Plant Circular RNA Database

Detail information of Zm00001d044573_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d044573_circ_g.1
					
						ID in PlantcircBase
						zma_circ_007924
					
						Alias
						Zm03circ00142
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 232117761-232117954  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d044573						
					
						Parent gene annotation
						
							Pre-mRNA-processing protein 40A
							
						Parent gene strand
						+
					
						Alternative splicing
						
							NA						
					
						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  
						
							AG-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
						Zm00001d044573_T055:1
Zm00001d044573_T033:1
Zm00001d044573_T012:1
Zm00001d044573_T025:1
Zm00001d044573_T026:1
Zm00001d044573_T027:1
Zm00001d044573_T032:1
Zm00001d044573_T072:1
Zm00001d044573_T028:1
Zm00001d044573_T051:1
Zm00001d044573_T069:1
Zm00001d044573_T003:1
Zm00001d044573_T024:1
Zm00001d044573_T005:1
Zm00001d044573_T019:1
Zm00001d044573_T067:1
Zm00001d044573_T031:1
Zm00001d044573_T004:1
Zm00001d044573_T021:1
Zm00001d044573_T001:1
Zm00001d044573_T020:1
Zm00001d044573_T013:1
Zm00001d044573_T039:1
Zm00001d044573_T006:1
Zm00001d044573_T065:1
Zm00001d044573_T070:1
Zm00001d044573_T016:1
Zm00001d044573_T002:1
Zm00001d044573_T044:1
Zm00001d044573_T029:1
Zm00001d044573_T007:1
Zm00001d044573_T010:1
Zm00001d044573_T022:1
Zm00001d044573_T018:1
Zm00001d044573_T041:1
Zm00001d044573_T017:1
Zm00001d044573_T047:1
Zm00001d044573_T034:1
Zm00001d044573_T054:1
Zm00001d044573_T023:1
Zm00001d044573_T068:1

General Information
CircRNA Name	Zm00001d044573_circ_g.1
ID in PlantcircBase	zma_circ_007924
Alias	Zm03circ00142
Organism	Zea mays
Position	chr3: 232117761-232117954 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d044573
Parent gene annotation	Pre-mRNA-processing protein 40A
Parent gene strand	+
Alternative splicing	NA
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	AG-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	Zm00001d044573_T055:1 Zm00001d044573_T033:1 Zm00001d044573_T012:1 Zm00001d044573_T025:1 Zm00001d044573_T026:1 Zm00001d044573_T027:1 Zm00001d044573_T032:1 Zm00001d044573_T072:1 Zm00001d044573_T028:1 Zm00001d044573_T051:1 Zm00001d044573_T069:1 Zm00001d044573_T003:1 Zm00001d044573_T024:1 Zm00001d044573_T005:1 Zm00001d044573_T019:1 Zm00001d044573_T067:1 Zm00001d044573_T031:1 Zm00001d044573_T004:1 Zm00001d044573_T021:1 Zm00001d044573_T001:1 Zm00001d044573_T020:1 Zm00001d044573_T013:1 Zm00001d044573_T039:1 Zm00001d044573_T006:1 Zm00001d044573_T065:1 Zm00001d044573_T070:1 Zm00001d044573_T016:1 Zm00001d044573_T002:1 Zm00001d044573_T044:1 Zm00001d044573_T029:1 Zm00001d044573_T007:1 Zm00001d044573_T010:1 Zm00001d044573_T022:1 Zm00001d044573_T018:1 Zm00001d044573_T041:1 Zm00001d044573_T017:1 Zm00001d044573_T047:1 Zm00001d044573_T034:1 Zm00001d044573_T054:1 Zm00001d044573_T023:1 Zm00001d044573_T068:1

			
						 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  
						
							AGAGAGAAAAGGAGAAAGGGAAGGATCGATCAAGGAGAGATGAAATGGAGTTTGATGGTGCTGA
TTTGAACACCCATGGTGCAAAAGATAAGAAAAGgcaaaaagagagaaagagcgtgaggagaaag
agaagaagaaagagaaagaaaggaaggagaaagaacgcaaagaaaaagaaagagaccaccggga
gg

						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: 194
Transcript exons: 232117761-232117954
GCAAAAAGAGAGAAAGAGCGTGAGGAGAAAGAGAAGAAGAAAGAGAAAGAAAGGAAGGAGAAAG
AACGCAAAGAAAAAGAAAGAGACCACCGGGAGGAGAGAGAAAAGGAGAAAGGGAAGGATCGATC
AAGGAGAGATGAAATGGAGTTTGATGGTGCTGATTTGAACACCCATGGTGCAAAAGATAAGAAA
AG
						
						Genomic sequence
						
							GCAAAAAGAGAGAAAGAGCGTGAGGAGAAAGAGAAGAAGAAAGAGAAAGAAAGGAAGGAGAAAG
AACGCAAAGAAAAAGAAAGAGACCACCGGGAGGAGAGAGAAAAGGAGAAAGGGAAGGATCGATC
AAGGAGAGATGAAATGGAGTTTGATGGTGCTGATTTGAACACCCATGGTGCAAAAGATAAGAAA
AG

Sequences
Splice junction sequence	AGAGAGAAAAGGAGAAAGGGAAGGATCGATCAAGGAGAGATGAAATGGAGTTTGATGGTGCTGA TTTGAACACCCATGGTGCAAAAGATAAGAAAAGgcaaaaagagagaaagagcgtgaggagaaag agaagaagaaagagaaagaaaggaaggagaaagaacgcaaagaaaaagaaagagaccaccggga gg
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: 194 Transcript exons: 232117761-232117954 GCAAAAAGAGAGAAAGAGCGTGAGGAGAAAGAGAAGAAGAAAGAGAAAGAAAGGAAGGAGAAAG AACGCAAAGAAAAAGAAAGAGACCACCGGGAGGAGAGAGAAAAGGAGAAAGGGAAGGATCGATC AAGGAGAGATGAAATGGAGTTTGATGGTGCTGATTTGAACACCCATGGTGCAAAAGATAAGAAA AG
Genomic sequence	GCAAAAAGAGAGAAAGAGCGTGAGGAGAAAGAGAAGAAGAAAGAGAAAGAAAGGAAGGAGAAAG AACGCAAAGAAAAAGAAAGAGACCACCGGGAGGAGAGAGAAAAGGAGAAAGGGAAGGATCGATC AAGGAGAGATGAAATGGAGTTTGATGGTGCTGATTTGAACACCCATGGTGCAAAAGATAAGAAA AG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.336632753

Conservation Information
Conserved circRNAs	NA
PMCS	0.336632753

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							232117903-232117923(+)
						
						Potential amino acid sequence
						
							MEFDGADLNTHGAKDKKRQKERKSVRRKRRRKRKKGRRKNAKKKKETTGRREKRRKGRIDQGEM
KWSLMVLI*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	232117903-232117923(+)
Potential amino acid sequence	MEFDGADLNTHGAKDKKRQKERKSVRRKRRRKRKKGRRKNAKKKKETTGRREKRRKGRIDQGEM KWSLMVLI*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d044573_circ_g.1

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