Plant Circular RNA Database

Detail information of Os02g0119400_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os02g0119400_circ_g.3
					
						ID in PlantcircBase
						osa_circ_012796
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 1023102-1024414  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os02g0119400						
					
						Parent gene annotation
						
							Similar to Syntaxin 52 (AtSYP52). (Os02t0119400-01)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os02g0119400_circ_g.4 Os02g0119400_circ_g.5 Os02g0119400_circ_g.6 						
					
						Support reads
						2
					
						Tissues
						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  
						
							CT-AC							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
						Os02t0119400-01:3

General Information
CircRNA Name	Os02g0119400_circ_g.3
ID in PlantcircBase	osa_circ_012796
Alias	NA
Organism	Oryza sativa
Position	chr2: 1023102-1024414 JBrowse»
Reference genome	IRGSP-1.0.38
Type	ue-circRNA
Identification method	CIRCexplorer
Parent gene	Os02g0119400
Parent gene annotation	Similar to Syntaxin 52 (AtSYP52). (Os02t0119400-01)
Parent gene strand	-
Alternative splicing	Os02g0119400_circ_g.4 Os02g0119400_circ_g.5 Os02g0119400_circ_g.6
Support reads	2
Tissues	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	CT-AC 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	Os02t0119400-01:3

			
						 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  
						
							ACCCCTATCGGCGATCATGGAGGTGACGTCATCCGCGAGCCTGGACGCCTCGCTGTACTCCCTC
ACCCATGGATCCGAAGACGACGCCATTCCTTCCTTCctttcataacttgcctctgaagtgaaac
gattccttggttatccaaaccagctactctactcatatcatcagctgctttcttactctgacca
agcaaatc

									
								

					

						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: 431
Transcript exons: 1023102-1023205,1023352-1023453,1024190-1024414
CTTTCATAACTTGCCTCTGAAGTGAAACGATTCCTTGGTTATCCAAACCAGCTACTCTACTCAT
ATCATCAGCTGCTTTCTTACTCTGACCAAGCAAATCCTCCCTGTTTGCAAAGTTTGACATGTTG
AAACTTGTAGCCATCTGCTTTGCTCTAGATTTCAGATTTGAAAGCATGTCTTGTCGCTTATGCA
ACTCCTTGTCCGTGATGGACTTGGGAGGAATCCTGGACAGCAAGGCCTCGAGGCTATCGAGCCT
AGTCCCGAGGATGGTTATCTTCCTCCGAATGGCCGAGGTGTGGCGCATGATCTCCGGCCCCGAC
TGCGGGAGCGAACCCCTATCGGCGATCATGGAGGTGACGTCATCCGCGAGCCTGGACGCCTCGC
TGTACTCCCTCACCCATGGATCCGAAGACGACGCCATTCCTTCCTTC
						
					

						Genomic sequence
						
							CTTTCATAACTTGCCTCTGAAGTGAAACGATTCCTTGGTTATCCAAACCAGCTACTCTACTCAT
ATCATCAGCTGCTTTCTTACTCTGACCAAGCAAATCCTCCCTAAAAATACAAACAAAGATTTCC
ATTAATATGCTTCTGAACAAATTGCAACATGTCAAAGCATCAACCAGTTATCTTTATTTCGAGA
GAACAAGGCAAATAACTGTATCAGGCTACCAGGTTGATATCTGAGAACAAGAACAGACCTGTTT
GCAAAGTTTGACATGTTGAAACTTGTAGCCATCTGCTTTGCTCTAGATTTCAGATTTGAAAGCA
TGTCTTGTCGCTTATGCAACTCCTTGTCCGTGCTGCATAATGAGAGAACAGCATGAATACCAGT
AGCAATCTTTTTTTTTCACTAGAATCATAATCCCGAATTGCCGATAATCCCTCAGATATAGGGA
GAAATATCGAACAGCATCTACTTTAATGAAGTCTCAACCCAGGCACACAAGAGTAACCAACTCT
AATTTAGTGTTCGATCCAGAAGGTGAATCACAAGGGTGAAAAGTGGACAGGTCAACGTGTAAGG
GTAACAATTCTAAATGAATTCGATCGCGGCGTAAGTTAATCAGGGGACCGACAGATTCCATAAG
ATTTGTACAAGCTAACTGTGATTCCATCACCAACATATGAACAACCCATATTAGTACGCAAACA
GAAATTAAGTAGTAGCAGTGTTATGAAGGAAGGAAGGAAGCAACACATGAACTTTGGAGGAATC
CTGGACAGCAACGCTTCTAATTTATCTCGTAATGAAGTCTCAACCCCAGGCACACAAGTGCAAC
CAACTCTAATTTATCTCGTATCTCTCTCTCCATAAGTTTGATCCAGCAGGTGAATCACAAGGGT
GAAAAGTGGACAGGTCAGTGTGCAAAGAGTAACAATTCTAATCGAATTCGATTCCGCCTTAAGT
TAAACCAGGACCAGAGACATTCCTTAACATTTATACAAGCTAATAACTGCGACTCCAACACCAT
CAATCCATCATATGAACAACCCATATTAGTACACAAACAGAAAATAAGTAGAAGAGTGGTATAC
ATGGACTTGGGAGGAATCCTGGACAGCAAGGCCTCGAGGCTATCGAGCCTAGTCCCGAGGATGG
TTATCTTCCTCCGAATGGCCGAGGTGTGGCGCATGATCTCCGGCCCCGACTGCGGGAGCGAACC
CCTATCGGCGATCATGGAGGTGACGTCATCCGCGAGCCTGGACGCCTCGCTGTACTCCCTCACC
CATGGATCCGAAGACGACGCCATTCCTTCCTTC
						
					

			
		

Sequences
Splice junction sequence	ACCCCTATCGGCGATCATGGAGGTGACGTCATCCGCGAGCCTGGACGCCTCGCTGTACTCCCTC ACCCATGGATCCGAAGACGACGCCATTCCTTCCTTCctttcataacttgcctctgaagtgaaac gattccttggttatccaaaccagctactctactcatatcatcagctgctttcttactctgacca agcaaatc
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: 431 Transcript exons: 1023102-1023205,1023352-1023453,1024190-1024414 CTTTCATAACTTGCCTCTGAAGTGAAACGATTCCTTGGTTATCCAAACCAGCTACTCTACTCAT ATCATCAGCTGCTTTCTTACTCTGACCAAGCAAATCCTCCCTGTTTGCAAAGTTTGACATGTTG AAACTTGTAGCCATCTGCTTTGCTCTAGATTTCAGATTTGAAAGCATGTCTTGTCGCTTATGCA ACTCCTTGTCCGTGATGGACTTGGGAGGAATCCTGGACAGCAAGGCCTCGAGGCTATCGAGCCT AGTCCCGAGGATGGTTATCTTCCTCCGAATGGCCGAGGTGTGGCGCATGATCTCCGGCCCCGAC TGCGGGAGCGAACCCCTATCGGCGATCATGGAGGTGACGTCATCCGCGAGCCTGGACGCCTCGC TGTACTCCCTCACCCATGGATCCGAAGACGACGCCATTCCTTCCTTC
Genomic sequence	CTTTCATAACTTGCCTCTGAAGTGAAACGATTCCTTGGTTATCCAAACCAGCTACTCTACTCAT ATCATCAGCTGCTTTCTTACTCTGACCAAGCAAATCCTCCCTAAAAATACAAACAAAGATTTCC ATTAATATGCTTCTGAACAAATTGCAACATGTCAAAGCATCAACCAGTTATCTTTATTTCGAGA GAACAAGGCAAATAACTGTATCAGGCTACCAGGTTGATATCTGAGAACAAGAACAGACCTGTTT GCAAAGTTTGACATGTTGAAACTTGTAGCCATCTGCTTTGCTCTAGATTTCAGATTTGAAAGCA TGTCTTGTCGCTTATGCAACTCCTTGTCCGTGCTGCATAATGAGAGAACAGCATGAATACCAGT AGCAATCTTTTTTTTTCACTAGAATCATAATCCCGAATTGCCGATAATCCCTCAGATATAGGGA GAAATATCGAACAGCATCTACTTTAATGAAGTCTCAACCCAGGCACACAAGAGTAACCAACTCT AATTTAGTGTTCGATCCAGAAGGTGAATCACAAGGGTGAAAAGTGGACAGGTCAACGTGTAAGG GTAACAATTCTAAATGAATTCGATCGCGGCGTAAGTTAATCAGGGGACCGACAGATTCCATAAG ATTTGTACAAGCTAACTGTGATTCCATCACCAACATATGAACAACCCATATTAGTACGCAAACA GAAATTAAGTAGTAGCAGTGTTATGAAGGAAGGAAGGAAGCAACACATGAACTTTGGAGGAATC CTGGACAGCAACGCTTCTAATTTATCTCGTAATGAAGTCTCAACCCCAGGCACACAAGTGCAAC CAACTCTAATTTATCTCGTATCTCTCTCTCCATAAGTTTGATCCAGCAGGTGAATCACAAGGGT GAAAAGTGGACAGGTCAGTGTGCAAAGAGTAACAATTCTAATCGAATTCGATTCCGCCTTAAGT TAAACCAGGACCAGAGACATTCCTTAACATTTATACAAGCTAATAACTGCGACTCCAACACCAT CAATCCATCATATGAACAACCCATATTAGTACACAAACAGAAAATAAGTAGAAGAGTGGTATAC ATGGACTTGGGAGGAATCCTGGACAGCAAGGCCTCGAGGCTATCGAGCCTAGTCCCGAGGATGG TTATCTTCCTCCGAATGGCCGAGGTGTGGCGCATGATCTCCGGCCCCGACTGCGGGAGCGAACC CCTATCGGCGATCATGGAGGTGACGTCATCCGCGAGCCTGGACGCCTCGCTGTACTCCCTCACC CATGGATCCGAAGACGACGCCATTCCTTCCTTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.120283974

Conservation Information
Conserved circRNAs	NA
PMCS	0.120283974

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							1023436-1023118(+)
1023371-1023107(+)
1024406-1024379(-)
						
						Potential amino acid sequence
						
							MQLLVRDGLGRNPGQQGLEAIEPSPEDGYLPPNGRGVAHDLRPRLRERTPIGDHGGDVIREPGR
LAVLPHPWIRRRRHSFLPFITCL*(+)
MLKLVAICFALDFRFESMSCRLCNSLSVMDLGGILDSKASRLSSLVPRMVIFLRMAEVWRMISG
PDCGSEPLSAIMEVTSSASLDASLYSLTHGSEDDAIPSFLS*(+)
MASSSDPWVREYSEASRLADDVTSMIADRGSLPQSGPEIMRHTSAIRRKITILGTRLDSLEALL
SRIPPKSITDKELHKRQDMLSNLKSRAKQMATSFNMSNFANREDLLGQSKKAADDMSRVAGLDN
QGIVSLQRQVMKGRKEWRRLRIHG*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	1023436-1023118(+) 1023371-1023107(+) 1024406-1024379(-)
Potential amino acid sequence	MQLLVRDGLGRNPGQQGLEAIEPSPEDGYLPPNGRGVAHDLRPRLRERTPIGDHGGDVIREPGR LAVLPHPWIRRRRHSFLPFITCL(+) MLKLVAICFALDFRFESMSCRLCNSLSVMDLGGILDSKASRLSSLVPRMVIFLRMAEVWRMISG PDCGSEPLSAIMEVTSSASLDASLYSLTHGSEDDAIPSFLS(+) MASSSDPWVREYSEASRLADDVTSMIADRGSLPQSGPEIMRHTSAIRRKITILGTRLDSLEALL SRIPPKSITDKELHKRQDMLSNLKSRAKQMATSFNMSNFANREDLLGQSKKAADDMSRVAGLDN QGIVSLQRQVMKGRKEWRRLRIHG*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os02g0119400_circ_g.3

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