Plant Circular RNA Database

Detail information of Zm00001d046786_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d046786_circ_g.4
					
						ID in PlantcircBase
						zma_circ_000475
					
						Alias
						NA
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 105955983-105956134  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Zm00001d046786						
					
						Parent gene annotation
						
							Photosystem I chlorophyll a/b-binding protein 3-1 chloroplastic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d046786_circ_g.1 Zm00001d046786_circ_g.2 Zm00001d046786_circ_g.3 Zm00001d046786_circ_g.5 Zm00001d046786_circ_g.6 Zm00001d046786_circ_g.7 Zm00001d046786_circ_g.8 Zm00001d046786_circ_g.9 Zm00001d046786_circ_g.10 Zm00001d046786_circ_g.11 Zm00001d046786_circ_g.12 Zm00001d046786_circ_g.13 Zm00001d046786_circ_g.14 Zm00001d046786_circ_g.15 						
					
						Support reads
						16
					
						Tissues
						shoot
					
						Exon boundary  
						
							No-No							"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
						Zm00001d046786_T001:1

General Information
CircRNA Name	Zm00001d046786_circ_g.4
ID in PlantcircBase	zma_circ_000475
Alias	NA
Organism	Zea mays
Position	chr9: 105955983-105956134 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	SMALT, Segemehl
Parent gene	Zm00001d046786
Parent gene annotation	Photosystem I chlorophyll a/b-binding protein 3-1 chloroplastic
Parent gene strand	-
Alternative splicing	Zm00001d046786_circ_g.1 Zm00001d046786_circ_g.2 Zm00001d046786_circ_g.3 Zm00001d046786_circ_g.5 Zm00001d046786_circ_g.6 Zm00001d046786_circ_g.7 Zm00001d046786_circ_g.8 Zm00001d046786_circ_g.9 Zm00001d046786_circ_g.10 Zm00001d046786_circ_g.11 Zm00001d046786_circ_g.12 Zm00001d046786_circ_g.13 Zm00001d046786_circ_g.14 Zm00001d046786_circ_g.15
Support reads	16
Tissues	shoot
Exon boundary	No-No "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	Zm00001d046786_T001:1

			
						 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  
						
							GATGCACCACGTTCTAGTGGAACTTGAGGCTGGTGAGCACGTTGTTGTTGACGGGGTCGGCGAG
GTGGTCGAGCAGgttcctttacaacacgcatgcatctagctttccacagcaaacaactggcggc
ggcggcggcagcagcaggtatgct

						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: 152
Transcript exons: 105955983-105956134
GTTCCTTTACAACACGCATGCATCTAGCTTTCCACAGCAAACAACTGGCGGCGGCGGCGGCAGC
AGCAGGTATGCTGATGCACCACGTTCTAGTGGAACTTGAGGCTGGTGAGCACGTTGTTGTTGAC
GGGGTCGGCGAGGTGGTCGAGCAG
						
						Genomic sequence
						
							GTTCCTTTACAACACGCATGCATCTAGCTTTCCACAGCAAACAACTGGCGGCGGCGGCGGCAGC
AGCAGGTATGCTGATGCACCACGTTCTAGTGGAACTTGAGGCTGGTGAGCACGTTGTTGTTGAC
GGGGTCGGCGAGGTGGTCGAGCAG

Sequences
Splice junction sequence	GATGCACCACGTTCTAGTGGAACTTGAGGCTGGTGAGCACGTTGTTGTTGACGGGGTCGGCGAG GTGGTCGAGCAGgttcctttacaacacgcatgcatctagctttccacagcaaacaactggcggc ggcggcggcagcagcaggtatgct
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: 152 Transcript exons: 105955983-105956134 GTTCCTTTACAACACGCATGCATCTAGCTTTCCACAGCAAACAACTGGCGGCGGCGGCGGCAGC AGCAGGTATGCTGATGCACCACGTTCTAGTGGAACTTGAGGCTGGTGAGCACGTTGTTGTTGAC GGGGTCGGCGAGGTGGTCGAGCAG
Genomic sequence	GTTCCTTTACAACACGCATGCATCTAGCTTTCCACAGCAAACAACTGGCGGCGGCGGCGGCAGC AGCAGGTATGCTGATGCACCACGTTCTAGTGGAACTTGAGGCTGGTGAGCACGTTGTTGTTGAC GGGGTCGGCGAGGTGGTCGAGCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.173844467

Conservation Information
Conserved circRNAs	NA
PMCS	0.173844467

			
						 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
						Lu et al., 2015

circRNA

Detail information of Zm00001d046786_circ_g.4

Address

Any questions?

Supported by