Plant Circular RNA Database

Detail information of Os09g0244900_circ_g.1

			
						 General Information
					
						CircRNA Name
						Os09g0244900_circ_g.1
					
						ID in PlantcircBase
						osa_circ_038519
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 3373187-3373607  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, PcircRNA_finder
					
						Parent gene
						
							Os09g0244900						
					
						Parent gene annotation
						
							Transport protein particle (TRAPP) component domain containing p
rotein. (Os09t0244900-01);Transport protein particle (TRAPP) com
ponent domain containing protein. (Os09t0244900-02);Transport pr
otein particle (TRAPP) component domain containing protein. (Os0
9t0244900-03);Transport protein particle (TRAPP) component domai
n containing protein. (Os09t0244900-04)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						Support reads
						15
					
						Tissues
						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
						Os09t0244900-04:2
Os09t0244900-02:2
Os09t0244900-01:2
Os09t0244900-03:2

General Information
CircRNA Name	Os09g0244900_circ_g.1
ID in PlantcircBase	osa_circ_038519
Alias	NA
Organism	Oryza sativa
Position	chr9: 3373187-3373607 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, PcircRNA_finder
Parent gene	Os09g0244900
Parent gene annotation	Transport protein particle (TRAPP) component domain containing p rotein. (Os09t0244900-01);Transport protein particle (TRAPP) com ponent domain containing protein. (Os09t0244900-02);Transport pr otein particle (TRAPP) component domain containing protein. (Os0 9t0244900-03);Transport protein particle (TRAPP) component domai n containing protein. (Os09t0244900-04)
Parent gene strand	+
Alternative splicing	NA
Support reads	15
Tissues	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	Os09t0244900-04:2 Os09t0244900-02:2 Os09t0244900-01:2 Os09t0244900-03:2

			
						 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  
						
							AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGT
GTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATatataccatggagcgccctcgatttagt
gatcatcttgaagcaatcaaatttatctgcaaagacttttggtcagagctattcaagaagcaga
ttgacaat

						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: 347
Transcript exons: 3373187-3373304,3373379-3373607
ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGAC
TTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGGGAACATTTG
TTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCTATAGATCCATCTGTAGAGAGCAT
GGATGCAACTGACAATGACTCTGCAACACTAGGGGATAGCGCAGCCCAAACAACAAGCATGCTT
CTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCA
CTGCAGACATGTCCAACCTTCCAGCAT
						
						Genomic sequence
						
							ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGAC
TTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGGTAATGAATT
TAAAATTCGTACCTTATTTTGCGCTTGTGACAGAACTGATGTTACTTGACTTCCCTATATGCAG
GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCTATAGATCCATCTG
TAGAGAGCATGGATGCAACTGACAATGACTCTGCAACACTAGGGGATAGCGCAGCCCAAACAAC
AAGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCG
TGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT

Sequences
Splice junction sequence	AGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGT GTTCTGTCACTGCAGACATGTCCAACCTTCCAGCATatataccatggagcgccctcgatttagt gatcatcttgaagcaatcaaatttatctgcaaagacttttggtcagagctattcaagaagcaga ttgacaat
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: 347 Transcript exons: 3373187-3373304,3373379-3373607 ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGAC TTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGGGAACATTTG TTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCTATAGATCCATCTGTAGAGAGCAT GGATGCAACTGACAATGACTCTGCAACACTAGGGGATAGCGCAGCCCAAACAACAAGCATGCTT CTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCGTGTTCTGTCA CTGCAGACATGTCCAACCTTCCAGCAT
Genomic sequence	ATATACCATGGAGCGCCCTCGATTTAGTGATCATCTTGAAGCAATCAAATTTATCTGCAAAGAC TTTTGGTCAGAGCTATTCAAGAAGCAGATTGACAATCTTAAAACTAATCATAGGGTAATGAATT TAAAATTCGTACCTTATTTTGCGCTTGTGACAGAACTGATGTTACTTGACTTCCCTATATGCAG GGAACATTTGTTCTTCAAGATAACCGTTTCCGGTGGCTTACTCGTGTTTCTATAGATCCATCTG TAGAGAGCATGGATGCAACTGACAATGACTCTGCAACACTAGGGGATAGCGCAGCCCAAACAAC AAGCATGCTTCTGTACTTTCCATGCGGGATAATAAGAGGTGCCTTGACCAATTTGGGTATTTCG TGTTCTGTCACTGCAGACATGTCCAACCTTCCAGCAT

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_009745 osi_circ_016943 						
					
						PMCS
						0.553628345

Conservation Information
Conserved circRNAs	osi_circ_009745 osi_circ_016943
PMCS	0.553628345

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3373529-3373430(+)
3373195-3373430(+)
3373222-3373395(-)
						
						Potential amino acid sequence
						
							MRDNKRCLDQFGYFVFCHCRHVQPSSIYTMERPRFSDHLEAIKFICKDFWSELFKKQIDNLKTN
HRGTFVLQDNRFRWLTRVSIDPSVESMDATDNDSATLGDSAAQTTSMLLYFPCGIIRGALTNLG
ISCSVTADMSNLPAYIPWSALDLVIILKQSNLSAKTFGQSYSRSRLTILKLIIGEHLFFKITVS
GGLLVFL*(+)
MERPRFSDHLEAIKFICKDFWSELFKKQIDNLKTNHRGTFVLQDNRFRWLTRVSIDPSVESMDA
TDNDSATLGDSAAQTTSMLLYFPCGIIRGALTNLGISCSVTADMSNLPAYIPWSALDLVIILKQ
SNLSAKTFGQSYSRSRLTILKLIIGEHLFFKITVSGGLLVFL*(+)
MITKSRALHGIYAGRLDMSAVTEHEIPKLVKAPLIIPHGKYRSMLVVWAALSPSVAESLSVASM
LSTDGSIETRVSHRKRLS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3373529-3373430(+) 3373195-3373430(+) 3373222-3373395(-)
Potential amino acid sequence	MRDNKRCLDQFGYFVFCHCRHVQPSSIYTMERPRFSDHLEAIKFICKDFWSELFKKQIDNLKTN HRGTFVLQDNRFRWLTRVSIDPSVESMDATDNDSATLGDSAAQTTSMLLYFPCGIIRGALTNLG ISCSVTADMSNLPAYIPWSALDLVIILKQSNLSAKTFGQSYSRSRLTILKLIIGEHLFFKITVS GGLLVFL(+) MERPRFSDHLEAIKFICKDFWSELFKKQIDNLKTNHRGTFVLQDNRFRWLTRVSIDPSVESMDA TDNDSATLGDSAAQTTSMLLYFPCGIIRGALTNLGISCSVTADMSNLPAYIPWSALDLVIILKQ SNLSAKTFGQSYSRSRLTILKLIIGEHLFFKITVSGGLLVFL(+) MITKSRALHGIYAGRLDMSAVTEHEIPKLVKAPLIIPHGKYRSMLVVWAALSPSVAESLSVASM LSTDGSIETRVSHRKRLS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0244900_circ_g.1

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