Plant Circular RNA Database

Detail information of Zm00001d002396_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d002396_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007068
					
						Alias
						Zm02circ00018
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 11926764-11927109  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d002396						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 9 plasma membrane-type
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d002396_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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
						Zm00001d002396_T014:3
Zm00001d002396_T012:3
Zm00001d002396_T021:3
Zm00001d002396_T023:3
Zm00001d002396_T019:2
Zm00001d002396_T016:3
Zm00001d002396_T002:3
Zm00001d002396_T017:3
Zm00001d002396_T025:3
Zm00001d002396_T005:3
Zm00001d002396_T010:3
Zm00001d002396_T018:3
Zm00001d002396_T001:3
Zm00001d002396_T003:3
Zm00001d002396_T024:3
Zm00001d002396_T022:3
Zm00001d002396_T026:3
Zm00001d002396_T004:3
Zm00001d002396_T006:3

General Information
CircRNA Name	Zm00001d002396_circ_g.3
ID in PlantcircBase	zma_circ_007068
Alias	Zm02circ00018
Organism	Zea mays
Position	chr2: 11926764-11927109 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d002396
Parent gene annotation	Calcium-transporting ATPase 9 plasma membrane-type
Parent gene strand	+
Alternative splicing	Zm00001d002396_circ_g.2
Support reads	NA
Tissues	leaf, endosperm
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	Zm00001d002396_T014:3 Zm00001d002396_T012:3 Zm00001d002396_T021:3 Zm00001d002396_T023:3 Zm00001d002396_T019:2 Zm00001d002396_T016:3 Zm00001d002396_T002:3 Zm00001d002396_T017:3 Zm00001d002396_T025:3 Zm00001d002396_T005:3 Zm00001d002396_T010:3 Zm00001d002396_T018:3 Zm00001d002396_T001:3 Zm00001d002396_T003:3 Zm00001d002396_T024:3 Zm00001d002396_T022:3 Zm00001d002396_T026:3 Zm00001d002396_T004:3 Zm00001d002396_T006:3

			
						 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  
						
							TTCCTATGGAATGTAGGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATC
TGCAGTGACAAGACTGGCACCTTAACTTTAAATCAGgtcactattgtggtcgtggctgttccag
aaggactaccattagctgtcacactgacgtaagcatggtttgtgtgttattttctgccagccct
ttcgtccc

						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
						
							GTCACTATTGTGGTCGTGGCTGTTCCAGAAGGACTACCATTAGCTGTCACACTGACGTAAGCAT
GGTTTGTGTGTTATTTTCTGCCAGCCCTTTCGTCCCTTGCCACTCAACATACTTTATTTTTGTC
AGGCTTGCTTTCTCAATGCGCAAAATGATGAAGGACAAGGCTCTGGTATGTTCCCAACTTTCTA
TACCTTGGTTTTGTCATACTACTTGATCCGACATTGAATGCTTTGCACGCTCACTTCCTATGGA
ATGTAGGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACA
AGACTGGCACCTTAACTTTAAATCAG

Sequences
Splice junction sequence	TTCCTATGGAATGTAGGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATC TGCAGTGACAAGACTGGCACCTTAACTTTAAATCAGgtcactattgtggtcgtggctgttccag aaggactaccattagctgtcacactgacgtaagcatggtttgtgtgttattttctgccagccct ttcgtccc
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	GTCACTATTGTGGTCGTGGCTGTTCCAGAAGGACTACCATTAGCTGTCACACTGACGTAAGCAT GGTTTGTGTGTTATTTTCTGCCAGCCCTTTCGTCCCTTGCCACTCAACATACTTTATTTTTGTC AGGCTTGCTTTCTCAATGCGCAAAATGATGAAGGACAAGGCTCTGGTATGTTCCCAACTTTCTA TACCTTGGTTTTGTCATACTACTTGATCCGACATTGAATGCTTTGCACGCTCACTTCCTATGGA ATGTAGGTCAGGAGGCTTTCTGCATGTGAAACGATGGGTTCTGCCACAACAATCTGCAGTGACA AGACTGGCACCTTAACTTTAAATCAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.19219882

Conservation Information
Conserved circRNAs	NA
PMCS	0.19219882

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							11926908-11927106(+)
						
						Potential amino acid sequence
						
							MRKMMKDKALVRRLSACETMGSATTICSDKTGTLTLNQVTIVVVAVPEGLPLAVTLTLAFSMRK
MMKDKALVRRLSACETMGSATTICSDKTGTLTLNQVTIVVVAVPEGLPLAVTLTLAFSMRKMMK
DKALVRRLSACETMGSATTICSDKTGTLTLNQVTIVVVAVPEGLPLAVTLTLAFSMRKMMKDKA
LVRRLSACETMGSATTICSDKTGTLTLNQ(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	11926908-11927106(+)
Potential amino acid sequence	MRKMMKDKALVRRLSACETMGSATTICSDKTGTLTLNQVTIVVVAVPEGLPLAVTLTLAFSMRK MMKDKALVRRLSACETMGSATTICSDKTGTLTLNQVTIVVVAVPEGLPLAVTLTLAFSMRKMMK DKALVRRLSACETMGSATTICSDKTGTLTLNQVTIVVVAVPEGLPLAVTLTLAFSMRKMMKDKA LVRRLSACETMGSATTICSDKTGTLTLNQ(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d002396_circ_g.3

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