Plant Circular RNA Database

Detail information of Zm00001d004125_circ_g.4

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d004125_circ_g.4
					

						ID in PlantcircBase
						zma_circ_007219
					

						Alias
						zma_circ_0001104
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 84504955-84505338  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d004125						
					

						Parent gene annotation
						
							 acetyl-CoA carboxylase2
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d004125_circ_g.2 Zm00001d004125_circ_g.3 						
					

						Support reads
						NA
					

						Tissues
						leaf, 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  
						
							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
						Zm00001d004125_T075:2
Zm00001d004125_T115:1
Zm00001d004125_T012:2
Zm00001d004125_T041:2
Zm00001d004125_T149:2
Zm00001d004125_T081:2
Zm00001d004125_T093:2
Zm00001d004125_T179:2
Zm00001d004125_T131:2
Zm00001d004125_T112:2
Zm00001d004125_T088:2
Zm00001d004125_T144:2
Zm00001d004125_T177:2
Zm00001d004125_T140:2
Zm00001d004125_T158:2
Zm00001d004125_T060:2
Zm00001d004125_T054:2
Zm00001d004125_T178:2
Zm00001d004125_T118:2
Zm00001d004125_T068:2
Zm00001d004125_T032:2
Zm00001d004125_T022:2
Zm00001d004125_T114:2
Zm00001d004125_T091:2
Zm00001d004125_T090:2
Zm00001d004125_T098:2
Zm00001d004125_T082:2
Zm00001d004125_T116:2
Zm00001d004125_T143:2
Zm00001d004125_T055:2
Zm00001d004125_T005:2
Zm00001d004125_T156:2
Zm00001d004125_T168:2
Zm00001d004125_T001:2
Zm00001d004125_T153:2
Zm00001d004125_T073:2
Zm00001d004125_T164:2
Zm00001d004125_T125:2
Zm00001d004125_T057:2
Zm00001d004125_T139:2
Zm00001d004125_T108:2
Zm00001d004125_T048:2
Zm00001d004125_T063:2
Zm00001d004125_T157:2
Zm00001d004125_T127:2
Zm00001d004125_T121:2
Zm00001d004125_T150:2
Zm00001d004125_T103:2
Zm00001d004125_T183:1
Zm00001d004125_T038:2
Zm00001d004125_T100:2
Zm00001d004125_T110:2
Zm00001d004125_T036:2
Zm00001d004125_T046:2
Zm00001d004125_T097:2
Zm00001d004125_T077:2
Zm00001d004125_T076:2
Zm00001d004125_T071:2
Zm00001d004125_T006:2
Zm00001d004125_T064:2
Zm00001d004125_T004:2
Zm00001d004125_T078:2
Zm00001d004125_T070:2
Zm00001d004125_T136:2
Zm00001d004125_T167:2
Zm00001d004125_T107:2
Zm00001d004125_T031:2
Zm00001d004125_T003:2
Zm00001d004125_T074:2
Zm00001d004125_T165:2
Zm00001d004125_T062:2
Zm00001d004125_T084:2
Zm00001d004125_T035:2
Zm00001d004125_T134:2
Zm00001d004125_T154:2
Zm00001d004125_T182:2
Zm00001d004125_T007:2
Zm00001d004125_T130:2
Zm00001d004125_T181:2
Zm00001d004125_T013:2
Zm00001d004125_T172:2
Zm00001d004125_T027:2
Zm00001d004125_T126:2
Zm00001d004125_T086:2
Zm00001d004125_T123:2
Zm00001d004125_T129:2
Zm00001d004125_T101:2
Zm00001d004125_T039:2
Zm00001d004125_T174:2
Zm00001d004125_T159:2
Zm00001d004125_T163:1
Zm00001d004125_T059:2
Zm00001d004125_T170:2
Zm00001d004125_T135:2
Zm00001d004125_T105:2
Zm00001d004125_T094:2
Zm00001d004125_T089:2
Zm00001d004125_T147:2
Zm00001d004125_T037:2
Zm00001d004125_T096:2
Zm00001d004125_T072:2
Zm00001d004125_T020:2
Zm00001d004125_T030:2
Zm00001d004125_T067:2
Zm00001d004125_T066:2
Zm00001d004125_T023:2
Zm00001d004125_T043:2
Zm00001d004125_T061:2
Zm00001d004125_T092:2
Zm00001d004125_T162:2
Zm00001d004125_T087:2
Zm00001d004125_T002:2
Zm00001d004125_T024:2
Zm00001d004125_T015:2
Zm00001d004125_T132:2
Zm00001d004125_T085:2
Zm00001d004125_T095:2
Zm00001d004125_T171:2
Zm00001d004125_T051:2

					

			
		

General Information
CircRNA Name	Zm00001d004125_circ_g.4
ID in PlantcircBase	zma_circ_007219
Alias	zma_circ_0001104
Organism	Zea mays
Position	chr2: 84504955-84505338 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d004125
Parent gene annotation	acetyl-CoA carboxylase2
Parent gene strand	+
Alternative splicing	Zm00001d004125_circ_g.2 Zm00001d004125_circ_g.3
Support reads	NA
Tissues	leaf, 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	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	Zm00001d004125_T075:2 Zm00001d004125_T115:1 Zm00001d004125_T012:2 Zm00001d004125_T041:2 Zm00001d004125_T149:2 Zm00001d004125_T081:2 Zm00001d004125_T093:2 Zm00001d004125_T179:2 Zm00001d004125_T131:2 Zm00001d004125_T112:2 Zm00001d004125_T088:2 Zm00001d004125_T144:2 Zm00001d004125_T177:2 Zm00001d004125_T140:2 Zm00001d004125_T158:2 Zm00001d004125_T060:2 Zm00001d004125_T054:2 Zm00001d004125_T178:2 Zm00001d004125_T118:2 Zm00001d004125_T068:2 Zm00001d004125_T032:2 Zm00001d004125_T022:2 Zm00001d004125_T114:2 Zm00001d004125_T091:2 Zm00001d004125_T090:2 Zm00001d004125_T098:2 Zm00001d004125_T082:2 Zm00001d004125_T116:2 Zm00001d004125_T143:2 Zm00001d004125_T055:2 Zm00001d004125_T005:2 Zm00001d004125_T156:2 Zm00001d004125_T168:2 Zm00001d004125_T001:2 Zm00001d004125_T153:2 Zm00001d004125_T073:2 Zm00001d004125_T164:2 Zm00001d004125_T125:2 Zm00001d004125_T057:2 Zm00001d004125_T139:2 Zm00001d004125_T108:2 Zm00001d004125_T048:2 Zm00001d004125_T063:2 Zm00001d004125_T157:2 Zm00001d004125_T127:2 Zm00001d004125_T121:2 Zm00001d004125_T150:2 Zm00001d004125_T103:2 Zm00001d004125_T183:1 Zm00001d004125_T038:2 Zm00001d004125_T100:2 Zm00001d004125_T110:2 Zm00001d004125_T036:2 Zm00001d004125_T046:2 Zm00001d004125_T097:2 Zm00001d004125_T077:2 Zm00001d004125_T076:2 Zm00001d004125_T071:2 Zm00001d004125_T006:2 Zm00001d004125_T064:2 Zm00001d004125_T004:2 Zm00001d004125_T078:2 Zm00001d004125_T070:2 Zm00001d004125_T136:2 Zm00001d004125_T167:2 Zm00001d004125_T107:2 Zm00001d004125_T031:2 Zm00001d004125_T003:2 Zm00001d004125_T074:2 Zm00001d004125_T165:2 Zm00001d004125_T062:2 Zm00001d004125_T084:2 Zm00001d004125_T035:2 Zm00001d004125_T134:2 Zm00001d004125_T154:2 Zm00001d004125_T182:2 Zm00001d004125_T007:2 Zm00001d004125_T130:2 Zm00001d004125_T181:2 Zm00001d004125_T013:2 Zm00001d004125_T172:2 Zm00001d004125_T027:2 Zm00001d004125_T126:2 Zm00001d004125_T086:2 Zm00001d004125_T123:2 Zm00001d004125_T129:2 Zm00001d004125_T101:2 Zm00001d004125_T039:2 Zm00001d004125_T174:2 Zm00001d004125_T159:2 Zm00001d004125_T163:1 Zm00001d004125_T059:2 Zm00001d004125_T170:2 Zm00001d004125_T135:2 Zm00001d004125_T105:2 Zm00001d004125_T094:2 Zm00001d004125_T089:2 Zm00001d004125_T147:2 Zm00001d004125_T037:2 Zm00001d004125_T096:2 Zm00001d004125_T072:2 Zm00001d004125_T020:2 Zm00001d004125_T030:2 Zm00001d004125_T067:2 Zm00001d004125_T066:2 Zm00001d004125_T023:2 Zm00001d004125_T043:2 Zm00001d004125_T061:2 Zm00001d004125_T092:2 Zm00001d004125_T162:2 Zm00001d004125_T087:2 Zm00001d004125_T002:2 Zm00001d004125_T024:2 Zm00001d004125_T015:2 Zm00001d004125_T132:2 Zm00001d004125_T085:2 Zm00001d004125_T095:2 Zm00001d004125_T171:2 Zm00001d004125_T051:2

			
						 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  
						
							GGGATGCATAAGGGAGAAATGAGTATTAAGGATAACATGGAAGATTTAGTCTCTGCCCCATTAC
CTGTTGAAGATGCTCTGATTTCTTTGTTTGATTACActaagcttgtaacggcacttatggaaaa
gctggtttatccaaatcctggtggttacagggatctgttagttcgcttttcttccctcaatcat
aaaagata

						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
						
							CTAAGCTTGTAACGGCACTTATGGAAAAGCTGGTTTATCCAAATCCTGGTGGTTACAGGGATCT
GTTAGTTCGCTTTTCTTCCCTCAATCATAAAAGATATTATAAGGTGCAGTGGTTAGAAATAACT
TAGATAGATATTCCCATTATAATTTATTTTGATATTTTTCCTAATGAATTCCATGCATCTTAAT
AAACACAGTTGGCCCTTAAAGCAAGTGAACTTCTTGAACAAACCAAACTAAGTGAACTCCGTGC
AAGCGTTGCAAGAAGCCTTTCGGATCTGGGGATGCATAAGGGAGAAATGAGTATTAAGGATAAC
ATGGAAGATTTAGTCTCTGCCCCATTACCTGTTGAAGATGCTCTGATTTCTTTGTTTGATTACA

Sequences
Splice junction sequence	GGGATGCATAAGGGAGAAATGAGTATTAAGGATAACATGGAAGATTTAGTCTCTGCCCCATTAC CTGTTGAAGATGCTCTGATTTCTTTGTTTGATTACActaagcttgtaacggcacttatggaaaa gctggtttatccaaatcctggtggttacagggatctgttagttcgcttttcttccctcaatcat aaaagata
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	CTAAGCTTGTAACGGCACTTATGGAAAAGCTGGTTTATCCAAATCCTGGTGGTTACAGGGATCT GTTAGTTCGCTTTTCTTCCCTCAATCATAAAAGATATTATAAGGTGCAGTGGTTAGAAATAACT TAGATAGATATTCCCATTATAATTTATTTTGATATTTTTCCTAATGAATTCCATGCATCTTAAT AAACACAGTTGGCCCTTAAAGCAAGTGAACTTCTTGAACAAACCAAACTAAGTGAACTCCGTGC AAGCGTTGCAAGAAGCCTTTCGGATCTGGGGATGCATAAGGGAGAAATGAGTATTAAGGATAAC ATGGAAGATTTAGTCTCTGCCCCATTACCTGTTGAAGATGCTCTGATTTCTTTGTTTGATTACA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.154704796

Conservation Information
Conserved circRNAs	NA
PMCS	0.154704796

			
						 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
						Ma et al., 2021b

circRNA

Detail information of Zm00001d004125_circ_g.4

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