Plant Circular RNA Database

Detail information of GLYMA_20G244900_circ_g.13

			
						 General Information
					
						CircRNA Name
						GLYMA_20G244900_circ_g.13
					
						ID in PlantcircBase
						gma_circ_005358
					
						Alias
						Gm20circRNA2399
					
						Organism
						
							Glycine max						
					
						Position
						
							chr20: 47542230-47548065  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI
					
						Parent gene
						
							GLYMA_20G244900						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_20G244900_circ_g.14 						
					
						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  
						
							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
						KRG93041:4

General Information
CircRNA Name	GLYMA_20G244900_circ_g.13
ID in PlantcircBase	gma_circ_005358
Alias	Gm20circRNA2399
Organism	Glycine max
Position	chr20: 47542230-47548065 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI
Parent gene	GLYMA_20G244900
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_20G244900_circ_g.14
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	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	KRG93041:4

			
						 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  
						
							TTCAAGGATAGCAGAAACCATTCTGAGTCTTAGATTTTTCATCTTTCAATATGGTATCGTGTAC
AAGCTTAATGTGAAAGGAACAAGTACTTCACTGACGtatcaagcaactggccgcgggtttgttg
ttcgccatatcaaattttcagagaactacagactctactctcgtagtcattttgttaaagggtg
agacgtgc

						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	TTCAAGGATAGCAGAAACCATTCTGAGTCTTAGATTTTTCATCTTTCAATATGGTATCGTGTAC AAGCTTAATGTGAAAGGAACAAGTACTTCACTGACGtatcaagcaactggccgcgggtttgttg ttcgccatatcaaattttcagagaactacagactctactctcgtagtcattttgttaaagggtg agacgtgc
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
						0.042457924

Conservation Information
Conserved circRNAs	NA
PMCS	0.042457924

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							47545615-47548062(+)
						
						Potential amino acid sequence
						
							MALSWLFAPYLFNPSGFEWQKVVEDFRDWTNWLLYRGGIGVKGEESWEAWWEEELAHIRSLGSR
IAETILSLRFFIFQYGIVYKLNVKGTSTSLTYQATGRGFVVRHIKFSENYRLYSRSHFVKGLEV
ALLLIVYLAYGYNEGGALSYILLSISSWFMALSWLFAPYLFNPSGFEWQKVVEDFRDWTNWLLY
RGGIGVKGEESWEAWWEEELAHIRSLGSRIAETILSLRFFIFQYGIVYKLNVKGTSTSLTYQAT
GRGFVVRHIKFSENYRLYSRSHFVKGLEVALLLIVYLAYGYNEGGALSYILLSISSWFMALSWL
FAPYLFNPSGFEWQKVVEDFRDWTNWLLYRGGIGVKGEESWEAWWEEELAHIRSLGSRIAETIL
SLRFFIFQYGIVYKLNVKGTSTSLTYQATGRGFVVRHIKFSENYRLYSRSHFVKGLEVALLLIV
YLAYGYNEGGALSYILLSISSWFMALSWLFAPYLFNPSGFEWQKVVEDFRDWTNWLLYRGGIGV
KGEESWEAWWEEELAHIRSLGSRIAETILSLRFFIFQYGIVYKLNVKGTSTSLT(+)
						
						Sponge-miRNAs
						
							gma-miR1533 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	47545615-47548062(+)
Potential amino acid sequence	MALSWLFAPYLFNPSGFEWQKVVEDFRDWTNWLLYRGGIGVKGEESWEAWWEEELAHIRSLGSR IAETILSLRFFIFQYGIVYKLNVKGTSTSLTYQATGRGFVVRHIKFSENYRLYSRSHFVKGLEV ALLLIVYLAYGYNEGGALSYILLSISSWFMALSWLFAPYLFNPSGFEWQKVVEDFRDWTNWLLY RGGIGVKGEESWEAWWEEELAHIRSLGSRIAETILSLRFFIFQYGIVYKLNVKGTSTSLTYQAT GRGFVVRHIKFSENYRLYSRSHFVKGLEVALLLIVYLAYGYNEGGALSYILLSISSWFMALSWL FAPYLFNPSGFEWQKVVEDFRDWTNWLLYRGGIGVKGEESWEAWWEEELAHIRSLGSRIAETIL SLRFFIFQYGIVYKLNVKGTSTSLTYQATGRGFVVRHIKFSENYRLYSRSHFVKGLEVALLLIV YLAYGYNEGGALSYILLSISSWFMALSWLFAPYLFNPSGFEWQKVVEDFRDWTNWLLYRGGIGV KGEESWEAWWEEELAHIRSLGSRIAETILSLRFFIFQYGIVYKLNVKGTSTSLT(+)
Sponge-miRNAs	gma-miR1533
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a

circRNA

Detail information of GLYMA_20G244900_circ_g.13

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