Plant Circular RNA Database

Detail information of Os01g0908200_circ_g.4

			
						 General Information
					
						CircRNA Name
						Os01g0908200_circ_g.4
					
						ID in PlantcircBase
						osa_circ_005355
					
						Alias
						Os_ciR2239
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr1: 39546537-39546843  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, circseq_cup, find_circ
					
						Parent gene
						
							Os01g0908200						
					
						Parent gene annotation
						
							Member of the Bric-a-Brac/Tramtrack/Broad (BTB) family, BT1/BT2 
ortholog, Negative regulation of nitrate uptake and nitrogen use
 efficiency (Os01t0908200-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os01g0908200_circ_g.5 Os01g0908200_circ_g.6 						
					
						Support reads
						5/12/12
					
						Tissues
						root/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
						Os01t0908200-01:1

General Information
CircRNA Name	Os01g0908200_circ_g.4
ID in PlantcircBase	osa_circ_005355
Alias	Os_ciR2239
Organism	Oryza sativa
Position	chr1: 39546537-39546843 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, circseq_cup, find_circ
Parent gene	Os01g0908200
Parent gene annotation	Member of the Bric-a-Brac/Tramtrack/Broad (BTB) family, BT1/BT2 ortholog, Negative regulation of nitrate uptake and nitrogen use efficiency (Os01t0908200-01)
Parent gene strand	+
Alternative splicing	Os01g0908200_circ_g.5 Os01g0908200_circ_g.6
Support reads	5/12/12
Tissues	root/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	Os01t0908200-01:1

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							Yes							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   
						
							F: CTCGCCAAGGAGTTCAAGG
 R: CGCTCTTCTCGTCAATCTCC
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	Yes 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	F: CTCGCCAAGGAGTTCAAGG R: CGCTCTTCTCGTCAATCTCC 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  
						
							GTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCCAGGAGAACGACCCCTGGCTCGAG
CTCGACATCCTCCAGCGCCTCCACGACGCCGACCTGtggtgatgaggaggagattgacgagaag
agcgcggcgcagatgctggtgctggcgcacgcgtaccgggtgccgtggctgaagcggcggtgcg
agggggcg

						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: 251
Transcript exons: 39546537-39546612,39546669-39546843
TGGTGATGAGGAGGAGATTGACGAGAAGAGCGCGGCGCAGATGCTGGTGCTGGCGCACGCGTAC
CGGGTGCCGTGGGGACACGATGCAGCTGGCGGCGCTGTGCGACGCGCCGCAGCTGCACCTGCGC
TGCACCAGGCTGCTCGCCAAGGAGTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCC
AGGAGAACGACCCCTGGCTCGAGCTCGACATCCTCCAGCGCCTCCACGACGCCGACCTG
Transcript length: 307
Transcript exons: 39546537-39546843
TGGTGATGAGGAGGAGATTGACGAGAAGAGCGCGGCGCAGATGCTGGTGCTGGCGCACGCGTAC
CGGGTGCCGTGGCTGAAGCGGCGGTGCGAGGGGGCGATCGGGTCGCGGCTCACGGCGGAGTCGG
TGGTGGACACGATGCAGCTGGCGGCGCTGTGCGACGCGCCGCAGCTGCACCTGCGCTGCACCAG
GCTGCTCGCCAAGGAGTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCCAGGAGAAC
GACCCCTGGCTCGAGCTCGACATCCTCCAGCGCCTCCACGACGCCGACCTG
						
						Genomic sequence
						
							TGGTGATGAGGAGGAGATTGACGAGAAGAGCGCGGCGCAGATGCTGGTGCTGGCGCACGCGTAC
CGGGTGCCGTGGCTGAAGCGGCGGTGCGAGGGGGCGATCGGGTCGCGGCTCACGGCGGAGTCGG
TGGTGGACACGATGCAGCTGGCGGCGCTGTGCGACGCGCCGCAGCTGCACCTGCGCTGCACCAG
GCTGCTCGCCAAGGAGTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCCAGGAGAAC
GACCCCTGGCTCGAGCTCGACATCCTCCAGCGCCTCCACGACGCCGACCTG

Sequences
Splice junction sequence	GTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCCAGGAGAACGACCCCTGGCTCGAG CTCGACATCCTCCAGCGCCTCCACGACGCCGACCTGtggtgatgaggaggagattgacgagaag agcgcggcgcagatgctggtgctggcgcacgcgtaccgggtgccgtggctgaagcggcggtgcg agggggcg
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: 251 Transcript exons: 39546537-39546612,39546669-39546843 TGGTGATGAGGAGGAGATTGACGAGAAGAGCGCGGCGCAGATGCTGGTGCTGGCGCACGCGTAC CGGGTGCCGTGGGGACACGATGCAGCTGGCGGCGCTGTGCGACGCGCCGCAGCTGCACCTGCGC TGCACCAGGCTGCTCGCCAAGGAGTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCC AGGAGAACGACCCCTGGCTCGAGCTCGACATCCTCCAGCGCCTCCACGACGCCGACCTG Transcript length: 307 Transcript exons: 39546537-39546843 TGGTGATGAGGAGGAGATTGACGAGAAGAGCGCGGCGCAGATGCTGGTGCTGGCGCACGCGTAC CGGGTGCCGTGGCTGAAGCGGCGGTGCGAGGGGGCGATCGGGTCGCGGCTCACGGCGGAGTCGG TGGTGGACACGATGCAGCTGGCGGCGCTGTGCGACGCGCCGCAGCTGCACCTGCGCTGCACCAG GCTGCTCGCCAAGGAGTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCCAGGAGAAC GACCCCTGGCTCGAGCTCGACATCCTCCAGCGCCTCCACGACGCCGACCTG
Genomic sequence	TGGTGATGAGGAGGAGATTGACGAGAAGAGCGCGGCGCAGATGCTGGTGCTGGCGCACGCGTAC CGGGTGCCGTGGCTGAAGCGGCGGTGCGAGGGGGCGATCGGGTCGCGGCTCACGGCGGAGTCGG TGGTGGACACGATGCAGCTGGCGGCGCTGTGCGACGCGCCGCAGCTGCACCTGCGCTGCACCAG GCTGCTCGCCAAGGAGTTCAAGGCCGTGGAGAAGACCGAGGCGTGGCGATTCCTCCAGGAGAAC GACCCCTGGCTCGAGCTCGACATCCTCCAGCGCCTCCACGACGCCGACCTG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_002597* osi_circ_011081 						
					
						PMCS
						0.486725841

Conservation Information
Conserved circRNAs	osi_circ_002597* osi_circ_011081
PMCS	0.486725841

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							39546578-39546539(+)
39546817-39546748(-)
						
						Potential amino acid sequence
						
							MLVLAHAYRVPWLKRRCEGAIGSRLTAESVVDTMQLAALCDAPQLHLRCTRLLAKEFKAVEKTE
AWRFLQENDPWLELDILQRLHDADLW*(+)
MSSSSQGSFSWRNRHASVFSTALNSLASSLVQRRCSCGASHSAASCIVSTTDSAVSRDPIAPSH
RRFSHGTRYACASTSICAALFSSISSSSPQVGVVEALEDVELEPGVVLLEESPRLGLLHGLELL
GEQPGAAQVQLRRVAQRRQLHRVHHRLRREPRPDRPLAPPLQPRHPVRVRQHQHLRRALLVNLL
LITTGRRRGGAGGCRARARGRSPGGIATPRSSPRP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	39546578-39546539(+) 39546817-39546748(-)
Potential amino acid sequence	MLVLAHAYRVPWLKRRCEGAIGSRLTAESVVDTMQLAALCDAPQLHLRCTRLLAKEFKAVEKTE AWRFLQENDPWLELDILQRLHDADLW(+) MSSSSQGSFSWRNRHASVFSTALNSLASSLVQRRCSCGASHSAASCIVSTTDSAVSRDPIAPSH RRFSHGTRYACASTSICAALFSSISSSSPQVGVVEALEDVELEPGVVLLEESPRLGLLHGLELL GEQPGAAQVQLRRVAQRRQLHRVHHRLRREPRPDRPLAPPLQPRHPVRVRQHQHLRRALLVNLL LITTGRRRGGAGGCRARARGRSPGGIATPRSSPRP(-)
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 Os01g0908200_circ_g.4

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