Plant Circular RNA Database

Detail information of Zm00001d041889_circ_g.16

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d041889_circ_g.16
					

						ID in PlantcircBase
						zma_circ_004232
					

						Alias
						ear_test_circ_002074
					

						Organism
						
							Zea mays						
					

						Position
						
							chr3: 142438881-142439043  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							ui-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d041889						
					

						Parent gene annotation
						
							protein_coding
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d041889_circ_g.1 Zm00001d041889_circ_g.2 Zm00001d041889_circ_g.3 Zm00001d041889_circ_g.4 Zm00001d041889_circ_g.5 Zm00001d041889_circ_g.6 Zm00001d041889_circ_g.7 Zm00001d041889_circ_g.8 Zm00001d041889_circ_g.9 Zm00001d041889_circ_g.10 Zm00001d041889_circ_g.11 Zm00001d041889_circ_g.12 Zm00001d041889_circ_g.13 Zm00001d041889_circ_g.14 Zm00001d041889_circ_g.15 Zm00001d041889_circ_g.17 Zm00001d041889_circ_g.18 Zm00001d041889_circ_g.19 						
					

						Support reads
						NA
					

						Tissues
						ear
					

						Exon boundary  
						
							No-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-CA							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
						Zm00001d041889_T048:1
Zm00001d041889_T140:1
Zm00001d041889_T086:1
Zm00001d041889_T075:1
Zm00001d041889_T034:1
Zm00001d041889_T019:1
Zm00001d041889_T016:1
Zm00001d041889_T096:1
Zm00001d041889_T135:1
Zm00001d041889_T103:1
Zm00001d041889_T079:1
Zm00001d041889_T145:1
Zm00001d041889_T116:1
Zm00001d041889_T045:1
Zm00001d041889_T003:1
Zm00001d041889_T018:1
Zm00001d041889_T001:1
Zm00001d041889_T070:1
Zm00001d041889_T101:1
Zm00001d041889_T047:1
Zm00001d041889_T136:1
Zm00001d041889_T094:1
Zm00001d041889_T029:1
Zm00001d041889_T107:1
Zm00001d041889_T134:1
Zm00001d041889_T066:1
Zm00001d041889_T117:1
Zm00001d041889_T137:1
Zm00001d041889_T106:1
Zm00001d041889_T138:1
Zm00001d041889_T108:1
Zm00001d041889_T031:1
Zm00001d041889_T039:1
Zm00001d041889_T068:1
Zm00001d041889_T129:1
Zm00001d041889_T115:1
Zm00001d041889_T033:1
Zm00001d041889_T092:1
Zm00001d041889_T085:1
Zm00001d041889_T090:1
Zm00001d041889_T097:1
Zm00001d041889_T082:1
Zm00001d041889_T059:1
Zm00001d041889_T139:1
Zm00001d041889_T146:1
Zm00001d041889_T077:1
Zm00001d041889_T036:1
Zm00001d041889_T025:1
Zm00001d041889_T054:1
Zm00001d041889_T061:1
Zm00001d041889_T114:1
Zm00001d041889_T089:1
Zm00001d041889_T143:1
Zm00001d041889_T099:1
Zm00001d041889_T051:1
Zm00001d041889_T035:1
Zm00001d041889_T041:1
Zm00001d041889_T012:1
Zm00001d041889_T081:1
Zm00001d041889_T147:1
Zm00001d041889_T065:1
Zm00001d041889_T007:1
Zm00001d041889_T141:1
Zm00001d041889_T010:1
Zm00001d041889_T064:1
Zm00001d041889_T057:1
Zm00001d041889_T087:1
Zm00001d041889_T144:1
Zm00001d041889_T002:1
Zm00001d041889_T042:1
Zm00001d041889_T131:1
Zm00001d041889_T113:1
Zm00001d041889_T083:1
Zm00001d041889_T005:1
Zm00001d041889_T102:1
Zm00001d041889_T142:1
Zm00001d041889_T027:1
Zm00001d041889_T014:1
Zm00001d041889_T049:1
Zm00001d041889_T021:1
Zm00001d041889_T062:1
Zm00001d041889_T132:1
Zm00001d041889_T022:1

					

			
		

General Information
CircRNA Name	Zm00001d041889_circ_g.16
ID in PlantcircBase	zma_circ_004232
Alias	ear_test_circ_002074
Organism	Zea mays
Position	chr3: 142438881-142439043 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	find_circ
Parent gene	Zm00001d041889
Parent gene annotation	protein_coding
Parent gene strand	+
Alternative splicing	Zm00001d041889_circ_g.1 Zm00001d041889_circ_g.2 Zm00001d041889_circ_g.3 Zm00001d041889_circ_g.4 Zm00001d041889_circ_g.5 Zm00001d041889_circ_g.6 Zm00001d041889_circ_g.7 Zm00001d041889_circ_g.8 Zm00001d041889_circ_g.9 Zm00001d041889_circ_g.10 Zm00001d041889_circ_g.11 Zm00001d041889_circ_g.12 Zm00001d041889_circ_g.13 Zm00001d041889_circ_g.14 Zm00001d041889_circ_g.15 Zm00001d041889_circ_g.17 Zm00001d041889_circ_g.18 Zm00001d041889_circ_g.19
Support reads	NA
Tissues	ear
Exon boundary	No-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-CA 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	Zm00001d041889_T048:1 Zm00001d041889_T140:1 Zm00001d041889_T086:1 Zm00001d041889_T075:1 Zm00001d041889_T034:1 Zm00001d041889_T019:1 Zm00001d041889_T016:1 Zm00001d041889_T096:1 Zm00001d041889_T135:1 Zm00001d041889_T103:1 Zm00001d041889_T079:1 Zm00001d041889_T145:1 Zm00001d041889_T116:1 Zm00001d041889_T045:1 Zm00001d041889_T003:1 Zm00001d041889_T018:1 Zm00001d041889_T001:1 Zm00001d041889_T070:1 Zm00001d041889_T101:1 Zm00001d041889_T047:1 Zm00001d041889_T136:1 Zm00001d041889_T094:1 Zm00001d041889_T029:1 Zm00001d041889_T107:1 Zm00001d041889_T134:1 Zm00001d041889_T066:1 Zm00001d041889_T117:1 Zm00001d041889_T137:1 Zm00001d041889_T106:1 Zm00001d041889_T138:1 Zm00001d041889_T108:1 Zm00001d041889_T031:1 Zm00001d041889_T039:1 Zm00001d041889_T068:1 Zm00001d041889_T129:1 Zm00001d041889_T115:1 Zm00001d041889_T033:1 Zm00001d041889_T092:1 Zm00001d041889_T085:1 Zm00001d041889_T090:1 Zm00001d041889_T097:1 Zm00001d041889_T082:1 Zm00001d041889_T059:1 Zm00001d041889_T139:1 Zm00001d041889_T146:1 Zm00001d041889_T077:1 Zm00001d041889_T036:1 Zm00001d041889_T025:1 Zm00001d041889_T054:1 Zm00001d041889_T061:1 Zm00001d041889_T114:1 Zm00001d041889_T089:1 Zm00001d041889_T143:1 Zm00001d041889_T099:1 Zm00001d041889_T051:1 Zm00001d041889_T035:1 Zm00001d041889_T041:1 Zm00001d041889_T012:1 Zm00001d041889_T081:1 Zm00001d041889_T147:1 Zm00001d041889_T065:1 Zm00001d041889_T007:1 Zm00001d041889_T141:1 Zm00001d041889_T010:1 Zm00001d041889_T064:1 Zm00001d041889_T057:1 Zm00001d041889_T087:1 Zm00001d041889_T144:1 Zm00001d041889_T002:1 Zm00001d041889_T042:1 Zm00001d041889_T131:1 Zm00001d041889_T113:1 Zm00001d041889_T083:1 Zm00001d041889_T005:1 Zm00001d041889_T102:1 Zm00001d041889_T142:1 Zm00001d041889_T027:1 Zm00001d041889_T014:1 Zm00001d041889_T049:1 Zm00001d041889_T021:1 Zm00001d041889_T062:1 Zm00001d041889_T132:1 Zm00001d041889_T022:1

			
						 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  
						
							TAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCATGATAATGACAGAATAGC
TGAAGAGACTGATAAAGgaccatgaagagcaaagcaatgtgttcggagaacggagagttagctt
ggaagcaaatgccaacgagcctgaggaaaagaacc

						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
						
							GACCATGAAGAGCAAAGCAATGTGTTCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACG
AGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCA
TGATAATGACAGAATAGCTGAAGAGACTGATAAAG

Sequences
Splice junction sequence	TAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCATGATAATGACAGAATAGC TGAAGAGACTGATAAAGgaccatgaagagcaaagcaatgtgttcggagaacggagagttagctt ggaagcaaatgccaacgagcctgaggaaaagaacc
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	GACCATGAAGAGCAAAGCAATGTGTTCGGAGAACGGAGAGTTAGCTTGGAAGCAAATGCCAACG AGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCA TGATAATGACAGAATAGCTGAAGAGACTGATAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.164447546

Conservation Information
Conserved circRNAs	NA
PMCS	0.164447546

			
						 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

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Detail information of Zm00001d041889_circ_g.16

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