Plant Circular RNA Database

Detail information of GLYMA_13G185900_circ_ig.2

			
						 General Information
					
						CircRNA Name
						GLYMA_13G185900_circ_ig.2
					
						ID in PlantcircBase
						gma_circ_006960
					
						Alias
						gma-circRNA1828
					
						Organism
						
							Glycine max						
					
						Position
						
							chr13: 29966167-29968180  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							ig-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							NA						
					
						Parent gene annotation
						
							NA							
					
						Parent gene strand
						NA
					
						Alternative splicing
						
							GLYMA_13G185900_circ_ig.1 GLYMA_13G185900_circ_ig.3 GLYMA_13G185900_circ_ig.4 GLYMA_13G185900_circ_ig.5 GLYMA_13G185900_circ_ig.6 GLYMA_13G185900_circ_ig.7 GLYMA_13G185900_circ_ig.8 GLYMA_13G185900_circ_ig.9 GLYMA_13G185900_circ_ig.10 GLYMA_13G185900_circ_ig.11 						
					
						Support reads
						NA
					
						Tissues
						flower bud
					
						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_13G185900_circ_ig.2
ID in PlantcircBase	gma_circ_006960
Alias	gma-circRNA1828
Organism	Glycine max
Position	chr13: 29966167-29968180 JBrowse»
Reference genome	v2.0.38
Type	ig-circRNA
Identification method	find_circ
Parent gene	NA
Parent gene annotation	NA
Parent gene strand	NA
Alternative splicing	GLYMA_13G185900_circ_ig.1 GLYMA_13G185900_circ_ig.3 GLYMA_13G185900_circ_ig.4 GLYMA_13G185900_circ_ig.5 GLYMA_13G185900_circ_ig.6 GLYMA_13G185900_circ_ig.7 GLYMA_13G185900_circ_ig.8 GLYMA_13G185900_circ_ig.9 GLYMA_13G185900_circ_ig.10 GLYMA_13G185900_circ_ig.11
Support reads	NA
Tissues	flower bud
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  
						
							ACCCAGGCCAACATTAATGAAGAGATTTTCACACACACAAAAAAATGATGGTCCAAGCTTCTAG
GCTCACCAGGCCATGGTGGACTGTGATTGCAGCAACctgttatccctccactgttgggaatggg
aggtgttcgctgttctgtgaaaccagcctcacgcagtgccctccactctaagaaccaggagacc
tatgcctt

									
								

					

						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
						
							CTGTTATCCCTCCACTGTTGGGAATGGGAGGTGTTCGCTGTTCTGTGAAACCAGCCTCACGCAG
TGCCCTCCACTCTAAGAACCAGGAGACCTATGCCTTCGCTTAGGTCCCATGATTCAATTCTCAA
CTTGGAGCGGACAGGCCAACACATTGCAGCCGCAGCCCAACCCAGCAAAGCCAAAGAACTGTTC
CATCACCTTGGTGCCCCCACTTGAGTCACAAGCTGACGTAACTCAACTCGGCATTCAGACAACT
TTGTCAGAGGGCATATAAAGATTTTGTTGTCTCCTTTTCTTTCCTATGTGGGACATAAGTAAGA
AGAAAGTTTGCAGTTTAACACTAACAATCTCAAAGAGCTTCTTTCTGGATGAAATGAAAGATAA
ATTGGATTAATTTGGGGAAAACAAAAGATTGTAATTTGTACTATATGCTTTGGTATAAGTTGTT
AGATGTTTGTATTCCTCCCTGCGGAAGCAAAAACACAGAGAAATGCAGCCTGTTCAACTAGTTA
CATATTGGACAGTTTAGCATGTCTTTATTTAAAATCTTGTACATTTGATTTTTCTCTGCAGCTT
TTCATACACGATAGCTTTTGTTTAAGGAGTGTCTTTCTATTGGCATTTCAAAATGTGATCAATT
ATTCTGATACTAAAGATTAAAGAATGCCAAACATAAACATTTATAATGTTAAATATGTTTAAGT
TTTGAACTGAAATCCTACACAGAACAGGTAACATTCCCCTATTCTTCATACGTGTGTGCTCATT
GTGTTTTTTTTTATAATATCTAGAAATTAACAACAAAGGGTGCATGTGTAGCAGGTTAAAGCCT
AGGATAAGGCGCTAAGCAGAGGAACCGATGGCATGAAGCTATGAAGATTCAAAGCTGTGGCATA
TATGAATTTTGTTGGTCTAGTTTTGTTTTGTCTAATTTTTTTATTTTTACTGTTTCATCCCACC
TACAAATTCTCAGGTTTATTAGTGAGTGAGAGTGTGGTATAGTTCATGACTTTAGATTGCTCTT
TATATCATCTTACCTTGGATGCTTTAGATTGTAGAGAATATATATAGGAGCATATGATGTAAAG
GAGAAAAATAATAGCCATCAAAATGTCAAGACTGTTTTTGGCACCACAAGATTCAAAACTATTT
AATTTTTTCTTTAATTTTTTTGGTACCACAAGAATGTTATTTTAAAAGAAAAAATAGCTTGCCT
TCATGGTTGCAACTTGTAAGAAGTTTCTTGTTATATTCAGTATAATATGTTGAATTTGATCCTC
TTAATTTTTCCTTTTGTGTTTAATAATAATCTTTATGGTTGGGTTTTGATAAAGGATCCATAAA
GGTGTTTGTGGTTGTTACGAATACATTTGCAGACTTGCACTCATATTACTAGTATCTATCTTTA
ATTTTCTATTGTCTGATGGATTGCAAAGAAATTATAACTGTGACCCATGTTTGAAACCTCAATC
GCAAGGTTTTAAATATTGGTCGCGGTCATGTTACGGTTTTGGTATATTTGTTGATATCGTGACA
AATTACAGGATAGATGCAGTCTTAATTGTGTCATGTTTTGCTGCGGACAATTAAAAACCTTGAT
GTTTTAGACCAAATCATGGTTCTGTAGATAATATTTTCATTTTCAAGAGTTTCTAAGTGAATCA
AATATGGTACATGGCTGAAGAGGGTAACCATTTTTTACCAGTGAGTATTGGTACCCAACAACTT
CAAAAGTAAATCTCATCTCATGATAGAGAGGTATTAAGAAAAAAAAACTCAAATAGAGGGATTG
TTGGGATGGATGTGGATCTGATCTTTGCTCATTTGAATTGCATTTGCAGAAGCTATTTATCTAA
TAACTAGACTTTAGTTATCTTACACAATCATGTGGTTGTAGCACAAAAAAAATGCCCAACCCAG
GCCAACATTAATGAAGAGATTTTCACACACACAAAAAAATGATGGTCCAAGCTTCTAGGCTCAC
CAGGCCATGGTGGACTGTGATTGCAGCAAC
						
					

			
		

Sequences
Splice junction sequence	ACCCAGGCCAACATTAATGAAGAGATTTTCACACACACAAAAAAATGATGGTCCAAGCTTCTAG GCTCACCAGGCCATGGTGGACTGTGATTGCAGCAACctgttatccctccactgttgggaatggg aggtgttcgctgttctgtgaaaccagcctcacgcagtgccctccactctaagaaccaggagacc tatgcctt
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	CTGTTATCCCTCCACTGTTGGGAATGGGAGGTGTTCGCTGTTCTGTGAAACCAGCCTCACGCAG TGCCCTCCACTCTAAGAACCAGGAGACCTATGCCTTCGCTTAGGTCCCATGATTCAATTCTCAA CTTGGAGCGGACAGGCCAACACATTGCAGCCGCAGCCCAACCCAGCAAAGCCAAAGAACTGTTC CATCACCTTGGTGCCCCCACTTGAGTCACAAGCTGACGTAACTCAACTCGGCATTCAGACAACT TTGTCAGAGGGCATATAAAGATTTTGTTGTCTCCTTTTCTTTCCTATGTGGGACATAAGTAAGA AGAAAGTTTGCAGTTTAACACTAACAATCTCAAAGAGCTTCTTTCTGGATGAAATGAAAGATAA ATTGGATTAATTTGGGGAAAACAAAAGATTGTAATTTGTACTATATGCTTTGGTATAAGTTGTT AGATGTTTGTATTCCTCCCTGCGGAAGCAAAAACACAGAGAAATGCAGCCTGTTCAACTAGTTA CATATTGGACAGTTTAGCATGTCTTTATTTAAAATCTTGTACATTTGATTTTTCTCTGCAGCTT TTCATACACGATAGCTTTTGTTTAAGGAGTGTCTTTCTATTGGCATTTCAAAATGTGATCAATT ATTCTGATACTAAAGATTAAAGAATGCCAAACATAAACATTTATAATGTTAAATATGTTTAAGT TTTGAACTGAAATCCTACACAGAACAGGTAACATTCCCCTATTCTTCATACGTGTGTGCTCATT GTGTTTTTTTTTATAATATCTAGAAATTAACAACAAAGGGTGCATGTGTAGCAGGTTAAAGCCT AGGATAAGGCGCTAAGCAGAGGAACCGATGGCATGAAGCTATGAAGATTCAAAGCTGTGGCATA TATGAATTTTGTTGGTCTAGTTTTGTTTTGTCTAATTTTTTTATTTTTACTGTTTCATCCCACC TACAAATTCTCAGGTTTATTAGTGAGTGAGAGTGTGGTATAGTTCATGACTTTAGATTGCTCTT TATATCATCTTACCTTGGATGCTTTAGATTGTAGAGAATATATATAGGAGCATATGATGTAAAG GAGAAAAATAATAGCCATCAAAATGTCAAGACTGTTTTTGGCACCACAAGATTCAAAACTATTT AATTTTTTCTTTAATTTTTTTGGTACCACAAGAATGTTATTTTAAAAGAAAAAATAGCTTGCCT TCATGGTTGCAACTTGTAAGAAGTTTCTTGTTATATTCAGTATAATATGTTGAATTTGATCCTC TTAATTTTTCCTTTTGTGTTTAATAATAATCTTTATGGTTGGGTTTTGATAAAGGATCCATAAA GGTGTTTGTGGTTGTTACGAATACATTTGCAGACTTGCACTCATATTACTAGTATCTATCTTTA ATTTTCTATTGTCTGATGGATTGCAAAGAAATTATAACTGTGACCCATGTTTGAAACCTCAATC GCAAGGTTTTAAATATTGGTCGCGGTCATGTTACGGTTTTGGTATATTTGTTGATATCGTGACA AATTACAGGATAGATGCAGTCTTAATTGTGTCATGTTTTGCTGCGGACAATTAAAAACCTTGAT GTTTTAGACCAAATCATGGTTCTGTAGATAATATTTTCATTTTCAAGAGTTTCTAAGTGAATCA AATATGGTACATGGCTGAAGAGGGTAACCATTTTTTACCAGTGAGTATTGGTACCCAACAACTT CAAAAGTAAATCTCATCTCATGATAGAGAGGTATTAAGAAAAAAAAACTCAAATAGAGGGATTG TTGGGATGGATGTGGATCTGATCTTTGCTCATTTGAATTGCATTTGCAGAAGCTATTTATCTAA TAACTAGACTTTAGTTATCTTACACAATCATGTGGTTGTAGCACAAAAAAAATGCCCAACCCAG GCCAACATTAATGAAGAGATTTTCACACACACAAAAAAATGATGGTCCAAGCTTCTAGGCTCAC CAGGCCATGGTGGACTGTGATTGCAGCAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						1.019939336

Conservation Information
Conserved circRNAs	NA
PMCS	1.019939336

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

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

			
						 Other Information
					
						References
						Chen et al., 2018

circRNA

Detail information of GLYMA_13G185900_circ_ig.2

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