Plant Circular RNA Database

Detail information of Zm00001d049543_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d049543_circ_g.3
					
						ID in PlantcircBase
						zma_circ_001657
					
						Alias
						circ2231
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 34080717-34080965  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRCexplor2
					
						Parent gene
						
							Zm00001d049543						
					
						Parent gene annotation
						
							 circadian clock associated1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d049543_circ_g.4 Zm00001d049543_circ_g.5 Zm00001d049543_circ_g.6 Zm00001d049543_circ_g.7 Zm00001d049543_circ_g.8 Zm00001d049543_circ_g.9 						
					
						Support reads
						16
					
						Tissues
						seedling leaves
					
						Exon boundary  
						
							No-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-CA							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
						Zm00001d049543_T013:2
Zm00001d049543_T014:2
Zm00001d049543_T002:2
Zm00001d049543_T003:1
Zm00001d049543_T015:2
Zm00001d049543_T010:2
Zm00001d049543_T016:2
Zm00001d049543_T012:1
Zm00001d049543_T001:2

General Information
CircRNA Name	Zm00001d049543_circ_g.3
ID in PlantcircBase	zma_circ_001657
Alias	circ2231
Organism	Zea mays
Position	chr4: 34080717-34080965 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRCexplor2
Parent gene	Zm00001d049543
Parent gene annotation	circadian clock associated1
Parent gene strand	+
Alternative splicing	Zm00001d049543_circ_g.4 Zm00001d049543_circ_g.5 Zm00001d049543_circ_g.6 Zm00001d049543_circ_g.7 Zm00001d049543_circ_g.8 Zm00001d049543_circ_g.9
Support reads	16
Tissues	seedling leaves
Exon boundary	No-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-CA 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	Zm00001d049543_T013:2 Zm00001d049543_T014:2 Zm00001d049543_T002:2 Zm00001d049543_T003:1 Zm00001d049543_T015:2 Zm00001d049543_T010:2 Zm00001d049543_T016:2 Zm00001d049543_T012:1 Zm00001d049543_T001:2

			
						 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  
						
							ATATGATTCTAGAGTTGAAGATAAGGAGTGGAGCTAGGTTTAAACTCTGGTGACTTGGTTGTTG
CGTGCAACGAATCAACTATGCTGAGTTTTTCTGTAGgtttacggaagtgtttggccctagaagg
tgcgcttgatctcttcttctgatagcgctttacatcttgtgcatgcttttgattggttttatga
atctaatc

						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
						
							GTTTACGGAAGTGTTTGGCCCTAGAAGGTGCGCTTGATCTCTTCTTCTGATAGCGCTTTACATC
TTGTGCATGCTTTTGATTGGTTTTATGAATCTAATCCATTTGTTTTCTTGGAATGGTTGCATAA
TTTGAAAACTTGCGAGTTTTAATATGATTCTAGAGTTGAAGATAAGGAGTGGAGCTAGGTTTAA
ACTCTGGTGACTTGGTTGTTGCGTGCAACGAATCAACTATGCTGAGTTTTTCTGTAG

Sequences
Splice junction sequence	ATATGATTCTAGAGTTGAAGATAAGGAGTGGAGCTAGGTTTAAACTCTGGTGACTTGGTTGTTG CGTGCAACGAATCAACTATGCTGAGTTTTTCTGTAGgtttacggaagtgtttggccctagaagg tgcgcttgatctcttcttctgatagcgctttacatcttgtgcatgcttttgattggttttatga atctaatc
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	GTTTACGGAAGTGTTTGGCCCTAGAAGGTGCGCTTGATCTCTTCTTCTGATAGCGCTTTACATC TTGTGCATGCTTTTGATTGGTTTTATGAATCTAATCCATTTGTTTTCTTGGAATGGTTGCATAA TTTGAAAACTTGCGAGTTTTAATATGATTCTAGAGTTGAAGATAAGGAGTGGAGCTAGGTTTAA ACTCTGGTGACTTGGTTGTTGCGTGCAACGAATCAACTATGCTGAGTTTTTCTGTAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.108433768

Conservation Information
Conserved circRNAs	NA
PMCS	0.108433768

			
						 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
						Chen et al., 2017b

circRNA

Detail information of Zm00001d049543_circ_g.3

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