Plant Circular RNA Database

Detail information of Zm00001d009562_circ_g.3

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d009562_circ_g.3
					

						ID in PlantcircBase
						zma_circ_005645
					

						Alias
						root_test_circ_002843
					

						Organism
						
							Zea mays						
					

						Position
						
							chr8: 70205173-70205315  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d009562						
					

						Parent gene annotation
						
							Putative homeodomain-like transcription factor superfamily prote
in  
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							NA						
					

						Support reads
						NA
					

						Tissues
						root
					

						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-AA							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
						Zm00001d009562_T023:1
Zm00001d009562_T040:1
Zm00001d009562_T043:1
Zm00001d009562_T024:1
Zm00001d009562_T041:1
Zm00001d009562_T044:1
Zm00001d009562_T087:1
Zm00001d009562_T008:1
Zm00001d009562_T019:1
Zm00001d009562_T012:1
Zm00001d009562_T082:1
Zm00001d009562_T028:1
Zm00001d009562_T006:1
Zm00001d009562_T052:1
Zm00001d009562_T049:1
Zm00001d009562_T005:1
Zm00001d009562_T051:1
Zm00001d009562_T036:1
Zm00001d009562_T015:1
Zm00001d009562_T039:1
Zm00001d009562_T003:1
Zm00001d009562_T017:1
Zm00001d009562_T037:1
Zm00001d009562_T027:1
Zm00001d009562_T067:1
Zm00001d009562_T058:1
Zm00001d009562_T045:1
Zm00001d009562_T014:1
Zm00001d009562_T009:1
Zm00001d009562_T060:1
Zm00001d009562_T018:1
Zm00001d009562_T079:1
Zm00001d009562_T057:1
Zm00001d009562_T035:1
Zm00001d009562_T031:1
Zm00001d009562_T007:1
Zm00001d009562_T022:1
Zm00001d009562_T038:1
Zm00001d009562_T002:1
Zm00001d009562_T004:1
Zm00001d009562_T046:1
Zm00001d009562_T069:1
Zm00001d009562_T063:1
Zm00001d009562_T062:1
Zm00001d009562_T066:1
Zm00001d009562_T021:1
Zm00001d009562_T020:1
Zm00001d009562_T011:1
Zm00001d009562_T034:1
Zm00001d009562_T030:1
Zm00001d009562_T013:1
Zm00001d009562_T025:1
Zm00001d009562_T064:1
Zm00001d009562_T050:1
Zm00001d009562_T016:1
Zm00001d009562_T029:1
Zm00001d009562_T033:1
Zm00001d009562_T010:1
Zm00001d009562_T026:1
Zm00001d009562_T001:1

					

			
		

General Information
CircRNA Name	Zm00001d009562_circ_g.3
ID in PlantcircBase	zma_circ_005645
Alias	root_test_circ_002843
Organism	Zea mays
Position	chr8: 70205173-70205315 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d009562
Parent gene annotation	Putative homeodomain-like transcription factor superfamily prote in
Parent gene strand	+
Alternative splicing	NA
Support reads	NA
Tissues	root
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-AA 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	Zm00001d009562_T023:1 Zm00001d009562_T040:1 Zm00001d009562_T043:1 Zm00001d009562_T024:1 Zm00001d009562_T041:1 Zm00001d009562_T044:1 Zm00001d009562_T087:1 Zm00001d009562_T008:1 Zm00001d009562_T019:1 Zm00001d009562_T012:1 Zm00001d009562_T082:1 Zm00001d009562_T028:1 Zm00001d009562_T006:1 Zm00001d009562_T052:1 Zm00001d009562_T049:1 Zm00001d009562_T005:1 Zm00001d009562_T051:1 Zm00001d009562_T036:1 Zm00001d009562_T015:1 Zm00001d009562_T039:1 Zm00001d009562_T003:1 Zm00001d009562_T017:1 Zm00001d009562_T037:1 Zm00001d009562_T027:1 Zm00001d009562_T067:1 Zm00001d009562_T058:1 Zm00001d009562_T045:1 Zm00001d009562_T014:1 Zm00001d009562_T009:1 Zm00001d009562_T060:1 Zm00001d009562_T018:1 Zm00001d009562_T079:1 Zm00001d009562_T057:1 Zm00001d009562_T035:1 Zm00001d009562_T031:1 Zm00001d009562_T007:1 Zm00001d009562_T022:1 Zm00001d009562_T038:1 Zm00001d009562_T002:1 Zm00001d009562_T004:1 Zm00001d009562_T046:1 Zm00001d009562_T069:1 Zm00001d009562_T063:1 Zm00001d009562_T062:1 Zm00001d009562_T066:1 Zm00001d009562_T021:1 Zm00001d009562_T020:1 Zm00001d009562_T011:1 Zm00001d009562_T034:1 Zm00001d009562_T030:1 Zm00001d009562_T013:1 Zm00001d009562_T025:1 Zm00001d009562_T064:1 Zm00001d009562_T050:1 Zm00001d009562_T016:1 Zm00001d009562_T029:1 Zm00001d009562_T033:1 Zm00001d009562_T010:1 Zm00001d009562_T026:1 Zm00001d009562_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  
						
							ATGATGGGTGATGGGAGCGACGATAATGATGAGGATGCTGAAGGAGATGAGGGTGAGGAAGATG
GAGAGGAcctatgaatgaggaatatggtgagcatatttcaggctatccaagagacaattccgac
tccagacccgtacag

						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
						
							CCTATGAATGAGGAATATGGTGAGCATATTTCAGGCTATCCAAGAGACAATTCCGACTCCAGAC
CCGTACAGATGATGGGTGATGGGAGCGACGATAATGATGAGGATGCTGAAGGAGATGAGGGTGA
GGAAGATGGAGAGGA

Sequences
Splice junction sequence	ATGATGGGTGATGGGAGCGACGATAATGATGAGGATGCTGAAGGAGATGAGGGTGAGGAAGATG GAGAGGAcctatgaatgaggaatatggtgagcatatttcaggctatccaagagacaattccgac tccagacccgtacag
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	CCTATGAATGAGGAATATGGTGAGCATATTTCAGGCTATCCAAGAGACAATTCCGACTCCAGAC CCGTACAGATGATGGGTGATGGGAGCGACGATAATGATGAGGATGCTGAAGGAGATGAGGGTGA GGAAGATGGAGAGGA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.280305128

Conservation Information
Conserved circRNAs	NA
PMCS	0.280305128

			
						 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
						Tang et al., 2018

circRNA

Detail information of Zm00001d009562_circ_g.3

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