Plant Circular RNA Database

Detail information of GLYMA_20G177000_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_20G177000_circ_g.2
					
						ID in PlantcircBase
						gma_circ_007790
					
						Alias
						gma-circRNA2783
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 41416178-41417890  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							GLYMA_20G177000						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_20G177000_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						flower bud
					
						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  
						
							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
						KRG91832:3
KRG91834:3
KRG91831:3
KRG91827:3
KRG91828:3
KRG91830:3
KRG91833:3
KRG91829:3

General Information
CircRNA Name	GLYMA_20G177000_circ_g.2
ID in PlantcircBase	gma_circ_007790
Alias	gma-circRNA2783
Organism	Glycine max
Position	chr20: 41416178-41417890 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	find_circ
Parent gene	GLYMA_20G177000
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_20G177000_circ_g.1
Support reads	NA
Tissues	flower bud
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	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	KRG91832:3 KRG91834:3 KRG91831:3 KRG91827:3 KRG91828:3 KRG91830:3 KRG91833:3 KRG91829:3

			
						 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  
						
							AAAATAGAAACAGTTACTTGAGACGAAGAGTCACTTGTGAGGCCAGGAATAACTACAACAATGG
GAACAGATTCATCTTCAGAAGCAACATCACCAGAAAcagaatattagctccaatactagttcca
acaacaaacagaggtgccatggatttctctttatggagataattaaccactgcgcggatatcct
cagtccat

									
								

					

						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
						
							CAGAATATTAGCTCCAATACTAGTTCCAACAACAAACAGAGGTGCCATGGATTTCTCTTTATGG
AGATAATTAACCACTGCGCGGATATCCTCAGTCCATCCAGCATTGTAGGAAAAACCAGACTGAA
ATTATTTATTATTTTAATAAGAAAAGGCGTTACAAGAGGAAGAAAACTGTCAAGACCATAACAT
GAAATTGATATACAAATGCAAAACAATCCCAATATTATAATAAAAAGGAATGCAATGATTTTCA
ACTACAAGTGTTAACTGTTACCTCCCCACATTTAAGATCTATTATCTAACCACGATTGCTTCCT
ACAGAAGATACTATGAAAGGGGTAAAGGCAATCAAACAAGCACGCCCTTGACCCTTTTACAGTT
TTCAACCGATAGATATTTCTAGAACCTTTTTTCTTGACATACAAATAGATTGGCAAGCTTTGTC
TTGTCTACTCGATTTGCTTATTCATACACCACATACAAACAGACCCTTCACCGAATAACTTAAA
AGTGATTTAGCTGCTTAAGGGAAAGTATAATATAAAGGCTGATCAGTGGTTATGGGTATCGACA
GCATTCAAGTTATGTTTTGAAAGTGTATCAACCCCTTATTTCTATATATTTCTAGCTTGCAGAA
AAACTAACCGTGATTGAAACACCTCCAAAACCTCGGTGGTTACAGATAACAACCTTCCATCCAC
GCTTTGCAGTGTGATACGCAAGATGTTTGATATACTATCAACATGAGAGCATGAAAAGAAAAAG
GAAAAATAAACTGTAGGAACTAAGACTTCATTACAGTATAAATGAATCTCCTAATCAAAATCAA
GCGAAAATTTGAAAAATAATGAATATTCATAAGGATACAAGGAAATATTTATTGTCTTTGATGA
TTAACGATAGAATAAATTAATAAAACAATAGTGTTCAATACACTTTCCTATTTTTACGACTAGT
ATAAGGGAAGCAATTGTTCATTTTAGCATTAACACCTCAGCATGCATCAAATTTCAACCTGACG
ACTAAGCTAGGGAGTTTTAGCTGGAACTATATAAGTAACTAGTATATAACTATGAGGACAATGA
TATTAATACAATCAAATTACAAGCCCTGATCTAGCAGCTGTCAAGTAACTGCCAACAGAGTAGG
GATAAACATGTGATTTTCCCCGATCCCCATTTAGTAGAAAAAAAAAATCAACGATGGAGACAAC
ATTAACAATCAGGCATACAAGAACTAAATTAAAATACAACAGACTGTTACATTGTCATCTAATC
ATTAGATTGTTGACTTTAGTAATATCTATTTTTGTTCCGGTATAGACCGTTCCTGGTTTGGGAG
ACCTAGCCAGAGCATTCAAGTTTGTGTGTGTAATCCCCCTAGTCTCTAGCTCAAGGGTTTTTTT
ATTCTAGTCTCCAATCTCAATCTATCTCCATGATGACCATTGAGCATCAAAGCGGACAATGCCT
CACATGATGAGGAGATCCTAACTATACATGAGGATTTGAGGTCGTAACAACTTTAAAAGTAATA
ATATAGTAATTATCAATTAGTTGAGGACATAGTAAAAATATTCTTCTTTAGTCCAAGGGTATAT
GAAAAATAAAGTCAAAATAGAAACAGTTACTTGAGACGAAGAGTCACTTGTGAGGCCAGGAATA
ACTACAACAATGGGAACAGATTCATCTTCAGAAGCAACATCACCAGAAA
						
					

			
		

Sequences
Splice junction sequence	AAAATAGAAACAGTTACTTGAGACGAAGAGTCACTTGTGAGGCCAGGAATAACTACAACAATGG GAACAGATTCATCTTCAGAAGCAACATCACCAGAAAcagaatattagctccaatactagttcca acaacaaacagaggtgccatggatttctctttatggagataattaaccactgcgcggatatcct cagtccat
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	CAGAATATTAGCTCCAATACTAGTTCCAACAACAAACAGAGGTGCCATGGATTTCTCTTTATGG AGATAATTAACCACTGCGCGGATATCCTCAGTCCATCCAGCATTGTAGGAAAAACCAGACTGAA ATTATTTATTATTTTAATAAGAAAAGGCGTTACAAGAGGAAGAAAACTGTCAAGACCATAACAT GAAATTGATATACAAATGCAAAACAATCCCAATATTATAATAAAAAGGAATGCAATGATTTTCA ACTACAAGTGTTAACTGTTACCTCCCCACATTTAAGATCTATTATCTAACCACGATTGCTTCCT ACAGAAGATACTATGAAAGGGGTAAAGGCAATCAAACAAGCACGCCCTTGACCCTTTTACAGTT TTCAACCGATAGATATTTCTAGAACCTTTTTTCTTGACATACAAATAGATTGGCAAGCTTTGTC TTGTCTACTCGATTTGCTTATTCATACACCACATACAAACAGACCCTTCACCGAATAACTTAAA AGTGATTTAGCTGCTTAAGGGAAAGTATAATATAAAGGCTGATCAGTGGTTATGGGTATCGACA GCATTCAAGTTATGTTTTGAAAGTGTATCAACCCCTTATTTCTATATATTTCTAGCTTGCAGAA AAACTAACCGTGATTGAAACACCTCCAAAACCTCGGTGGTTACAGATAACAACCTTCCATCCAC GCTTTGCAGTGTGATACGCAAGATGTTTGATATACTATCAACATGAGAGCATGAAAAGAAAAAG GAAAAATAAACTGTAGGAACTAAGACTTCATTACAGTATAAATGAATCTCCTAATCAAAATCAA GCGAAAATTTGAAAAATAATGAATATTCATAAGGATACAAGGAAATATTTATTGTCTTTGATGA TTAACGATAGAATAAATTAATAAAACAATAGTGTTCAATACACTTTCCTATTTTTACGACTAGT ATAAGGGAAGCAATTGTTCATTTTAGCATTAACACCTCAGCATGCATCAAATTTCAACCTGACG ACTAAGCTAGGGAGTTTTAGCTGGAACTATATAAGTAACTAGTATATAACTATGAGGACAATGA TATTAATACAATCAAATTACAAGCCCTGATCTAGCAGCTGTCAAGTAACTGCCAACAGAGTAGG GATAAACATGTGATTTTCCCCGATCCCCATTTAGTAGAAAAAAAAAATCAACGATGGAGACAAC ATTAACAATCAGGCATACAAGAACTAAATTAAAATACAACAGACTGTTACATTGTCATCTAATC ATTAGATTGTTGACTTTAGTAATATCTATTTTTGTTCCGGTATAGACCGTTCCTGGTTTGGGAG ACCTAGCCAGAGCATTCAAGTTTGTGTGTGTAATCCCCCTAGTCTCTAGCTCAAGGGTTTTTTT ATTCTAGTCTCCAATCTCAATCTATCTCCATGATGACCATTGAGCATCAAAGCGGACAATGCCT CACATGATGAGGAGATCCTAACTATACATGAGGATTTGAGGTCGTAACAACTTTAAAAGTAATA ATATAGTAATTATCAATTAGTTGAGGACATAGTAAAAATATTCTTCTTTAGTCCAAGGGTATAT GAAAAATAAAGTCAAAATAGAAACAGTTACTTGAGACGAAGAGTCACTTGTGAGGCCAGGAATA ACTACAACAATGGGAACAGATTCATCTTCAGAAGCAACATCACCAGAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.219973127

Conservation Information
Conserved circRNAs	NA
PMCS	0.219973127

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							41416905-41416244(+)
41416286-41417883(-)
41416227-41417845(-)
						
						Potential amino acid sequence
						
							MFDILRRRVTCEARNNYNNGNRFIFRSNITRNRILAPILVPTTNRGAMDFSLWR*(+)
MLDGLRISAQWLIISIKRNPWHLCLLLELVLELIFCFW*(-)
MAPLFVVGTSIGANILFLVMLLLKMNLFPLL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						cytoplasmic male sterility

Functional Information
Coding potential	Y
Potential coding position	41416905-41416244(+) 41416286-41417883(-) 41416227-41417845(-)
Potential amino acid sequence	MFDILRRRVTCEARNNYNNGNRFIFRSNITRNRILAPILVPTTNRGAMDFSLWR(+) MLDGLRISAQWLIISIKRNPWHLCLLLELVLELIFCFW(-) MAPLFVVGTSIGANILFLVMLLLKMNLFPLL*(-)
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_20G177000_circ_g.2

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