Plant Circular RNA Database

Detail information of Os02g0146700_circ_g.3

			
						 General Information
					
						CircRNA Name
						Os02g0146700_circ_g.3
					
						ID in PlantcircBase
						osa_circ_013125
					
						Alias
						Os_ciR7938
					
						Organism
						
							Oryza sativa						
					
						Position
						
							chr2: 2566842-2567374  JBrowse»						
					
						Reference genome
						
							IRGSP-1.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, find_circ
					
						Parent gene
						
							Os02g0146700						
					
						Parent gene annotation
						
							Similar to predicted protein. (Os02t0146700-01);Similar to PSMD2
 subunit (Fragment). (Os02t0146700-02)
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Os02g0141300_circ_g.1 Os02g0141300_circ_igg.1 Os02g0141300_circ_g.2 Os02g0141300_circ_g.3 Os02g0141300_circ_g.4 Os02g0141300_circ_g.5 Os02g0141300_circ_g.6 Os02g0141300_circ_g.7 Os02g0142250_circ_ag.1 Os02g0142300_circ_g.1 Os02g0142450_circ_g.1 Os02g0142450_circ_g.2 Os02g0142450_circ_g.3 Os02g0142500_circ_igg.1 Os02g0142500_circ_ag.1 Os02g0142500_circ_ag.2 Os02g0143100_circ_g.1 Os02g0143100_circ_g.2 Os02g0143100_circ_g.3 Os02g0143100_circ_g.4 Os02g0143100_circ_g.5 Os02g0143100_circ_g.6 Os02g0143100_circ_g.7 Os02g0143200_circ_g.1 Os02g0143200_circ_g.2 Os02g0145000_circ_g.1 EPlOSAG00000039494_circ_ig.1 EPlOSAG00000039494_circ_ig.2 ENSRNA049472287_circ_ig.1 Os02g0146500_circ_g.1 Os02g0146500_circ_g.2 Os02g0146600_circ_g.1 Os02g0146600_circ_g.2 Os02g0146600_circ_g.3 Os02g0146700_circ_g.1 Os02g0146700_circ_g.2 Os02g0146700_circ_g.4 Os02g0146700_circ_g.5 Os02g0146900_circ_g.1 Os02g0147100_circ_ag.1 Os02g0147100_circ_ag.2 Os02g0147100_circ_ag.3 Os02g0147100_circ_ag.4 Os02g0147100_circ_ag.5 Os02g0147700_circ_igg.1 Os02g0147700_circ_igg.2 						
					
						Support reads
						2/1
					
						Tissues
						root/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
						Os02t0146700-01:3
Os02t0146700-02:3

General Information
CircRNA Name	Os02g0146700_circ_g.3
ID in PlantcircBase	osa_circ_013125
Alias	Os_ciR7938
Organism	Oryza sativa
Position	chr2: 2566842-2567374 JBrowse»
Reference genome	IRGSP-1.0.38
Type	e-circRNA
Identification method	CIRCexplorer, find_circ
Parent gene	Os02g0146700
Parent gene annotation	Similar to predicted protein. (Os02t0146700-01);Similar to PSMD2 subunit (Fragment). (Os02t0146700-02)
Parent gene strand	+
Alternative splicing	Os02g0141300_circ_g.1 Os02g0141300_circ_igg.1 Os02g0141300_circ_g.2 Os02g0141300_circ_g.3 Os02g0141300_circ_g.4 Os02g0141300_circ_g.5 Os02g0141300_circ_g.6 Os02g0141300_circ_g.7 Os02g0142250_circ_ag.1 Os02g0142300_circ_g.1 Os02g0142450_circ_g.1 Os02g0142450_circ_g.2 Os02g0142450_circ_g.3 Os02g0142500_circ_igg.1 Os02g0142500_circ_ag.1 Os02g0142500_circ_ag.2 Os02g0143100_circ_g.1 Os02g0143100_circ_g.2 Os02g0143100_circ_g.3 Os02g0143100_circ_g.4 Os02g0143100_circ_g.5 Os02g0143100_circ_g.6 Os02g0143100_circ_g.7 Os02g0143200_circ_g.1 Os02g0143200_circ_g.2 Os02g0145000_circ_g.1 EPlOSAG00000039494_circ_ig.1 EPlOSAG00000039494_circ_ig.2 ENSRNA049472287_circ_ig.1 Os02g0146500_circ_g.1 Os02g0146500_circ_g.2 Os02g0146600_circ_g.1 Os02g0146600_circ_g.2 Os02g0146600_circ_g.3 Os02g0146700_circ_g.1 Os02g0146700_circ_g.2 Os02g0146700_circ_g.4 Os02g0146700_circ_g.5 Os02g0146900_circ_g.1 Os02g0147100_circ_ag.1 Os02g0147100_circ_ag.2 Os02g0147100_circ_ag.3 Os02g0147100_circ_ag.4 Os02g0147100_circ_ag.5 Os02g0147700_circ_igg.1 Os02g0147700_circ_igg.2
Support reads	2/1
Tissues	root/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	Os02t0146700-01:3 Os02t0146700-02:3

			
						 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  
						
							TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACA
TTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGtcaatgcagtatgtgaagcaggtctaca
ccgcaactgaggatcttcagctcaaaaagcagttctcattcatcattgcacgccatgtataaat
ctctcacg

						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: 348
Transcript exons: 2566842-2566925,2567028-2567186,2567270-2567374
TCAATGCAGTATGTGAAGCAGGTCTACACCGCAACTGAGGATCTTCAGCTCAAAAAGCAGTTCT
CATTCATCATTGCACGCCATGGTTTGGCCATGGAGATTGACGACGAGATAGCTGCCGATGGCAA
TGATAAGGAGGGTTTGCAAGAAATCGTTAATAATAGTAAGCTGAGTGAGGGGTACCTCACCCTT
GCTCGAGATATCGAAGTGATGGAAGCAAAATCTCCAGAGGATATATATAAGGTCCATTTAATTG
ATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAA
TGCATTCGTAAATGCTGGATTTGGTCAG
						
						Genomic sequence
						
							TCAATGCAGTATGTGAAGCAGGTCTACACCGCAACTGAGGATCTTCAGCTCAAAAAGCAGTTCT
CATTCATCATTGCACGCCATGTATAAATCTCTCACGCACTATCTACCTTGGTTGCCACCTTTTG
CATCTTATGCTAAAAGTAGCAATCCCTTAAATTTGACCCAAGCGCTTCTCTTCTGCAGGGTTTG
GCCATGGAGATTGACGACGAGATAGCTGCCGATGGCAATGATAAGGAGGGTTTGCAAGAAATCG
TTAATAATAGTAAGCTGAGTGAGGGGTACCTCACCCTTGCTCGAGATATCGAAGTGATGGAAGC
AAAATCTCCAGAGGATATATATAAGGTCATCTATATTTTACTATCAATGTTTATTAAGGTTGCT
TTTTTCATTCATAATAATTAATATTTGTATTTAACAATCTACAGGTCCATTTAATTGATGGGCG
TGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTC
GTAAATGCTGGATTTGGTCAG

Sequences
Splice junction sequence	TTTAATTGATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACA TTTGTAAATGCATTCGTAAATGCTGGATTTGGTCAGtcaatgcagtatgtgaagcaggtctaca ccgcaactgaggatcttcagctcaaaaagcagttctcattcatcattgcacgccatgtataaat ctctcacg
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: 348 Transcript exons: 2566842-2566925,2567028-2567186,2567270-2567374 TCAATGCAGTATGTGAAGCAGGTCTACACCGCAACTGAGGATCTTCAGCTCAAAAAGCAGTTCT CATTCATCATTGCACGCCATGGTTTGGCCATGGAGATTGACGACGAGATAGCTGCCGATGGCAA TGATAAGGAGGGTTTGCAAGAAATCGTTAATAATAGTAAGCTGAGTGAGGGGTACCTCACCCTT GCTCGAGATATCGAAGTGATGGAAGCAAAATCTCCAGAGGATATATATAAGGTCCATTTAATTG ATGGGCGTGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAA TGCATTCGTAAATGCTGGATTTGGTCAG
Genomic sequence	TCAATGCAGTATGTGAAGCAGGTCTACACCGCAACTGAGGATCTTCAGCTCAAAAAGCAGTTCT CATTCATCATTGCACGCCATGTATAAATCTCTCACGCACTATCTACCTTGGTTGCCACCTTTTG CATCTTATGCTAAAAGTAGCAATCCCTTAAATTTGACCCAAGCGCTTCTCTTCTGCAGGGTTTG GCCATGGAGATTGACGACGAGATAGCTGCCGATGGCAATGATAAGGAGGGTTTGCAAGAAATCG TTAATAATAGTAAGCTGAGTGAGGGGTACCTCACCCTTGCTCGAGATATCGAAGTGATGGAAGC AAAATCTCCAGAGGATATATATAAGGTCATCTATATTTTACTATCAATGTTTATTAAGGTTGCT TTTTTCATTCATAATAATTAATATTTGTATTTAACAATCTACAGGTCCATTTAATTGATGGGCG TGGTGCCAGCTCCAGTCTTGATTCTGCAAGACAAAATTTAGCTGCAACATTTGTAAATGCATTC GTAAATGCTGGATTTGGTCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_012126 osi_circ_002660 osi_circ_011171 						
					
						PMCS
						0.387693809

Conservation Information
Conserved circRNAs	osi_circ_012126 osi_circ_002660 osi_circ_011171
PMCS	0.387693809

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2566846-2567371(+)
						
						Potential amino acid sequence
						
							MQYVKQVYTATEDLQLKKQFSFIIARHGLAMEIDDEIAADGNDKEGLQEIVNNSKLSEGYLTLA
RDIEVMEAKSPEDIYKVHLIDGRGASSSLDSARQNLAATFVNAFVNAGFGQSMQYVKQVYTATE
DLQLKKQFSFIIARHGLAMEIDDEIAADGNDKEGLQEIVNNSKLSEGYLTLARDIEVMEAKSPE
DIYKVHLIDGRGASSSLDSARQNLAATFVNAFVNAGFGQSMQYVKQVYTATEDLQLKKQFSFII
ARHGLAMEIDDEIAADGNDKEGLQEIVNNSKLSEGYLTLARDIEVMEAKSPEDIYKVHLIDGRG
ASSSLDSARQNLAATFVNAFVNAGFGQSMQYVKQVYTATEDLQLKKQFSFIIARHGLAMEIDDE
IAADGNDKEGLQEIVNNSKLSEGYLTLARDIEVMEAKSPEDIYKVHLIDGRGASSSLDSARQNL
AATFVNAFVNAGFGQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2566846-2567371(+)
Potential amino acid sequence	MQYVKQVYTATEDLQLKKQFSFIIARHGLAMEIDDEIAADGNDKEGLQEIVNNSKLSEGYLTLA RDIEVMEAKSPEDIYKVHLIDGRGASSSLDSARQNLAATFVNAFVNAGFGQSMQYVKQVYTATE DLQLKKQFSFIIARHGLAMEIDDEIAADGNDKEGLQEIVNNSKLSEGYLTLARDIEVMEAKSPE DIYKVHLIDGRGASSSLDSARQNLAATFVNAFVNAGFGQSMQYVKQVYTATEDLQLKKQFSFII ARHGLAMEIDDEIAADGNDKEGLQEIVNNSKLSEGYLTLARDIEVMEAKSPEDIYKVHLIDGRG ASSSLDSARQNLAATFVNAFVNAGFGQSMQYVKQVYTATEDLQLKKQFSFIIARHGLAMEIDDE IAADGNDKEGLQEIVNNSKLSEGYLTLARDIEVMEAKSPEDIYKVHLIDGRGASSSLDSARQNL AATFVNAFVNAGFGQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ye et al., 2015;Chu et al., 2017

circRNA

Detail information of Os02g0146700_circ_g.3

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