTGACC CATTTACTAATCAATGGATAGTAACATATATATATATATATCCATGTTGATTGAAGAGTAGATG ATGTTTTTGACCTGGTCGCTTTACTAATTCATGAGTATGTCATAATCATATACTCCCAACAACT TAACCCTCTATCCATTCACAGTTGAATCTATGGGACCTCATGGTCAACGGACGGCTGTTGTGTA CATAAAGGAGTGCATTACTCCAAAGAAATACCCGCGGCATCCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.131149436

Conservation Information
Conserved circRNAs	NA
PMCS	0.131149436

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7223361-7223970(+)
7223363-7223911(-)
						
						Potential amino acid sequence
						
							MLEICDVESMGPHGQRTAVVYIKECITPKKYPRHPAEYCLPLVRIDGLFIAAKGHNPHEEIKNA
KSAVHKLGASMLEICDVESMGPHGQRTAVVYIKECITPKKYPRHPAEYCLPLVRIDGLFIAAKG
HNPHEEIKNAKSAVHKLGASMLEICDVESMGPHGQRTAVVYIKECITPKKYPRHPAEYCLPLVR
IDGLFIAAKGHNPHEEIKNAKSAVHKLGASMLEICDVESMGPHGQRTAVVYIKECITPKKYPRH
P(+)
MEAPNLCTALLAFFISSWGLCPFAAINKPSIRTNGRQYSAGCRGYFFGVMHSFMYTTAVR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7223361-7223970(+) 7223363-7223911(-)
Potential amino acid sequence	MLEICDVESMGPHGQRTAVVYIKECITPKKYPRHPAEYCLPLVRIDGLFIAAKGHNPHEEIKNA KSAVHKLGASMLEICDVESMGPHGQRTAVVYIKECITPKKYPRHPAEYCLPLVRIDGLFIAAKG HNPHEEIKNAKSAVHKLGASMLEICDVESMGPHGQRTAVVYIKECITPKKYPRHPAEYCLPLVR IDGLFIAAKGHNPHEEIKNAKSAVHKLGASMLEICDVESMGPHGQRTAVVYIKECITPKKYPRH P(+) MEAPNLCTALLAFFISSWGLCPFAAINKPSIRTNGRQYSAGCRGYFFGVMHSFMYTTAVR*(-)
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 Os06g0239000_circ_g.3

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