Plant Circular RNA Database

Detail information of GLYMA_17G001100_circ_g.6

			
						 General Information
					
						CircRNA Name
						GLYMA_17G001100_circ_g.6
					
						ID in PlantcircBase
						gma_circ_004363
					
						Alias
						Gm17circRNA360, gma-circRNA2307
					
						Organism
						
							Glycine max						
					
						Position
						
							chr17: 112821-120230  JBrowse»						
					
						Reference genome
						
							v2.0.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						Tophat, CIRI, find_circ
					
						Parent gene
						
							GLYMA_17G001100						
					
						Parent gene annotation
						
							hypothetical protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							GLYMA_17G001100_circ_g.2 GLYMA_17G001100_circ_g.3 GLYMA_17G001100_circ_g.4 GLYMA_17G001100_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, root, stem, 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  
						
							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
						KRH01863:5

General Information
CircRNA Name	GLYMA_17G001100_circ_g.6
ID in PlantcircBase	gma_circ_004363
Alias	Gm17circRNA360, gma-circRNA2307
Organism	Glycine max
Position	chr17: 112821-120230 JBrowse»
Reference genome	v2.0.38
Type	e-circRNA
Identification method	Tophat, CIRI, find_circ
Parent gene	GLYMA_17G001100
Parent gene annotation	hypothetical protein
Parent gene strand	+
Alternative splicing	GLYMA_17G001100_circ_g.2 GLYMA_17G001100_circ_g.3 GLYMA_17G001100_circ_g.4 GLYMA_17G001100_circ_g.5
Support reads	NA
Tissues	leaf, root, stem, 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	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	KRH01863:5

			
						 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  
						
							TAAGTTATTGTTTTGCTTGTTGTTGATATTCCAGGGGGACCAAAGCTTGTCTGGCATTACTCAT
ATCATAGTTGATGAAGTTCATGAGAGGTCTTTGTTGgatatgttgaatatcagagctacgcttc
ctattgcagctctaaagggtgatatattgaaattgatggaggaacatgattttcttgttgtttg
tggggaaa

						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: 435
Transcript exons: 112821-112943,113089-113175,113495-113595,118847-118904,
120165-120230
GATATGTTGAATATCAGAGCTACGCTTCCTATTGCAGCTCTAAAGGGTGATATATTGAAATTGA
TGGAGGAACATGATTTTCTTGTTGTTTGTGGGGAAACAGGCTCTGGAAAGACAACTCAGGTTCC
ACAATTTATATTGGATGACATGATTGAGTCAGGACATGGTGGATATTGTAATATTATTTGCACG
CAACCACGGAGAATAGCGGCTGTTTCTGTGGCTGAAAGGGTCGCAGATGAGCGGTGCGAACCTT
CACCTGGTTCAGATGGTTCTTTGATTGGTTATCAAGTCCGTCTTGATAGTGCCAGGAATGAGAA
AACAAGGCTTCTGTTCTGTACAACAGGCATCCTTCTAAGAAAATTGATGGGGGACCAAAGCTTG
TCTGGCATTACTCATATCATAGTTGATGAAGTTCATGAGAGGTCTTTGTTG
						
						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	TAAGTTATTGTTTTGCTTGTTGTTGATATTCCAGGGGGACCAAAGCTTGTCTGGCATTACTCAT ATCATAGTTGATGAAGTTCATGAGAGGTCTTTGTTGgatatgttgaatatcagagctacgcttc ctattgcagctctaaagggtgatatattgaaattgatggaggaacatgattttcttgttgtttg tggggaaa
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: 435 Transcript exons: 112821-112943,113089-113175,113495-113595,118847-118904, 120165-120230 GATATGTTGAATATCAGAGCTACGCTTCCTATTGCAGCTCTAAAGGGTGATATATTGAAATTGA TGGAGGAACATGATTTTCTTGTTGTTTGTGGGGAAACAGGCTCTGGAAAGACAACTCAGGTTCC ACAATTTATATTGGATGACATGATTGAGTCAGGACATGGTGGATATTGTAATATTATTTGCACG CAACCACGGAGAATAGCGGCTGTTTCTGTGGCTGAAAGGGTCGCAGATGAGCGGTGCGAACCTT CACCTGGTTCAGATGGTTCTTTGATTGGTTATCAAGTCCGTCTTGATAGTGCCAGGAATGAGAA AACAAGGCTTCTGTTCTGTACAACAGGCATCCTTCTAAGAAAATTGATGGGGGACCAAAGCTTG TCTGGCATTACTCATATCATAGTTGATGAAGTTCATGAGAGGTCTTTGTTG
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
						0.286650922

Conservation Information
Conserved circRNAs	NA
PMCS	0.286650922

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							112825-120227(+)
						
						Potential amino acid sequence
						
							MLNIRATLPIAALKGDILKLMEEHDFLVVCGETGSGKTTQVPQFILDDMIESGHGGYCNIICTQ
PRRIAAVSVAERVADERCEPSPGSDGSLIGYQVRLDSARNEKTRLLFCTTGILLRKLMGDQSLS
GITHIIVDEVHERSLLDMLNIRATLPIAALKGDILKLMEEHDFLVVCGETGSGKTTQVPQFILD
DMIESGHGGYCNIICTQPRRIAAVSVAERVADERCEPSPGSDGSLIGYQVRLDSARNEKTRLLF
CTTGILLRKLMGDQSLSGITHIIVDEVHERSLLDMLNIRATLPIAALKGDILKLMEEHDFLVVC
GETGSGKTTQVPQFILDDMIESGHGGYCNIICTQPRRIAAVSVAERVADERCEPSPGSDGSLIG
YQVRLDSARNEKTRLLFCTTGILLRKLMGDQSLSGITHIIVDEVHERSLLDMLNIRATLPIAAL
KGDILKLMEEHDFLVVCGETGSGKTTQVPQFILDDMIESGHGGYCNIICTQPRRIAAVSVAERV
ADERCEPSPGSDGSLIGYQVRLDSARNEKTRLLFCTTGILLRKLMGDQSLSGITHIIVDEVHER
SLL(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	112825-120227(+)
Potential amino acid sequence	MLNIRATLPIAALKGDILKLMEEHDFLVVCGETGSGKTTQVPQFILDDMIESGHGGYCNIICTQ PRRIAAVSVAERVADERCEPSPGSDGSLIGYQVRLDSARNEKTRLLFCTTGILLRKLMGDQSLS GITHIIVDEVHERSLLDMLNIRATLPIAALKGDILKLMEEHDFLVVCGETGSGKTTQVPQFILD DMIESGHGGYCNIICTQPRRIAAVSVAERVADERCEPSPGSDGSLIGYQVRLDSARNEKTRLLF CTTGILLRKLMGDQSLSGITHIIVDEVHERSLLDMLNIRATLPIAALKGDILKLMEEHDFLVVC GETGSGKTTQVPQFILDDMIESGHGGYCNIICTQPRRIAAVSVAERVADERCEPSPGSDGSLIG YQVRLDSARNEKTRLLFCTTGILLRKLMGDQSLSGITHIIVDEVHERSLLDMLNIRATLPIAAL KGDILKLMEEHDFLVVCGETGSGKTTQVPQFILDDMIESGHGGYCNIICTQPRRIAAVSVAERV ADERCEPSPGSDGSLIGYQVRLDSARNEKTRLLFCTTGILLRKLMGDQSLSGITHIIVDEVHER SLL(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Zhao et al., 2017a; Chen et al., 2018

circRNA

Detail information of GLYMA_17G001100_circ_g.6

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