Plant Circular RNA Database

Detail information of Zm00001d013159_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d013159_circ_g.3
					
						ID in PlantcircBase
						zma_circ_000274
					
						Alias
						NA
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 5560589-5560735  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Zm00001d013159						
					
						Parent gene annotation
						
							 alpha tubulin3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d013159_circ_g.1 Zm00001d013159_circ_g.2 Zm00001d013159_circ_g.4 Zm00001d013159_circ_g.5 						
					
						Support reads
						2
					
						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  
						
							CT-AC							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
						Zm00001d013159_T001:1
Zm00001d013159_T002:1
Zm00001d013159_T003:1
Zm00001d013159_T004:1

General Information
CircRNA Name	Zm00001d013159_circ_g.3
ID in PlantcircBase	zma_circ_000274
Alias	NA
Organism	Zea mays
Position	chr5: 5560589-5560735 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	SMALT, Segemehl
Parent gene	Zm00001d013159
Parent gene annotation	alpha tubulin3
Parent gene strand	-
Alternative splicing	Zm00001d013159_circ_g.1 Zm00001d013159_circ_g.2 Zm00001d013159_circ_g.4 Zm00001d013159_circ_g.5
Support reads	2
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	CT-AC 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	Zm00001d013159_T001:1 Zm00001d013159_T002:1 Zm00001d013159_T003:1 Zm00001d013159_T004:1

			
						 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  
						
							CCTCCTCGTCACCGTCATCACTGCCGCCCTCTGCGGCGACCTCCTCGTAGTCCTTCTCCAGGGC
GGCCAGGTCacaaacaaaggtttttcaacaccacaacctggctcgacagccaaacagattcatg
caagcagatcagtattcct

						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: 147
Transcript exons: 5560589-5560735
ACAAACAAAGGTTTTTCAACACCACAACCTGGCTCGACAGCCAAACAGATTCATGCAAGCAGAT
CAGTATTCCTCCTCCTCGTCACCGTCATCACTGCCGCCCTCTGCGGCGACCTCCTCGTAGTCCT
TCTCCAGGGCGGCCAGGTC
						
						Genomic sequence
						
							ACAAACAAAGGTTTTTCAACACCACAACCTGGCTCGACAGCCAAACAGATTCATGCAAGCAGAT
CAGTATTCCTCCTCCTCGTCACCGTCATCACTGCCGCCCTCTGCGGCGACCTCCTCGTAGTCCT
TCTCCAGGGCGGCCAGGTC

Sequences
Splice junction sequence	CCTCCTCGTCACCGTCATCACTGCCGCCCTCTGCGGCGACCTCCTCGTAGTCCTTCTCCAGGGC GGCCAGGTCacaaacaaaggtttttcaacaccacaacctggctcgacagccaaacagattcatg caagcagatcagtattcct
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: 147 Transcript exons: 5560589-5560735 ACAAACAAAGGTTTTTCAACACCACAACCTGGCTCGACAGCCAAACAGATTCATGCAAGCAGAT CAGTATTCCTCCTCCTCGTCACCGTCATCACTGCCGCCCTCTGCGGCGACCTCCTCGTAGTCCT TCTCCAGGGCGGCCAGGTC
Genomic sequence	ACAAACAAAGGTTTTTCAACACCACAACCTGGCTCGACAGCCAAACAGATTCATGCAAGCAGAT CAGTATTCCTCCTCCTCGTCACCGTCATCACTGCCGCCCTCTGCGGCGACCTCCTCGTAGTCCT TCTCCAGGGCGGCCAGGTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.880252098

Conservation Information
Conserved circRNAs	NA
PMCS	0.880252098

			
						 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 Zm00001d013159_circ_g.3

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