Plant Circular RNA Database

Detail information of GLYMA_19G138000_circ_g.2

			
						 General Information
					
						CircRNA Name
						GLYMA_19G138000_circ_g.2
					
						ID in PlantcircBase
						gma_circ_004958
					
						Alias
						Gm19circRNA1496
					
						Organism
						
							Glycine max						
					
						Position
						
							chr19: 39937242-39937483  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat
					
						Parent gene
						
							GLYMA_19G138000						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							GLYMA_19G138000_circ_g.1 						
					
						Support reads
						NA
					
						Tissues
						root, stem
					
						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
						KRG95238:1
KRG95239:2
KRG95240:2

General Information
CircRNA Name	GLYMA_19G138000_circ_g.2
ID in PlantcircBase	gma_circ_004958
Alias	Gm19circRNA1496
Organism	Glycine max
Position	chr19: 39937242-39937483 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat
Parent gene	GLYMA_19G138000
Parent gene annotation	hypothetical protein
Parent gene strand	-
Alternative splicing	GLYMA_19G138000_circ_g.1
Support reads	NA
Tissues	root, stem
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	KRG95238:1 KRG95239:2 KRG95240:2

			
						 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  
						
							ACAAAACCGAAACGAACCTTGCTTTCCCTTCTTATTCTGATTTTGGTTCCACGTACTCTTATCC
CAAAGATGCGCTTCATAACGACCAGTCCACCTGTGCccaagtaaactggcgccaccaatcacga
accgttgtccaaccaaccaaccaattcacgaacaacaggaaaaaaaaaaaaacgaaacacgtaa
gcaatttc

						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: 92
Transcript exons: 39937242-39937250,39937401-39937483
CCAAGTAAACTTGCTTTCCCTTCTTATTCTGATTTTGGTTCCACGTACTCTTATCCCAAAGATG
CGCTTCATAACGACCAGTCCACCTGTGC
						
						Genomic sequence
						
							CCAAGTAAACTGGCGCCACCAATCACGAACCGTTGTCCAACCAACCAACCAATTCACGAACAAC
AGGAAAAAAAAAAAAACGAAACACGTAAGCAATTTCAGCCTTACACATGTTGAAACCCGAAACG
AAGAACAGAACAGAACAAAACCGAAACGAACCTTGCTTTCCCTTCTTATTCTGATTTTGGTTCC
ACGTACTCTTATCCCAAAGATGCGCTTCATAACGACCAGTCCACCTGTGC

Sequences
Splice junction sequence	ACAAAACCGAAACGAACCTTGCTTTCCCTTCTTATTCTGATTTTGGTTCCACGTACTCTTATCC CAAAGATGCGCTTCATAACGACCAGTCCACCTGTGCccaagtaaactggcgccaccaatcacga accgttgtccaaccaaccaaccaattcacgaacaacaggaaaaaaaaaaaaacgaaacacgtaa gcaatttc
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: 92 Transcript exons: 39937242-39937250,39937401-39937483 CCAAGTAAACTTGCTTTCCCTTCTTATTCTGATTTTGGTTCCACGTACTCTTATCCCAAAGATG CGCTTCATAACGACCAGTCCACCTGTGC
Genomic sequence	CCAAGTAAACTGGCGCCACCAATCACGAACCGTTGTCCAACCAACCAACCAATTCACGAACAAC AGGAAAAAAAAAAAAACGAAACACGTAAGCAATTTCAGCCTTACACATGTTGAAACCCGAAACG AAGAACAGAACAGAACAAAACCGAAACGAACCTTGCTTTCCCTTCTTATTCTGATTTTGGTTCC ACGTACTCTTATCCCAAAGATGCGCTTCATAACGACCAGTCCACCTGTGC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.368854534

Conservation Information
Conserved circRNAs	NA
PMCS	0.368854534

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							39937465-39937462(-)
						
						Potential amino acid sequence
						
							MKRIFGIRVRGTKIRIRRESKFTWAQVDWSL*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	39937465-39937462(-)
Potential amino acid sequence	MKRIFGIRVRGTKIRIRRESKFTWAQVDWSL*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_19G138000_circ_g.2

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