Plant Circular RNA Database

Detail information of Zm00001d041889_circ_g.9

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d041889_circ_g.9
					

						ID in PlantcircBase
						zma_circ_004226
					

						Alias
						ovule_test_circ_003033
					

						Organism
						
							Zea mays						
					

						Position
						
							chr3: 142438014-142438737  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-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.10 Zm00001d041889_circ_g.11 Zm00001d041889_circ_g.12 Zm00001d041889_circ_g.13 Zm00001d041889_circ_g.14 Zm00001d041889_circ_g.15 Zm00001d041889_circ_g.16 Zm00001d041889_circ_g.17 Zm00001d041889_circ_g.18 Zm00001d041889_circ_g.19 						
					

						Support reads
						NA
					

						Tissues
						ovule
					

						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-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
						Zm00001d041889_T059:3
Zm00001d041889_T145:3
Zm00001d041889_T061:3
Zm00001d041889_T141:3
Zm00001d041889_T081:3
Zm00001d041889_T022:3
Zm00001d041889_T102:1
Zm00001d041889_T001:3
Zm00001d041889_T016:3
Zm00001d041889_T086:2
Zm00001d041889_T082:2
Zm00001d041889_T048:3
Zm00001d041889_T051:3
Zm00001d041889_T021:2
Zm00001d041889_T057:3
Zm00001d041889_T065:3
Zm00001d041889_T034:2
Zm00001d041889_T129:3
Zm00001d041889_T103:3
Zm00001d041889_T041:3
Zm00001d041889_T087:3
Zm00001d041889_T131:3
Zm00001d041889_T003:3
Zm00001d041889_T064:3
Zm00001d041889_T031:1
Zm00001d041889_T139:3
Zm00001d041889_T135:3
Zm00001d041889_T075:1
Zm00001d041889_T138:4
Zm00001d041889_T073:3
Zm00001d041889_T114:2
Zm00001d041889_T070:3
Zm00001d041889_T106:3
Zm00001d041889_T143:2
Zm00001d041889_T068:2
Zm00001d041889_T042:3
Zm00001d041889_T107:2
Zm00001d041889_T049:3
Zm00001d041889_T132:3
Zm00001d041889_T079:3
Zm00001d041889_T115:2
Zm00001d041889_T142:2
Zm00001d041889_T097:3
Zm00001d041889_T101:1
Zm00001d041889_T140:1
Zm00001d041889_T099:1
Zm00001d041889_T012:3
Zm00001d041889_T066:3
Zm00001d041889_T007:3
Zm00001d041889_T035:3
Zm00001d041889_T033:3
Zm00001d041889_T077:2
Zm00001d041889_T027:3
Zm00001d041889_T134:3
Zm00001d041889_T029:1
Zm00001d041889_T144:2
Zm00001d041889_T085:1
Zm00001d041889_T116:1
Zm00001d041889_T025:3
Zm00001d041889_T094:3
Zm00001d041889_T113:3
Zm00001d041889_T010:1
Zm00001d041889_T083:3
Zm00001d041889_T036:3
Zm00001d041889_T117:3
Zm00001d041889_T092:3
Zm00001d041889_T047:2
Zm00001d041889_T136:3
Zm00001d041889_T137:3
Zm00001d041889_T062:3
Zm00001d041889_T045:1
Zm00001d041889_T014:3
Zm00001d041889_T054:3
Zm00001d041889_T090:3
Zm00001d041889_T002:3
Zm00001d041889_T039:1
Zm00001d041889_T108:3
Zm00001d041889_T096:3
Zm00001d041889_T005:3
Zm00001d041889_T019:3
Zm00001d041889_T018:3
Zm00001d041889_T089:3

					

			
		

General Information
CircRNA Name	Zm00001d041889_circ_g.9
ID in PlantcircBase	zma_circ_004226
Alias	ovule_test_circ_003033
Organism	Zea mays
Position	chr3: 142438014-142438737 JBrowse»
Reference genome	AGPv4.38
Type	u-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.10 Zm00001d041889_circ_g.11 Zm00001d041889_circ_g.12 Zm00001d041889_circ_g.13 Zm00001d041889_circ_g.14 Zm00001d041889_circ_g.15 Zm00001d041889_circ_g.16 Zm00001d041889_circ_g.17 Zm00001d041889_circ_g.18 Zm00001d041889_circ_g.19
Support reads	NA
Tissues	ovule
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-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	Zm00001d041889_T059:3 Zm00001d041889_T145:3 Zm00001d041889_T061:3 Zm00001d041889_T141:3 Zm00001d041889_T081:3 Zm00001d041889_T022:3 Zm00001d041889_T102:1 Zm00001d041889_T001:3 Zm00001d041889_T016:3 Zm00001d041889_T086:2 Zm00001d041889_T082:2 Zm00001d041889_T048:3 Zm00001d041889_T051:3 Zm00001d041889_T021:2 Zm00001d041889_T057:3 Zm00001d041889_T065:3 Zm00001d041889_T034:2 Zm00001d041889_T129:3 Zm00001d041889_T103:3 Zm00001d041889_T041:3 Zm00001d041889_T087:3 Zm00001d041889_T131:3 Zm00001d041889_T003:3 Zm00001d041889_T064:3 Zm00001d041889_T031:1 Zm00001d041889_T139:3 Zm00001d041889_T135:3 Zm00001d041889_T075:1 Zm00001d041889_T138:4 Zm00001d041889_T073:3 Zm00001d041889_T114:2 Zm00001d041889_T070:3 Zm00001d041889_T106:3 Zm00001d041889_T143:2 Zm00001d041889_T068:2 Zm00001d041889_T042:3 Zm00001d041889_T107:2 Zm00001d041889_T049:3 Zm00001d041889_T132:3 Zm00001d041889_T079:3 Zm00001d041889_T115:2 Zm00001d041889_T142:2 Zm00001d041889_T097:3 Zm00001d041889_T101:1 Zm00001d041889_T140:1 Zm00001d041889_T099:1 Zm00001d041889_T012:3 Zm00001d041889_T066:3 Zm00001d041889_T007:3 Zm00001d041889_T035:3 Zm00001d041889_T033:3 Zm00001d041889_T077:2 Zm00001d041889_T027:3 Zm00001d041889_T134:3 Zm00001d041889_T029:1 Zm00001d041889_T144:2 Zm00001d041889_T085:1 Zm00001d041889_T116:1 Zm00001d041889_T025:3 Zm00001d041889_T094:3 Zm00001d041889_T113:3 Zm00001d041889_T010:1 Zm00001d041889_T083:3 Zm00001d041889_T036:3 Zm00001d041889_T117:3 Zm00001d041889_T092:3 Zm00001d041889_T047:2 Zm00001d041889_T136:3 Zm00001d041889_T137:3 Zm00001d041889_T062:3 Zm00001d041889_T045:1 Zm00001d041889_T014:3 Zm00001d041889_T054:3 Zm00001d041889_T090:3 Zm00001d041889_T002:3 Zm00001d041889_T039:1 Zm00001d041889_T108:3 Zm00001d041889_T096:3 Zm00001d041889_T005:3 Zm00001d041889_T019:3 Zm00001d041889_T018:3 Zm00001d041889_T089:3

			
						 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  
						
							GAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGC
ATGATAATGACAGAATAGCTGAAGAGACTGATAAAGgagcatgaagaaaaatatgcagttagcc
ctatagccgttgaaaagagcttccgtcaggaagcaagtgcaattgaatctgcaggaaaacccct
aactgtca

						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
						
							GAGCATGAAGAAAAATATGCAGTTAGCCCTATAGCCGTTGAAAAGAGCTTCCGTCAGGAAGCAA
GTGCAATTGAATCTGCAGGAAAACCCCTAACTGTCATCTTTTCTAACGATCTCCACACCAAACA
TCTGCAACATGATTGTGATGTGCTAATTAAGGAGACTGGTGAAGGTAATATTGCATTAATACTT
GTTCCACAACTTGTTACTGATCTGCGGAGATGGTGATGAAAACTTGTGCTGTTTGCACTGTGTT
GACATTTTTTAAATGTATTCTTTCCCTTTCTCAGAAGTTTTAGCTCAGGAGAATTGTAATGACC
AGCCTGTTCCTGCCCAGACCGACCTAGAAATTAAGTTAAATGATGAACTTGCTGATCCGGGTAT
GGACCGTGTTTAATTTACCAATTTTAAACATACCGAGTTCTAAGTCAAGTTGTTGGCTACTTGT
AATTCTAATTGTTTTTAATAGGCTTTATATTTATTCTATCTGCAAAAGCTAGGCATATGTTTCA
TTGTCATTTGATGTCTTTTAAGTATCTGACATTTATTTTTTAAATGTATTCTTTCCCTTTATCA
GATGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCAACGAGCCTGAGGAAAAGA
ACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCATGATAATGACAGAAT
AGCTGAAGAGACTGATAAAG

Sequences
Splice junction sequence	GAGCCTGAGGAAAAGAACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGC ATGATAATGACAGAATAGCTGAAGAGACTGATAAAGgagcatgaagaaaaatatgcagttagcc ctatagccgttgaaaagagcttccgtcaggaagcaagtgcaattgaatctgcaggaaaacccct aactgtca
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	GAGCATGAAGAAAAATATGCAGTTAGCCCTATAGCCGTTGAAAAGAGCTTCCGTCAGGAAGCAA GTGCAATTGAATCTGCAGGAAAACCCCTAACTGTCATCTTTTCTAACGATCTCCACACCAAACA TCTGCAACATGATTGTGATGTGCTAATTAAGGAGACTGGTGAAGGTAATATTGCATTAATACTT GTTCCACAACTTGTTACTGATCTGCGGAGATGGTGATGAAAACTTGTGCTGTTTGCACTGTGTT GACATTTTTTAAATGTATTCTTTCCCTTTCTCAGAAGTTTTAGCTCAGGAGAATTGTAATGACC AGCCTGTTCCTGCCCAGACCGACCTAGAAATTAAGTTAAATGATGAACTTGCTGATCCGGGTAT GGACCGTGTTTAATTTACCAATTTTAAACATACCGAGTTCTAAGTCAAGTTGTTGGCTACTTGT AATTCTAATTGTTTTTAATAGGCTTTATATTTATTCTATCTGCAAAAGCTAGGCATATGTTTCA TTGTCATTTGATGTCTTTTAAGTATCTGACATTTATTTTTTAAATGTATTCTTTCCCTTTATCA GATGTTTTAGCTCAGGAGAATTGTAATGACCAGCCTGTTCCTGCCAACGAGCCTGAGGAAAAGA ACCTAGCTAACGTCATATCAACTGATCTCCACACCAAAACTCTGCAGCATGATAATGACAGAAT AGCTGAAGAGACTGATAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.13165747

Conservation Information
Conserved circRNAs	NA
PMCS	0.13165747

			
						 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 Zm00001d041889_circ_g.9

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