Plant Circular RNA Database

Detail information of AT1G15215_circ_g.3

			
						 General Information
					
						CircRNA Name
						AT1G15215_circ_g.3
					
						ID in PlantcircBase
						ath_circ_002654
					
						Alias
						Ath_circ_FC0355, AT1G15215_C1
					
						Organism
						
							Arabidpsis thaliana						
					
						Position
						
							chr1: 5239295-5239650  JBrowse»						
					
						Reference genome
						
							TAIR10.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRCexplorer, CIRI, CIRI-full, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI2
					
						Parent gene
						
							AT1G15215						
					
						Parent gene annotation
						
							SAWADEE HOMEODOMAIN protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							AT1G15215_circ_g.1 AT1G15215_circ_g.2 						
					
						Support reads
						12
					
						Tissues
						root, aerial, seed, whole_plant, leaf
					
						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
						AT1G15215.3:2
AT1G15215.2:2
AT1G15215.4:2

General Information
CircRNA Name	AT1G15215_circ_g.3
ID in PlantcircBase	ath_circ_002654
Alias	Ath_circ_FC0355, AT1G15215_C1
Organism	Arabidpsis thaliana
Position	chr1: 5239295-5239650 JBrowse»
Reference genome	TAIR10.38
Type	e-circRNA
Identification method	CIRCexplorer, CIRI, CIRI-full, KNIFE, PcircRNA_finder, circRNA_finder, circseq_cup, find_circ, CIRI2
Parent gene	AT1G15215
Parent gene annotation	SAWADEE HOMEODOMAIN protein
Parent gene strand	+
Alternative splicing	AT1G15215_circ_g.1 AT1G15215_circ_g.2
Support reads	12
Tissues	root, aerial, seed, whole_plant, leaf
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	AT1G15215.3:2 AT1G15215.2:2 AT1G15215.4:2

			
						 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  
						
							CTACTGTGATGGTCATGTTTTGAATATCAAGAGAGGGATTCATGATCACGCGAGATGTAACTGC
GTGTTTCTTGTTCGCTACGAGCTTGACAATACAGAGgaagtgcgtgtacggttttctgggttcg
acaaccgacacgatgagtgggtaaacgtcaaaacatcagtgcgtgagcggtctattcctgtaga
accatcag

									
								

					

						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: 164
Transcript exons: 5239295-5239424,5239617-5239650
GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT
CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGGAGAGTGAACGTTGGAGACCT
GCGTTTCTTGTTCGCTACGAGCTTGACAATACAGAG
Transcript length: 187
Transcript exons: 5239295-5239373,5239543-5239650
GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT
CAGTGCGTGAGCGGTCAAGCACTCTACTGTGATGGTCATGTTTTGAATATCAAGAGAGGGATTC
ATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCGCTACGAGCTTGACAATACAGAG
Transcript length: 214
Transcript exons: 5239295-5239401,5239544-5239650
GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT
CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGAAGCACTCTACTGTGATGGTC
ATGTTTTGAATATCAAGAGAGGGATTCATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCG
CTACGAGCTTGACAATACAGAG
Transcript length: 264
Transcript exons: 5239295-5239438,5239531-5239650
GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT
CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGGAGAGTGAACGTTGGAGACCT
GCTTCTATGTTTCCAAGAAAGAGAGGATCAAGCACTCTACTGTGATGGTCATGTTTTGAATATC
AAGAGAGGGATTCATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCGCTACGAGCTTGACA
ATACAGAG
Transcript length: 264
Transcript exons: 5239295-5239650
GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT
CAGTGCGTGAGCGGTCTATTCCTGTAGAACCTTCAGAGTGTGGGAGAGTGAACGTTGGAGACCT
GCTTCTATGTTTCCAAGAAAGAGAGGATCAAGCACTCTACTGTGATGGTCATGTTTTGAATATC
AAGAGAGGGATTCATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCGCTACGAGCTTGACA
ATACAGAG
						
					

						Genomic sequence
						
							GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT
CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGGAGAGTGAACGTTGGAGACCT
GCTTCTATGTTTCCAAGTAAGGCTGACTTTGATCTAATTATGAAGGATGGAACATTTAACAAAA
GAAATTTGAACTTAAAAATGAAAGTTGGGGTGGTTAATGAGCAGGAAAGAGAGGATCAAGCACT
CTACTGTGATGGTCATGTTTTGAATATCAAGAGAGGGATTCATGATCACGCGAGATGTAACTGC
GTGTTTCTTGTTCGCTACGAGCTTGACAATACAGAG
						
					

			
		

Sequences
Splice junction sequence	CTACTGTGATGGTCATGTTTTGAATATCAAGAGAGGGATTCATGATCACGCGAGATGTAACTGC GTGTTTCTTGTTCGCTACGAGCTTGACAATACAGAGgaagtgcgtgtacggttttctgggttcg acaaccgacacgatgagtgggtaaacgtcaaaacatcagtgcgtgagcggtctattcctgtaga accatcag
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: 164 Transcript exons: 5239295-5239424,5239617-5239650 GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGGAGAGTGAACGTTGGAGACCT GCGTTTCTTGTTCGCTACGAGCTTGACAATACAGAG Transcript length: 187 Transcript exons: 5239295-5239373,5239543-5239650 GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT CAGTGCGTGAGCGGTCAAGCACTCTACTGTGATGGTCATGTTTTGAATATCAAGAGAGGGATTC ATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCGCTACGAGCTTGACAATACAGAG Transcript length: 214 Transcript exons: 5239295-5239401,5239544-5239650 GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGAAGCACTCTACTGTGATGGTC ATGTTTTGAATATCAAGAGAGGGATTCATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCG CTACGAGCTTGACAATACAGAG Transcript length: 264 Transcript exons: 5239295-5239438,5239531-5239650 GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGGAGAGTGAACGTTGGAGACCT GCTTCTATGTTTCCAAGAAAGAGAGGATCAAGCACTCTACTGTGATGGTCATGTTTTGAATATC AAGAGAGGGATTCATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCGCTACGAGCTTGACA ATACAGAG Transcript length: 264 Transcript exons: 5239295-5239650 GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT CAGTGCGTGAGCGGTCTATTCCTGTAGAACCTTCAGAGTGTGGGAGAGTGAACGTTGGAGACCT GCTTCTATGTTTCCAAGAAAGAGAGGATCAAGCACTCTACTGTGATGGTCATGTTTTGAATATC AAGAGAGGGATTCATGATCACGCGAGATGTAACTGCGTGTTTCTTGTTCGCTACGAGCTTGACA ATACAGAG
Genomic sequence	GAAGTGCGTGTACGGTTTTCTGGGTTCGACAACCGACACGATGAGTGGGTAAACGTCAAAACAT CAGTGCGTGAGCGGTCTATTCCTGTAGAACCATCAGAGTGTGGGAGAGTGAACGTTGGAGACCT GCTTCTATGTTTCCAAGTAAGGCTGACTTTGATCTAATTATGAAGGATGGAACATTTAACAAAA GAAATTTGAACTTAAAAATGAAAGTTGGGGTGGTTAATGAGCAGGAAAGAGAGGATCAAGCACT CTACTGTGATGGTCATGTTTTGAATATCAAGAGAGGGATTCATGATCACGCGAGATGTAACTGC GTGTTTCTTGTTCGCTACGAGCTTGACAATACAGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.555975422

Conservation Information
Conserved circRNAs	NA
PMCS	0.555975422

			
						 Functional Information
					
						Coding potential
						N
					
						Potential coding position
						
							NA
						
						Potential amino acid sequence
						
							NA
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	N
Potential coding position	NA
Potential amino acid sequence	NA
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Chu et al., 2017;Chen et al., 2017a;Zhang et al., 2019

circRNA

Detail information of AT1G15215_circ_g.3

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