Plant Circular RNA Database

Detail information of GLYMA_05G213800_circ_ag.1

			
						 General Information
					
						CircRNA Name
						GLYMA_05G213800_circ_ag.1
					
						ID in PlantcircBase
						gma_circ_008253
					
						Alias
						circRNA2560
					
						Organism
						
							Glycine max						
					
						Position
						
							chr5: 39516673-39530658  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ag-circRNA							
									
						Identification method
						CIRI, CIRCexplorer
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							GLYMA_05G213800_circ_ag.2 GLYMA_05G213800_circ_ag.3 GLYMA_05G213800_circ_ag.4 GLYMA_05G214100_circ_ag.1 GLYMA_05G214100_circ_ag.2 GLYMA_05G214100_circ_ag.3 GLYMA_05G214100_circ_ag.4 						
					
						Support reads
						NA
					
						Tissues
						pod
					
						Exon boundary  
						
							NA-NA							"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
						NA

General Information
CircRNA Name	GLYMA_05G213800_circ_ag.1
ID in PlantcircBase	gma_circ_008253
Alias	circRNA2560
Organism	Glycine max
Position	chr5: 39516673-39530658 JBrowse»
Reference genome	v2.0.38
Type	ag-circRNA
Identification method	CIRI, CIRCexplorer
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	GLYMA_05G213800_circ_ag.2 GLYMA_05G213800_circ_ag.3 GLYMA_05G213800_circ_ag.4 GLYMA_05G214100_circ_ag.1 GLYMA_05G214100_circ_ag.2 GLYMA_05G214100_circ_ag.3 GLYMA_05G214100_circ_ag.4
Support reads	NA
Tissues	pod
Exon boundary	NA-NA "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	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  
						
							CATACTCCTGTGCAGATGAATCCAGCACATGCTCTACCAAGTGCAGGTCATCTTTCCGACATCT
CAATAGGACTGAAGGTTCTTTCAGTCTAAGCAAACActgaacaatgagatctttcagaaggttt
ctgtacacatgatcatcatgatgatgactcacagtcaaaagttccttggatgcagcttctttca
tggaactg

						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	CATACTCCTGTGCAGATGAATCCAGCACATGCTCTACCAAGTGCAGGTCATCTTTCCGACATCT CAATAGGACTGAAGGTTCTTTCAGTCTAAGCAAACActgaacaatgagatctttcagaaggttt ctgtacacatgatcatcatgatgatgactcacagtcaaaagttccttggatgcagcttctttca tggaactg
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
						1.038908789

Conservation Information
Conserved circRNAs	NA
PMCS	1.038908789

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							gma-miR5031 gma-miR1530 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						playing a post-transcriptional regulatory role in soybean oil synthesis

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	gma-miR5031 gma-miR1530
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	playing a post-transcriptional regulatory role in soybean oil synthesis

			
						 Other Information
					
						References
						Ma et al., 2021a

circRNA

Detail information of GLYMA_05G213800_circ_ag.1

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