Plant Circular RNA Database

Detail information of Os04g0659500_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0659500_circ_g.3
					
						ID in PlantcircBase
						osa_circ_025785
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 33651667-33652514  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0659500						
					
						Parent gene annotation
						
							Protein phosphatase 2C domain containing protein. (Os04t0659500-
01);Similar to OSIGBa0132E09-OSIGBa0108L24.16 protein. (Os04t065
9500-02)
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Os04g0659500_circ_g.1 Os04g0659500_circ_g.2 						
					
						Support reads
						3
					
						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
						Os04t0659500-02:3
Os04t0659500-01:3

General Information
CircRNA Name	Os04g0659500_circ_g.3
ID in PlantcircBase	osa_circ_025785
Alias	NA
Organism	Oryza sativa
Position	chr4: 33651667-33652514 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0659500
Parent gene annotation	Protein phosphatase 2C domain containing protein. (Os04t0659500- 01);Similar to OSIGBa0132E09-OSIGBa0108L24.16 protein. (Os04t065 9500-02)
Parent gene strand	-
Alternative splicing	Os04g0659500_circ_g.1 Os04g0659500_circ_g.2
Support reads	3
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	Os04t0659500-02:3 Os04t0659500-01:3

			
						 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  
						
							CTGCCCATCAACAGAGTCAATTCTTGTCTCGTAAAAGTCTTCCATGGAAGCCCTTTTACCAGGG
GAGCTCGCATACCCATAGCTAAACTTACCATTCTGGcatttccccccctgcatatgatagccct
agagtctccaacgtttgcaacaaagagacggtcaccaacaaggacagcggttgatgcagttgat
ccacactg

						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
						
							CATTTCCCCCCCTGCATATGATAGCCCTAGAGTCTCCAACGTTTGCAACAAAGAGACGGTCACC
AACAAGGACAGCGGTTGATGCAGTTGATCCACACTGGTTTTGACTGCTGTCAGATTCTAAGAAT
TCACTGTCGGTACTTTTATAAGCATCATCTACAGCAAACAATATCACGTGGTAGTTCTGTCAAT
TCTATACACAAAACTCAACATCTAGTGAATTATGGAAAGAGAACAAACCAATACCTATTGCCAC
TTTGGTGTCACTGATGAACTTTGGATGCCTTAGAAGATGACTGAAGAGATTCTGTTTAACATAC
TCAGCTACTTTAGCACCACCATGACCTATAAAATGAACTGTATGTTTAGCATTTATTTTTCCTA
AAATAAGCTCAAGAGCTTGGTATATCCACACTTCTAGTTCAATTTAAAGCATTGTGCCCTAGTA
TGAGTAATCTTTAAAACTTTCTCCATGGACTTCTCACCGTCATACTAGCTCTAACTGCGGAAAT
AAGAAATGTTACAAGGCAAATGAATTATTTTGAGCTTTTTTATACTATACAAGATTAGCAAAGG
AAACATAAATGGTATGTTCTTTTGGTACAAAAGAGAAAGGTCTAAAACTTGGAAGAGTGTAATC
TTAGAAATGTTCCTTTCTAAAATGATAAAGAATTATCAATGGGTAGAGATTATGCACGAATGTG
ACAAATTCATACATACCATCAAAAACTCCAAAAAGACCAATAATCTGCCCATCAACAGAGTCAA
TTCTTGTCTCGTAAAAGTCTTCCATGGAAGCCCTTTTACCAGGGGAGCTCGCATACCCATAGCT
AAACTTACCATTCTGG

Sequences
Splice junction sequence	CTGCCCATCAACAGAGTCAATTCTTGTCTCGTAAAAGTCTTCCATGGAAGCCCTTTTACCAGGG GAGCTCGCATACCCATAGCTAAACTTACCATTCTGGcatttccccccctgcatatgatagccct agagtctccaacgtttgcaacaaagagacggtcaccaacaaggacagcggttgatgcagttgat ccacactg
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	CATTTCCCCCCCTGCATATGATAGCCCTAGAGTCTCCAACGTTTGCAACAAAGAGACGGTCACC AACAAGGACAGCGGTTGATGCAGTTGATCCACACTGGTTTTGACTGCTGTCAGATTCTAAGAAT TCACTGTCGGTACTTTTATAAGCATCATCTACAGCAAACAATATCACGTGGTAGTTCTGTCAAT TCTATACACAAAACTCAACATCTAGTGAATTATGGAAAGAGAACAAACCAATACCTATTGCCAC TTTGGTGTCACTGATGAACTTTGGATGCCTTAGAAGATGACTGAAGAGATTCTGTTTAACATAC TCAGCTACTTTAGCACCACCATGACCTATAAAATGAACTGTATGTTTAGCATTTATTTTTCCTA AAATAAGCTCAAGAGCTTGGTATATCCACACTTCTAGTTCAATTTAAAGCATTGTGCCCTAGTA TGAGTAATCTTTAAAACTTTCTCCATGGACTTCTCACCGTCATACTAGCTCTAACTGCGGAAAT AAGAAATGTTACAAGGCAAATGAATTATTTTGAGCTTTTTTATACTATACAAGATTAGCAAAGG AAACATAAATGGTATGTTCTTTTGGTACAAAAGAGAAAGGTCTAAAACTTGGAAGAGTGTAATC TTAGAAATGTTCCTTTCTAAAATGATAAAGAATTATCAATGGGTAGAGATTATGCACGAATGTG ACAAATTCATACATACCATCAAAAACTCCAAAAAGACCAATAATCTGCCCATCAACAGAGTCAA TTCTTGTCTCGTAAAAGTCTTCCATGGAAGCCCTTTTACCAGGGGAGCTCGCATACCCATAGCT AAACTTACCATTCTGG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.230495548

Conservation Information
Conserved circRNAs	NA
PMCS	0.230495548

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							33651960-33651770(+)
33651685-33651993(-)
						
						Potential amino acid sequence
						
							MTEEILFNILSYFSTTMTILAFPPLHMIALESPTFATKRRSPTRTAVDAVDPHWF*(+)
MQGGKCQNGHGGAKVAEYVKQNLFSHLLRHPKFISDTKVAIDDAYKSTDSEFLESDSSQNQCGS
TASTAVLVGDRLFVANVGDSRAIICRGGNARMVMVVLK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	33651960-33651770(+) 33651685-33651993(-)
Potential amino acid sequence	MTEEILFNILSYFSTTMTILAFPPLHMIALESPTFATKRRSPTRTAVDAVDPHWF(+) MQGGKCQNGHGGAKVAEYVKQNLFSHLLRHPKFISDTKVAIDDAYKSTDSEFLESDSSQNQCGS TASTAVLVGDRLFVANVGDSRAIICRGGNARMVMVVLK(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0659500_circ_g.3

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