Plant Circular RNA Database

Detail information of Zm00001d001913_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d001913_circ_g.2
					
						ID in PlantcircBase
						zma_circ_000140
					
						Alias
						NA
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 2801707-2801811  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Zm00001d001913						
					
						Parent gene annotation
						
							Ubiquitin-conjugating enzyme E2 11
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d001913_circ_g.1 						
					
						Support reads
						7
					
						Tissues
						shoot
					
						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
						Zm00001d001913_T002:1
Zm00001d001913_T001:1
Zm00001d001913_T004:1
Zm00001d001913_T003:1
Zm00001d001913_T005:1

General Information
CircRNA Name	Zm00001d001913_circ_g.2
ID in PlantcircBase	zma_circ_000140
Alias	NA
Organism	Zea mays
Position	chr2: 2801707-2801811 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	SMALT, Segemehl
Parent gene	Zm00001d001913
Parent gene annotation	Ubiquitin-conjugating enzyme E2 11
Parent gene strand	+
Alternative splicing	Zm00001d001913_circ_g.1
Support reads	7
Tissues	shoot
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	Zm00001d001913_T002:1 Zm00001d001913_T001:1 Zm00001d001913_T004:1 Zm00001d001913_T003:1 Zm00001d001913_T005:1

			
						 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  
						
							TTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtgtctttccgc
accaaggttttccacccgaacatcaacagcaacggcagcat

						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: 105
Transcript exons: 2801707-2801811
GTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACA
TTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG
						
						Genomic sequence
						
							GTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACA
TTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG

Sequences
Splice junction sequence	TTGCCTTGACATTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAGgtgtctttccgc accaaggttttccacccgaacatcaacagcaacggcagcat
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: 105 Transcript exons: 2801707-2801811 GTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACA TTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG
Genomic sequence	GTGTCTTTCCGCACCAAGGTTTTCCACCCGAACATCAACAGCAACGGCAGCATTTGCCTTGACA TTCTTAAGGAACAGTGGAGTCCTGCTTTAACTATCTCAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_025862 						
					
						PMCS
						0.445402628

Conservation Information
Conserved circRNAs	osa_circ_025862
PMCS	0.445402628

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							2801773-2801709(-)
						
						Potential amino acid sequence
						
							MSRQMLPLLLMFGWKTLVRKDTFEIVKAGLHCSLRMSRQMLPLLLMFGWKTLVRKDTFEIVKAG
LHCSLRMSRQMLPLLLMFGWKTLVRKDTFEIVKAGLHCSLRMSRQMLPLLLMFGWKTLVRKD(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	2801773-2801709(-)
Potential amino acid sequence	MSRQMLPLLLMFGWKTLVRKDTFEIVKAGLHCSLRMSRQMLPLLLMFGWKTLVRKDTFEIVKAG LHCSLRMSRQMLPLLLMFGWKTLVRKDTFEIVKAGLHCSLRMSRQMLPLLLMFGWKTLVRKD(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Zm00001d001913_circ_g.2

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