Plant Circular RNA Database

Detail information of Os04g0487100_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0487100_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024297
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24341968-24342553  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0487100						
					
						Parent gene annotation
						
							Galactose oxidase/kelch, beta-propeller domain containing protei
n. (Os04t0487100-01)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os04g0479800_circ_igg.1 Os04g0480100_circ_g.1 Os04g0480100_circ_g.2 Os04g0480100_circ_g.3 Os04g0480100_circ_g.4 Os04g0480300_circ_g.1 Os04g0480400_circ_g.1 Os04g0480400_circ_g.2 Os04g0480700_circ_g.1 Os04g0480900_circ_g.1 Os04g0480900_circ_ag.1 Os04g0480900_circ_ag.2 Os04g0481000_circ_ig.1 Os04g0481100_circ_g.1 Os04g0481100_circ_g.2 Os04g0481100_circ_g.3 Os04g0481300_circ_g.1 Os04g0481400_circ_g.1 EPlOSAG00000043923_circ_ig.1 Os04g0482300_circ_g.1 Os04g0482700_circ_g.1 Os04g0482800_circ_g.1 Os04g0482800_circ_g.2 Os04g0482800_circ_g.3 Os04g0483200_circ_g.1 Os04g0483550_circ_g.1 Os04g0483600_circ_g.1 Os04g0483600_circ_g.2 Os04g0483600_circ_g.3 Os04g0483600_circ_g.4 Os04g0484800_circ_g.1 Os04g0484800_circ_g.2 Os04g0484800_circ_g.3 Os04g0484900_circ_g.1 Os04g0485000_circ_g.1 Os04g0485000_circ_g.2 Os04g0485100_circ_g.1 Os04g0485100_circ_g.2 Os04g0485200_circ_g.1 Os04g0485200_circ_g.2 Os04g0485300_circ_g.1 Os04g0485300_circ_g.2 Os04g0485300_circ_g.3 Os04g0485300_circ_g.4 Os04g0485300_circ_g.5 Os04g0485300_circ_g.6 Os04g0485300_circ_g.7 Os04g0485300_circ_g.8 Os04g0485300_circ_g.9 Os04g0485300_circ_g.10 Os04g0485300_circ_g.11 Os04g0485300_circ_g.12 Os04g0485300_circ_g.13 Os04g0485300_circ_g.14 Os04g0485300_circ_g.15 Os04g0485300_circ_g.16 Os04g0485601_circ_ig.1 Os04g0485800_circ_g.1 Os04g0486500_circ_g.1 Os04g0486500_circ_g.2 Os04g0486500_circ_g.3 Os04g0486500_circ_g.4 Os04g0486600_circ_g.1 Os04g0486600_circ_g.2 Os04g0486600_circ_g.3 Os04g0486600_circ_g.4 Os04g0486600_circ_g.5 Os04g0486600_circ_g.6 Os04g0486600_circ_g.7 Os04g0486600_circ_g.8 Os04g0486600_circ_g.9 Os04g0486600_circ_g.10 Os04g0486600_circ_g.11 Os04g0486900_circ_g.1 Os04g0486900_circ_g.2 Os04g0486950_circ_g.1 Os04g0487000_circ_g.1 Os04g0487100_circ_g.1 Os04g0487100_circ_g.2 Os04g0487200_circ_g.1 Os04g0488000_circ_g.1 Os04g0488000_circ_g.2 Os04g0488050_circ_g.1 Os04g0488050_circ_g.2 Os04g0488050_circ_g.3 Os04g0488050_circ_g.4 Os04g0488050_circ_g.5 Os04g0488050_circ_g.6 Os04g0488050_circ_g.7 Os04g0488000_circ_g.8 Os04g0488100_circ_g.1 						
					
						Support reads
						1
					
						Tissues
						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
						Os04t0487100-01:2

General Information
CircRNA Name	Os04g0487100_circ_g.3
ID in PlantcircBase	osa_circ_024297
Alias	NA
Organism	Oryza sativa
Position	chr4: 24341968-24342553 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0487100
Parent gene annotation	Galactose oxidase/kelch, beta-propeller domain containing protei n. (Os04t0487100-01)
Parent gene strand	+
Alternative splicing	Os04g0479800_circ_igg.1 Os04g0480100_circ_g.1 Os04g0480100_circ_g.2 Os04g0480100_circ_g.3 Os04g0480100_circ_g.4 Os04g0480300_circ_g.1 Os04g0480400_circ_g.1 Os04g0480400_circ_g.2 Os04g0480700_circ_g.1 Os04g0480900_circ_g.1 Os04g0480900_circ_ag.1 Os04g0480900_circ_ag.2 Os04g0481000_circ_ig.1 Os04g0481100_circ_g.1 Os04g0481100_circ_g.2 Os04g0481100_circ_g.3 Os04g0481300_circ_g.1 Os04g0481400_circ_g.1 EPlOSAG00000043923_circ_ig.1 Os04g0482300_circ_g.1 Os04g0482700_circ_g.1 Os04g0482800_circ_g.1 Os04g0482800_circ_g.2 Os04g0482800_circ_g.3 Os04g0483200_circ_g.1 Os04g0483550_circ_g.1 Os04g0483600_circ_g.1 Os04g0483600_circ_g.2 Os04g0483600_circ_g.3 Os04g0483600_circ_g.4 Os04g0484800_circ_g.1 Os04g0484800_circ_g.2 Os04g0484800_circ_g.3 Os04g0484900_circ_g.1 Os04g0485000_circ_g.1 Os04g0485000_circ_g.2 Os04g0485100_circ_g.1 Os04g0485100_circ_g.2 Os04g0485200_circ_g.1 Os04g0485200_circ_g.2 Os04g0485300_circ_g.1 Os04g0485300_circ_g.2 Os04g0485300_circ_g.3 Os04g0485300_circ_g.4 Os04g0485300_circ_g.5 Os04g0485300_circ_g.6 Os04g0485300_circ_g.7 Os04g0485300_circ_g.8 Os04g0485300_circ_g.9 Os04g0485300_circ_g.10 Os04g0485300_circ_g.11 Os04g0485300_circ_g.12 Os04g0485300_circ_g.13 Os04g0485300_circ_g.14 Os04g0485300_circ_g.15 Os04g0485300_circ_g.16 Os04g0485601_circ_ig.1 Os04g0485800_circ_g.1 Os04g0486500_circ_g.1 Os04g0486500_circ_g.2 Os04g0486500_circ_g.3 Os04g0486500_circ_g.4 Os04g0486600_circ_g.1 Os04g0486600_circ_g.2 Os04g0486600_circ_g.3 Os04g0486600_circ_g.4 Os04g0486600_circ_g.5 Os04g0486600_circ_g.6 Os04g0486600_circ_g.7 Os04g0486600_circ_g.8 Os04g0486600_circ_g.9 Os04g0486600_circ_g.10 Os04g0486600_circ_g.11 Os04g0486900_circ_g.1 Os04g0486900_circ_g.2 Os04g0486950_circ_g.1 Os04g0487000_circ_g.1 Os04g0487100_circ_g.1 Os04g0487100_circ_g.2 Os04g0487200_circ_g.1 Os04g0488000_circ_g.1 Os04g0488000_circ_g.2 Os04g0488050_circ_g.1 Os04g0488050_circ_g.2 Os04g0488050_circ_g.3 Os04g0488050_circ_g.4 Os04g0488050_circ_g.5 Os04g0488050_circ_g.6 Os04g0488050_circ_g.7 Os04g0488000_circ_g.8 Os04g0488100_circ_g.1
Support reads	1
Tissues	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	Os04t0487100-01:2

			
						 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  
						
							TGTTGTTGCTAATGATAAGCTACTTGTTATTGGTGGCCAAGAAGGAGATTTTATGGCGAAACCT
GGATCACCTATATTTAAATGTGTTAGAAGAAGTGAGatatgctccagccacacaactttggaga
ggcaggcttcatgtgatgggtggcagcaaggaggataggcatgaacctgggcttgaacattgga
gcattgca

						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
						
							ATATGCTCCAGCCACACAACTTTGGAGAGGCAGGCTTCATGTGATGGGTGGCAGCAAGGAGGAT
AGGCATGAACCTGGGCTTGAACATTGGAGCATTGCAGTAAAGGATGGGAAAGCCCTGGAAAACG
AGTGGAGGAGTGAGGTACCAATCCCACGTGGAGGCCCTCATAGGTCTATAACTCCCCCTCCACA
TGATTTCTATTGTTGCCATTTTTGTTGGAAAGTAATGTTGCTATACACCTGAATGGTCTTGATG
TTTAGCATCTGTTGTATTCAGATTTTTATGATGCCGCCCACAATATGTATGCTTCTAGGCTATT
TCTTTGATCAAGTATCTAAATTAAAATTAGTTCTGGGCCAGAAATATGTTTGTACGCCATACAA
AGTTCTTATGTGGCATATAAGTATATAACCTGTTTCCGAGAATGGTCCTGTTGTTAGCTTAGCA
GCTTAATCATGATTTTTCTCTTTTGATACCAGGGCTTGTGTTGTTGCTAATGATAAGCTACTTG
TTATTGGTGGCCAAGAAGGAGATTTTATGGCGAAACCTGGATCACCTATATTTAAATGTGTTAG
AAGAAGTGAG

Sequences
Splice junction sequence	TGTTGTTGCTAATGATAAGCTACTTGTTATTGGTGGCCAAGAAGGAGATTTTATGGCGAAACCT GGATCACCTATATTTAAATGTGTTAGAAGAAGTGAGatatgctccagccacacaactttggaga ggcaggcttcatgtgatgggtggcagcaaggaggataggcatgaacctgggcttgaacattgga gcattgca
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	ATATGCTCCAGCCACACAACTTTGGAGAGGCAGGCTTCATGTGATGGGTGGCAGCAAGGAGGAT AGGCATGAACCTGGGCTTGAACATTGGAGCATTGCAGTAAAGGATGGGAAAGCCCTGGAAAACG AGTGGAGGAGTGAGGTACCAATCCCACGTGGAGGCCCTCATAGGTCTATAACTCCCCCTCCACA TGATTTCTATTGTTGCCATTTTTGTTGGAAAGTAATGTTGCTATACACCTGAATGGTCTTGATG TTTAGCATCTGTTGTATTCAGATTTTTATGATGCCGCCCACAATATGTATGCTTCTAGGCTATT TCTTTGATCAAGTATCTAAATTAAAATTAGTTCTGGGCCAGAAATATGTTTGTACGCCATACAA AGTTCTTATGTGGCATATAAGTATATAACCTGTTTCCGAGAATGGTCCTGTTGTTAGCTTAGCA GCTTAATCATGATTTTTCTCTTTTGATACCAGGGCTTGTGTTGTTGCTAATGATAAGCTACTTG TTATTGGTGGCCAAGAAGGAGATTTTATGGCGAAACCTGGATCACCTATATTTAAATGTGTTAG AAGAAGTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.275227133

Conservation Information
Conserved circRNAs	NA
PMCS	0.275227133

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24342012-24342030(+)
24342076-24342030(+)
24342138-24342542(-)
						
						Potential amino acid sequence
						
							MGGSKEDRHEPGLEHWSIAVKDGKALENEWRSEVPIPRGGPHRACVVANDKLLVIGGQEGDFMA
KPGSPIFKCVRRSEICSSHTTLERQASCDGWQQGG*(+)
MGKPWKTSGGVRYQSHVEALIGLVLLLMISYLLLVAKKEILWRNLDHLYLNVLEEVRYAPATQL
WRGRLHVMGGSKEDRHEPGLEHWSIAVKDGKALENEWRSEVPIPRGGPHRACVVANDKLLVIGG
QEGDFMAKPGSPIFKCVRRSEICSSHTTLERQASCDGWQQGG*(+)
MRASTWDWYLTPPLVFQGFPILYCNAPMFKPRFMPILLAATHHMKPASPKLCGWSISHFF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24342012-24342030(+) 24342076-24342030(+) 24342138-24342542(-)
Potential amino acid sequence	MGGSKEDRHEPGLEHWSIAVKDGKALENEWRSEVPIPRGGPHRACVVANDKLLVIGGQEGDFMA KPGSPIFKCVRRSEICSSHTTLERQASCDGWQQGG(+) MGKPWKTSGGVRYQSHVEALIGLVLLLMISYLLLVAKKEILWRNLDHLYLNVLEEVRYAPATQL WRGRLHVMGGSKEDRHEPGLEHWSIAVKDGKALENEWRSEVPIPRGGPHRACVVANDKLLVIGG QEGDFMAKPGSPIFKCVRRSEICSSHTTLERQASCDGWQQGG(+) MRASTWDWYLTPPLVFQGFPILYCNAPMFKPRFMPILLAATHHMKPASPKLCGWSISHFF*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0487100_circ_g.3

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