Plant Circular RNA Database

Detail information of GLYMA_20G227200_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_20G227200_circ_g.2
					
						ID in PlantcircBase
						gma_circ_005316
					
						Alias
						Gm20circRNA468
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 46162027-46163376  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_20G227200						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_20G227200_circ_g.3 GLYMA_20G227200_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, 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
						KRG92725:3
KRG92728:3
KRG92727:3
KRG92726:3

General Information
CircRNA Name	GLYMA_20G227200_circ_g.2
ID in PlantcircBase	gma_circ_005316
Alias	Gm20circRNA468
Organism	Glycine max
Position	chr20: 46162027-46163376 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_20G227200
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_20G227200_circ_g.3 GLYMA_20G227200_circ_g.4
Support reads	NA
Tissues	leaf, 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	KRG92725:3 KRG92728:3 KRG92727:3 KRG92726:3

			
						 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  
						
							TGATGTTGATGGAAATTCTACGGATCCATTTATTGCAGCTGCCATTGCAAATGAAAGAGAATTA
GATCTTTCTGATGAGCAAAGGAGACAATTTAAAAAGgaacaacttgatggggctggcattgagc
ttcctagcctttataagttgattgaaagagaagctcctaatgtttgctccactgaagcatggaa
aaagagga

									
								

					

						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: 540
Transcript exons: 46162027-46162217,46162292-46162526,46163263-46163376
GAACAACTTGATGGGGCTGGCATTGAGCTTCCTAGCCTTTATAAGTTGATTGAAAGAGAAGCTC
CTAATGTTTGCTCCACTGAAGCATGGAAAAAGAGGAATCATTGGGTTGGCTCTCTGGCAACTGC
TGAAATTTCTGAGTCAATTGCTGATGCTGAGAAACATCTGCAAGTAAACAGACCTGTTAGAAGG
CGGCATGGTAAATTATTGGAAGAGGGTGCTAGTGGCTTTCTCCAAAAAAGACTCTGTGATGAAT
CCCAAGAGCCAGTAAAGAATGAGGGGGATTGGGATCTGTTCAATAAAATAGTTTCTGATGGGAG
TGGCACTGATGCTTCATTTGGCAGTAAGCATTGGGCTTCTGTTTATTTGGCCAGCACTCCACAG
CAAGCTGCCTTGATGGGACTCAAATTTCCTGGAGTTGATGAGGTGGAGGAGATTGATGATGTTG
ATGGAAATTCTACGGATCCATTTATTGCAGCTGCCATTGCAAATGAAAGAGAATTAGATCTTTC
TGATGAGCAAAGGAGACAATTTAAAAAG
						
					

						Genomic sequence
						
							GAACAACTTGATGGGGCTGGCATTGAGCTTCCTAGCCTTTATAAGTTGATTGAAAGAGAAGCTC
CTAATGTTTGCTCCACTGAAGCATGGAAAAAGAGGAATCATTGGGTTGGCTCTCTGGCAACTGC
TGAAATTTCTGAGTCAATTGCTGATGCTGAGAAACATCTGCAAGTAAACAGACCTGTTAGAAGG
TATGGTTCTTATATGGCATTGGATCTAGAAACAATCAAATATGTTATCTTATAAGTTTTTGGTG
TTGGTTCAGGCGGCATGGTAAATTATTGGAAGAGGGTGCTAGTGGCTTTCTCCAAAAAAGACTC
TGTGATGAATCCCAAGAGCCAGTAAAGAATGAGGGGGATTGGGATCTGTTCAATAAAATAGTTT
CTGATGGGAGTGGCACTGATGCTTCATTTGGCAGTAAGCATTGGGCTTCTGTTTATTTGGCCAG
CACTCCACAGCAAGCTGCCTTGATGGGACTCAAATTTCCTGGAGTTGATGAGGTGGAAAATACA
TTTTTGACTGTGTTTACTGCTGCTTTTTATATTCTTTTTATTGTATGTATATGTCAAAGGAATC
AAATGATGAGGAAGAAAGTTTAATTACTGGAGCGAGCTGTTGTTATTTTTTTCTATTCATCGTT
TGTTTTTCCCACCTACCCTTGAATTTGAGATGCCCTGAATTTGGATTCTTGATGATTTGGACTA
TATGTAGTTCTGTACGAATATATAAATAAATGTCAGGAAATGGCTGGGTAATGTCAGTGATGTT
ATTTTTATCCAATAAAAAAATGGCATTTGTAATTCATCTGTTCTCATGTTTCCTTGTAAAAATC
ATTTGTTGGGTTTTACTCAGTTACCGTCCCTAACATTGTAAAATGTAGCATGCACTGCCTTTCC
TTTTCCTGCTACTTACCTTGAATACCTGTTTAAATTTGTTAATTTGCCTCATAATTTGGCATTG
CCCTGGTGTGCATCAATCCTATGATTGTTGAGTTGTTGTTTAAGAATTGATGAATTATCTTTTG
CTCTGATTGTATGGTTTTGTTCTATATGTAGAAATTTGGTTAAGTTTTATGATATATGGAATTT
CGATCTTTTCAATGCATTCTTAAATTGTAGGCTTTTACATAATTTAATACATTATGACAGCTGT
TTCGTAAAGCATGTTCTTCACCATAGGTGATGTATGCTTACCATGTTAGTTACCTTTTTCTTTT
TGGAAATTCTTTTTCTTTAGGTGGAGGAGATTGATGATGTTGATGGAAATTCTACGGATCCATT
TATTGCAGCTGCCATTGCAAATGAAAGAGAATTAGATCTTTCTGATGAGCAAAGGAGACAATTT
AAAAAG
						
					

			
		

Sequences
Splice junction sequence	TGATGTTGATGGAAATTCTACGGATCCATTTATTGCAGCTGCCATTGCAAATGAAAGAGAATTA GATCTTTCTGATGAGCAAAGGAGACAATTTAAAAAGgaacaacttgatggggctggcattgagc ttcctagcctttataagttgattgaaagagaagctcctaatgtttgctccactgaagcatggaa aaagagga
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: 540 Transcript exons: 46162027-46162217,46162292-46162526,46163263-46163376 GAACAACTTGATGGGGCTGGCATTGAGCTTCCTAGCCTTTATAAGTTGATTGAAAGAGAAGCTC CTAATGTTTGCTCCACTGAAGCATGGAAAAAGAGGAATCATTGGGTTGGCTCTCTGGCAACTGC TGAAATTTCTGAGTCAATTGCTGATGCTGAGAAACATCTGCAAGTAAACAGACCTGTTAGAAGG CGGCATGGTAAATTATTGGAAGAGGGTGCTAGTGGCTTTCTCCAAAAAAGACTCTGTGATGAAT CCCAAGAGCCAGTAAAGAATGAGGGGGATTGGGATCTGTTCAATAAAATAGTTTCTGATGGGAG TGGCACTGATGCTTCATTTGGCAGTAAGCATTGGGCTTCTGTTTATTTGGCCAGCACTCCACAG CAAGCTGCCTTGATGGGACTCAAATTTCCTGGAGTTGATGAGGTGGAGGAGATTGATGATGTTG ATGGAAATTCTACGGATCCATTTATTGCAGCTGCCATTGCAAATGAAAGAGAATTAGATCTTTC TGATGAGCAAAGGAGACAATTTAAAAAG
Genomic sequence	GAACAACTTGATGGGGCTGGCATTGAGCTTCCTAGCCTTTATAAGTTGATTGAAAGAGAAGCTC CTAATGTTTGCTCCACTGAAGCATGGAAAAAGAGGAATCATTGGGTTGGCTCTCTGGCAACTGC TGAAATTTCTGAGTCAATTGCTGATGCTGAGAAACATCTGCAAGTAAACAGACCTGTTAGAAGG TATGGTTCTTATATGGCATTGGATCTAGAAACAATCAAATATGTTATCTTATAAGTTTTTGGTG TTGGTTCAGGCGGCATGGTAAATTATTGGAAGAGGGTGCTAGTGGCTTTCTCCAAAAAAGACTC TGTGATGAATCCCAAGAGCCAGTAAAGAATGAGGGGGATTGGGATCTGTTCAATAAAATAGTTT CTGATGGGAGTGGCACTGATGCTTCATTTGGCAGTAAGCATTGGGCTTCTGTTTATTTGGCCAG CACTCCACAGCAAGCTGCCTTGATGGGACTCAAATTTCCTGGAGTTGATGAGGTGGAAAATACA TTTTTGACTGTGTTTACTGCTGCTTTTTATATTCTTTTTATTGTATGTATATGTCAAAGGAATC AAATGATGAGGAAGAAAGTTTAATTACTGGAGCGAGCTGTTGTTATTTTTTTCTATTCATCGTT TGTTTTTCCCACCTACCCTTGAATTTGAGATGCCCTGAATTTGGATTCTTGATGATTTGGACTA TATGTAGTTCTGTACGAATATATAAATAAATGTCAGGAAATGGCTGGGTAATGTCAGTGATGTT ATTTTTATCCAATAAAAAAATGGCATTTGTAATTCATCTGTTCTCATGTTTCCTTGTAAAAATC ATTTGTTGGGTTTTACTCAGTTACCGTCCCTAACATTGTAAAATGTAGCATGCACTGCCTTTCC TTTTCCTGCTACTTACCTTGAATACCTGTTTAAATTTGTTAATTTGCCTCATAATTTGGCATTG CCCTGGTGTGCATCAATCCTATGATTGTTGAGTTGTTGTTTAAGAATTGATGAATTATCTTTTG CTCTGATTGTATGGTTTTGTTCTATATGTAGAAATTTGGTTAAGTTTTATGATATATGGAATTT CGATCTTTTCAATGCATTCTTAAATTGTAGGCTTTTACATAATTTAATACATTATGACAGCTGT TTCGTAAAGCATGTTCTTCACCATAGGTGATGTATGCTTACCATGTTAGTTACCTTTTTCTTTT TGGAAATTCTTTTTCTTTAGGTGGAGGAGATTGATGATGTTGATGGAAATTCTACGGATCCATT TATTGCAGCTGCCATTGCAAATGAAAGAGAATTAGATCTTTCTGATGAGCAAAGGAGACAATTT AAAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.464809028

Conservation Information
Conserved circRNAs	NA
PMCS	0.464809028

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							46162498-46163373(+)
46163352-46162072(+)
46162133-46163340(-)
46162051-46162465(-)
						
						Potential amino acid sequence
						
							MGLKFPGVDEVEEIDDVDGNSTDPFIAAAIANERELDLSDEQRRQFKKEQLDGAGIELPSLYKL
IEREAPNVCSTEAWKKRNHWVGSLATAEISESIADAEKHLQVNRPVRRRHGKLLEEGASGFLQK
RLCDESQEPVKNEGDWDLFNKIVSDGSGTDASFGSKHWASVYLASTPQQAALMGLKFPGVDEVE
EIDDVDGNSTDPFIAAAIANERELDLSDEQRRQFKKEQLDGAGIELPSLYKLIEREAPNVCSTE
AWKKRNHWVGSLATAEISESIADAEKHLQVNRPVRRRHGKLLEEGASGFLQKRLCDESQEPVKN
EGDWDLFNKIVSDGSGTDASFGSKHWASVYLASTPQQAALMGLKFPGVDEVEEIDDVDGNSTDP
FIAAAIANERELDLSDEQRRQFKKEQLDGAGIELPSLYKLIEREAPNVCSTEAWKKRNHWVGSL
ATAEISESIADAEKHLQVNRPVRRRHGKLLEEGASGFLQKRLCDESQEPVKNEGDWDLFNKIVS
DGSGTDASFGSKHWASVYLASTPQQAALMGLKFPGVDEVEEIDDVDGNSTDPFIAAAIANEREL
DLSDEQRRQFKK(+)
MSKGDNLKRNNLMGLALSFLAFIS*(+)
MIPLFPCFSGANIRSFSFNQLIKARKLNASPIKLFLFKLSPLLIRKI*(-)
MPAPSSCSFLNCLLCSSERSNSLSFAMAAAINGSVEFPSTSSISSTSSTPGNLSPIKAACCGVL
AK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	46162498-46163373(+) 46163352-46162072(+) 46162133-46163340(-) 46162051-46162465(-)
Potential amino acid sequence	MGLKFPGVDEVEEIDDVDGNSTDPFIAAAIANERELDLSDEQRRQFKKEQLDGAGIELPSLYKL IEREAPNVCSTEAWKKRNHWVGSLATAEISESIADAEKHLQVNRPVRRRHGKLLEEGASGFLQK RLCDESQEPVKNEGDWDLFNKIVSDGSGTDASFGSKHWASVYLASTPQQAALMGLKFPGVDEVE EIDDVDGNSTDPFIAAAIANERELDLSDEQRRQFKKEQLDGAGIELPSLYKLIEREAPNVCSTE AWKKRNHWVGSLATAEISESIADAEKHLQVNRPVRRRHGKLLEEGASGFLQKRLCDESQEPVKN EGDWDLFNKIVSDGSGTDASFGSKHWASVYLASTPQQAALMGLKFPGVDEVEEIDDVDGNSTDP FIAAAIANERELDLSDEQRRQFKKEQLDGAGIELPSLYKLIEREAPNVCSTEAWKKRNHWVGSL ATAEISESIADAEKHLQVNRPVRRRHGKLLEEGASGFLQKRLCDESQEPVKNEGDWDLFNKIVS DGSGTDASFGSKHWASVYLASTPQQAALMGLKFPGVDEVEEIDDVDGNSTDPFIAAAIANEREL DLSDEQRRQFKK(+) MSKGDNLKRNNLMGLALSFLAFIS(+) MIPLFPCFSGANIRSFSFNQLIKARKLNASPIKLFLFKLSPLLIRKI(-) MPAPSSCSFLNCLLCSSERSNSLSFAMAAAINGSVEFPSTSSISSTSSTPGNLSPIKAACCGVL AK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_20G227200_circ_g.2

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