Plant Circular RNA Database

Detail information of Os04g0486600_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os04g0486600_circ_g.3
					
						ID in PlantcircBase
						osa_circ_024283
					
						Alias
						NA
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr4: 24306430-24306977  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer
					
						Parent gene
						
							Os04g0486600						
					
						Parent gene annotation
						
							Similar to Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3
 (EC 1.2.1.12). (Os04t0486600-01);Similar to Glyceralde-3-phosph
ate dehydrogenase. (Os04t0486600-02)
							
						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.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 Os04g0487100_circ_g.3 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
						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
						Os04t0486600-01:3
Os04t0486600-02:2

General Information
CircRNA Name	Os04g0486600_circ_g.3
ID in PlantcircBase	osa_circ_024283
Alias	NA
Organism	Oryza sativa
Position	chr4: 24306430-24306977 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer
Parent gene	Os04g0486600
Parent gene annotation	Similar to Glyceraldehyde-3-phosphate dehydrogenase, cytosolic 3 (EC 1.2.1.12). (Os04t0486600-01);Similar to Glyceralde-3-phosph ate dehydrogenase. (Os04t0486600-02)
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.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 Os04g0487100_circ_g.3 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	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	Os04t0486600-01:3 Os04t0486600-02:2

			
						 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  
						
							CATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTGTGTCCAATGCT
AGCTGCACCACCAACTGCCTTGCTCCACTTGCCAAGacatacatgttcaagtatgacactgtgc
acggccagtggaagcatcatgaggttaaggtgaaggactccaagacccttctcttcggtgagaa
ggaggtca

						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
						
							ACATACATGTTCAAGTATGACACTGTGCACGGCCAGTGGAAGCATCATGAGGTTAAGGTGAAGG
ACTCCAAGACCCTTCTCTTCGGTGAGAAGGAGGTCACCGTGTTCGGCTGCAGGTTTGCTGTTTT
TTTCCCTCTCTGCTGTTGTCTGATGATATCATGAGCAGTATACCATATCGCTCAACCTTAATTT
CTCTGCTCAGGAACCCTGAGGAGATCCCATGGGGTGAGACTGGCGCTGAGTTTGTTGTGGAGTC
CACTGGTGTTTTCACTGACAAGGACAAGGCCGCTGCTCACCTGAAGGTATTTTCTGCGAAACCC
AACATGTCATTGTTTGATTGTGGTGTCATAACAATTCATATGAAGAATGATTCTCATGGTATCA
TATGCGTTTCAATATAGGGTGGTGCTAAGAAGGTCGTCATCTCTGCTCCCAGCAAGGATGCCCC
CATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTGTGTCCAATGCT
AGCTGCACCACCAACTGCCTTGCTCCACTTGCCAAG

Sequences
Splice junction sequence	CATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTGTGTCCAATGCT AGCTGCACCACCAACTGCCTTGCTCCACTTGCCAAGacatacatgttcaagtatgacactgtgc acggccagtggaagcatcatgaggttaaggtgaaggactccaagacccttctcttcggtgagaa ggaggtca
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	ACATACATGTTCAAGTATGACACTGTGCACGGCCAGTGGAAGCATCATGAGGTTAAGGTGAAGG ACTCCAAGACCCTTCTCTTCGGTGAGAAGGAGGTCACCGTGTTCGGCTGCAGGTTTGCTGTTTT TTTCCCTCTCTGCTGTTGTCTGATGATATCATGAGCAGTATACCATATCGCTCAACCTTAATTT CTCTGCTCAGGAACCCTGAGGAGATCCCATGGGGTGAGACTGGCGCTGAGTTTGTTGTGGAGTC CACTGGTGTTTTCACTGACAAGGACAAGGCCGCTGCTCACCTGAAGGTATTTTCTGCGAAACCC AACATGTCATTGTTTGATTGTGGTGTCATAACAATTCATATGAAGAATGATTCTCATGGTATCA TATGCGTTTCAATATAGGGTGGTGCTAAGAAGGTCGTCATCTCTGCTCCCAGCAAGGATGCCCC CATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTGTGTCCAATGCT AGCTGCACCACCAACTGCCTTGCTCCACTTGCCAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.444895453

Conservation Information
Conserved circRNAs	NA
PMCS	0.444895453

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							24306437-24306974(+)
24306872-24306487(+)
24306479-24306432(-)
24306439-24306724(-)
						
						Potential amino acid sequence
						
							MFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDK
AAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAKTYMFKYDTV
HGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDKAAAHLKG
GAKKVVISAPSKDAPMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAKTYMFKYDTVHGQWKHH
EVKVKDSKTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDKAAAHLKGGAKKVVI
SAPSKDAPMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAKTYMFKYDTVHGQWKHHEVKVKDS
KTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDA
PMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAK(+)
MPPCLLLVSMRRSTSLTSTLCPMLAAPPTALLHLPRHTCSSMTLCTASGSIMRLR*(+)
MMLPLAVHSVILEHVCLGKWSKAVGGAASIGHNVDVRLVLLLIDTNNKHGGILAGSRDDDLLST
TLQVSSGLVLVSENTSGLHNKLSASLTPWDLLRVPAAEHGDLLLTEEKGLGVLHLNLMMLPLAV
HSVILEHVCLGKWSKAVGGAASIGHNVDVRLVLLLIDTNNKHGGILAGSRDDDLLSTTLQVSSG
LVLVSENTSGLHNKLSASLTPWDLLRVPAAEHGDLLLTEEKGLGVLHLNLMMLPLAVHSVILEH
VCLGKWSKAVGGAASIGHNVDVRLVLLLIDTNNKHGGILAGSRDDDLLSTTLQVSSGLVLVSEN
TSGLHNKLSASLTPWDLLRVPAAEHGDLLLTEEKGLGVLHLNLMMLPLAVHSVILEHVC(-)
MYVLASGARQLVVQLALDTMSMSGLYSFSLTPTTNMGASLLGAEMTTFLAPPFR*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	24306437-24306974(+) 24306872-24306487(+) 24306479-24306432(-) 24306439-24306724(-)
Potential amino acid sequence	MFKYDTVHGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDK AAAHLKGGAKKVVISAPSKDAPMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAKTYMFKYDTV HGQWKHHEVKVKDSKTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDKAAAHLKG GAKKVVISAPSKDAPMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAKTYMFKYDTVHGQWKHH EVKVKDSKTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDKAAAHLKGGAKKVVI SAPSKDAPMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAKTYMFKYDTVHGQWKHHEVKVKDS KTLLFGEKEVTVFGCRNPEEIPWGETGAEFVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDA PMFVVGVNEKEYKPDIDIVSNASCTTNCLAPLAK(+) MPPCLLLVSMRRSTSLTSTLCPMLAAPPTALLHLPRHTCSSMTLCTASGSIMRLR(+) MMLPLAVHSVILEHVCLGKWSKAVGGAASIGHNVDVRLVLLLIDTNNKHGGILAGSRDDDLLST TLQVSSGLVLVSENTSGLHNKLSASLTPWDLLRVPAAEHGDLLLTEEKGLGVLHLNLMMLPLAV HSVILEHVCLGKWSKAVGGAASIGHNVDVRLVLLLIDTNNKHGGILAGSRDDDLLSTTLQVSSG LVLVSENTSGLHNKLSASLTPWDLLRVPAAEHGDLLLTEEKGLGVLHLNLMMLPLAVHSVILEH VCLGKWSKAVGGAASIGHNVDVRLVLLLIDTNNKHGGILAGSRDDDLLSTTLQVSSGLVLVSEN TSGLHNKLSASLTPWDLLRVPAAEHGDLLLTEEKGLGVLHLNLMMLPLAVHSVILEHVC(-) MYVLASGARQLVVQLALDTMSMSGLYSFSLTPTTNMGASLLGAEMTTFLAPPFR(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017

circRNA

Detail information of Os04g0486600_circ_g.3

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