Plant Circular RNA Database

Detail information of Os09g0535000_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os09g0535000_circ_g.3
					
						ID in PlantcircBase
						osa_circ_040017
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr9: 21034054-21034452  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os09g0535000						
					
						Parent gene annotation
						
							Similar to Triosephosphate isomerase. (Os09t0535000-01);Similar 
to Triosephosphate isomerase, chloroplast precursor (EC 5.3.1.1)
 (TIM) (Triose-phosphate isomerase). (Os09t0535000-02);Similar t
o Triosephosphate isomerase. (Os09t0535000-03)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os09g0535000_circ_g.1 Os09g0535000_circ_g.2 Os09g0535000_circ_g.4 						
					
						Support reads
						2
					
						Tissues
						shoot
					
						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
						Os09t0535000-02:2
Os09t0535000-01:2

General Information
CircRNA Name	Os09g0535000_circ_g.3
ID in PlantcircBase	osa_circ_040017
Alias	NA
Organism	Oryza sativa
Position	chr9: 21034054-21034452 JBrowse»
Reference genome	IRGSP-1.0.38
Type	u-circRNA
Identification method	CIRCexplorer
Parent gene	Os09g0535000
Parent gene annotation	Similar to Triosephosphate isomerase. (Os09t0535000-01);Similar to Triosephosphate isomerase, chloroplast precursor (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase). (Os09t0535000-02);Similar t o Triosephosphate isomerase. (Os09t0535000-03)
Parent gene strand	-
Alternative splicing	Os09g0535000_circ_g.1 Os09g0535000_circ_g.2 Os09g0535000_circ_g.4
Support reads	2
Tissues	shoot
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	Os09t0535000-02:2 Os09t0535000-01:2

			
						 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  
						
							CAAAAGTTTTCCCTGCTTCTCTCTCTTCCAACAGCTCCCCTATGCAGGCAATAACCTTTACATT
TTGACTCAAGGCATATGCAGCCTTCTTCCCAATAAActccatatataattcgaatgccggaagc
aacctcaggtgacacgttggttttcaaccaatcacgaacagcagcatgaacttcctgagcttgc
tcaggagt

						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: 307
Transcript exons: 21034054-21034227,21034320-21034452
CTCCATATATAATTCGAATGCCGGAAGCAACCTCAGGTGACACGTTGGTTTTCAACCAATCACG
AACAGCAGCATGAACTTCCTGAGCTTGCTCAGGAGTAGCAACTTTCCCGGTTCCAATAGCCCAA
ACAGGCTCATATGCAATTACTACATCCGCCCAGTTTGTAATACTGTCTGCAAAAGCCTTCATCT
GCTTAAAACAGACGTCAAAAGTTTTCCCTGCTTCTCTCTCTTCCAACAGCTCCCCTATGCAGGC
AATAACCTTTACATTTTGACTCAAGGCATATGCAGCCTTCTTCCCAATAAA
						
						Genomic sequence
						
							CTCCATATATAATTCGAATGCCGGAAGCAACCTCAGGTGACACGTTGGTTTTCAACCAATCACG
AACAGCAGCATGAACTTCCTGAGCTTGCTCAGGAGTAGCAACTTTCCCGGTTCCAATAGCCCAA
ACAGGCTCATATGCAATTACTACATCCGCCCAGTTTGTAATACTGTCTGAAAGCAACATGTTGA
TACATGAATCTTGTCTTCAGATGATGTAGGCTCATCAACCATTATTAATTTAACTCAAGATGAA
GAATTGTCACCTGCAAAAGCCTTCATCTGCTTAAAACAGACGTCAAAAGTTTTCCCTGCTTCTC
TCTCTTCCAACAGCTCCCCTATGCAGGCAATAACCTTTACATTTTGACTCAAGGCATATGCAGC
CTTCTTCCCAATAAA

Sequences
Splice junction sequence	CAAAAGTTTTCCCTGCTTCTCTCTCTTCCAACAGCTCCCCTATGCAGGCAATAACCTTTACATT TTGACTCAAGGCATATGCAGCCTTCTTCCCAATAAActccatatataattcgaatgccggaagc aacctcaggtgacacgttggttttcaaccaatcacgaacagcagcatgaacttcctgagcttgc tcaggagt
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: 307 Transcript exons: 21034054-21034227,21034320-21034452 CTCCATATATAATTCGAATGCCGGAAGCAACCTCAGGTGACACGTTGGTTTTCAACCAATCACG AACAGCAGCATGAACTTCCTGAGCTTGCTCAGGAGTAGCAACTTTCCCGGTTCCAATAGCCCAA ACAGGCTCATATGCAATTACTACATCCGCCCAGTTTGTAATACTGTCTGCAAAAGCCTTCATCT GCTTAAAACAGACGTCAAAAGTTTTCCCTGCTTCTCTCTCTTCCAACAGCTCCCCTATGCAGGC AATAACCTTTACATTTTGACTCAAGGCATATGCAGCCTTCTTCCCAATAAA
Genomic sequence	CTCCATATATAATTCGAATGCCGGAAGCAACCTCAGGTGACACGTTGGTTTTCAACCAATCACG AACAGCAGCATGAACTTCCTGAGCTTGCTCAGGAGTAGCAACTTTCCCGGTTCCAATAGCCCAA ACAGGCTCATATGCAATTACTACATCCGCCCAGTTTGTAATACTGTCTGAAAGCAACATGTTGA TACATGAATCTTGTCTTCAGATGATGTAGGCTCATCAACCATTATTAATTTAACTCAAGATGAA GAATTGTCACCTGCAAAAGCCTTCATCTGCTTAAAACAGACGTCAAAAGTTTTCCCTGCTTCTC TCTCTTCCAACAGCTCCCCTATGCAGGCAATAACCTTTACATTTTGACTCAAGGCATATGCAGC CTTCTTCCCAATAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.544579428

Conservation Information
Conserved circRNAs	NA
PMCS	0.544579428

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							21034128-21034062(+)
21034337-21034354(-)
21034061-21034354(-)
						
						Potential amino acid sequence
						
							MNFLSLLRSSNFPGSNSPNRLICNYYIRPVCNTVCKSLHLLKTDVKSFPCFSLFQQLPYAGNNL
YILTQGICSLLPNKLHI*(+)
MKAFADSITNWADVVIAYEPVWAIGTGKVATPEQAQEVHAAVRDWLKTNVSPEVASGIRIIYGV
YWEEGCICLESKCKGYCLHRGAVGRERSRENF*(-)
MEFIGKKAAYALSQNVKVIACIGELLEEREAGKTFDVCFKQMKAFADSITNWADVVIAYEPVWA
IGTGKVATPEQAQEVHAAVRDWLKTNVSPEVASGIRIIYGVYWEEGCICLESKCKGYCLHRGAV
GRERSRENF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	21034128-21034062(+) 21034337-21034354(-) 21034061-21034354(-)
Potential amino acid sequence	MNFLSLLRSSNFPGSNSPNRLICNYYIRPVCNTVCKSLHLLKTDVKSFPCFSLFQQLPYAGNNL YILTQGICSLLPNKLHI(+) MKAFADSITNWADVVIAYEPVWAIGTGKVATPEQAQEVHAAVRDWLKTNVSPEVASGIRIIYGV YWEEGCICLESKCKGYCLHRGAVGRERSRENF(-) MEFIGKKAAYALSQNVKVIACIGELLEEREAGKTFDVCFKQMKAFADSITNWADVVIAYEPVWA IGTGKVATPEQAQEVHAAVRDWLKTNVSPEVASGIRIIYGVYWEEGCICLESKCKGYCLHRGAV GRERSRENF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os09g0535000_circ_g.3

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