Plant Circular RNA Database

Detail information of GLYMA_18G249800_circ_ag.3

			
						 General Information
					
						CircRNA Name
						GLYMA_18G249800_circ_ag.3
					
						ID in PlantcircBase
						gma_circ_004805
					
						Alias
						Gm18ciRNA2858
					
						Organism
						
							Glycine max						
					
						Position
						
							chr18: 53641715-53679942  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						Tophat
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							GLYMA_18G249800_circ_ag.1 GLYMA_18G249800_circ_ag.2 GLYMA_18G249900_circ_ig.1 GLYMA_18G249900_circ_ig.2 GLYMA_18G249900_circ_ig.3 GLYMA_18G249900_circ_ig.4 GLYMA_18G250000_circ_ag.1 						
					
						Support reads
						NA
					
						Tissues
						stem
					
						Exon boundary  
						
							No-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-GC							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
						NA

General Information
CircRNA Name	GLYMA_18G249800_circ_ag.3
ID in PlantcircBase	gma_circ_004805
Alias	Gm18ciRNA2858
Organism	Glycine max
Position	chr18: 53641715-53679942 JBrowse»
Reference genome	v2.0.38
Type	ag-circRNA
Identification method	Tophat
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	GLYMA_18G249800_circ_ag.1 GLYMA_18G249800_circ_ag.2 GLYMA_18G249900_circ_ig.1 GLYMA_18G249900_circ_ig.2 GLYMA_18G249900_circ_ig.3 GLYMA_18G249900_circ_ig.4 GLYMA_18G250000_circ_ag.1
Support reads	NA
Tissues	stem
Exon boundary	No-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-GC 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	NA

			
						 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  
						
							AATGTCCCCAGCAAGAACATTATTTGGAAGAAAGCCAGCTCCAGTTATGGCTTCATTTTCATCT
AGAGGACCCAATAAGATTCAACCATCAATACTCAAGccgatgtgactgcgcctggtgtgaacat
acttgctgcctattcagaattggcaagtgcatcgaacttgctagtagacaatcgtcgagggttt
aaattcaa

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AATGTCCCCAGCAAGAACATTATTTGGAAGAAAGCCAGCTCCAGTTATGGCTTCATTTTCATCT AGAGGACCCAATAAGATTCAACCATCAATACTCAAGccgatgtgactgcgcctggtgtgaacat acttgctgcctattcagaattggcaagtgcatcgaacttgctagtagacaatcgtcgagggttt aaattcaa
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	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.003252561

Conservation Information
Conserved circRNAs	NA
PMCS	0.003252561

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							gma-miR1533 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	gma-miR1533
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_18G249800_circ_ag.3

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