Plant Circular RNA Database

Detail information of Zm00001d039537_circ_g.12

			
						 General Information
					
						CircRNA Name
						Zm00001d039537_circ_g.12
					
						ID in PlantcircBase
						zma_circ_007484
					
						Alias
						zma_circ_0001489
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 7527388-7529085  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d039537						
					
						Parent gene annotation
						
							Protein ALWAYS EARLY 3
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d039537_circ_g.2 Zm00001d039537_circ_g.3 Zm00001d039537_circ_g.4 Zm00001d039537_circ_g.5 Zm00001d039537_circ_g.6 Zm00001d039537_circ_g.7 Zm00001d039537_circ_g.8 Zm00001d039537_circ_g.9 Zm00001d039537_circ_g.10 Zm00001d039537_circ_g.11 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						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  
						
							CT-AC							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
						Zm00001d039537_T048:3
Zm00001d039537_T023:1
Zm00001d039537_T033:3
Zm00001d039537_T009:3
Zm00001d039537_T059:3
Zm00001d039537_T064:3
Zm00001d039537_T012:3
Zm00001d039537_T034:3
Zm00001d039537_T049:3
Zm00001d039537_T013:3
Zm00001d039537_T063:3
Zm00001d039537_T007:3
Zm00001d039537_T043:3
Zm00001d039537_T060:3
Zm00001d039537_T005:2
Zm00001d039537_T004:1
Zm00001d039537_T021:2
Zm00001d039537_T008:3
Zm00001d039537_T038:2
Zm00001d039537_T061:3
Zm00001d039537_T039:3
Zm00001d039537_T016:3
Zm00001d039537_T041:3
Zm00001d039537_T011:3
Zm00001d039537_T022:3
Zm00001d039537_T003:3
Zm00001d039537_T047:3
Zm00001d039537_T006:3
Zm00001d039537_T065:3
Zm00001d039537_T062:3
Zm00001d039537_T053:3
Zm00001d039537_T017:3
Zm00001d039537_T035:3
Zm00001d039537_T010:3
Zm00001d039537_T024:3
Zm00001d039537_T040:3
Zm00001d039537_T014:3
Zm00001d039537_T015:3

General Information
CircRNA Name	Zm00001d039537_circ_g.12
ID in PlantcircBase	zma_circ_007484
Alias	zma_circ_0001489
Organism	Zea mays
Position	chr3: 7527388-7529085 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	find_circ
Parent gene	Zm00001d039537
Parent gene annotation	Protein ALWAYS EARLY 3
Parent gene strand	-
Alternative splicing	Zm00001d039537_circ_g.2 Zm00001d039537_circ_g.3 Zm00001d039537_circ_g.4 Zm00001d039537_circ_g.5 Zm00001d039537_circ_g.6 Zm00001d039537_circ_g.7 Zm00001d039537_circ_g.8 Zm00001d039537_circ_g.9 Zm00001d039537_circ_g.10 Zm00001d039537_circ_g.11
Support reads	NA
Tissues	leaf, root
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	CT-AC 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	Zm00001d039537_T048:3 Zm00001d039537_T023:1 Zm00001d039537_T033:3 Zm00001d039537_T009:3 Zm00001d039537_T059:3 Zm00001d039537_T064:3 Zm00001d039537_T012:3 Zm00001d039537_T034:3 Zm00001d039537_T049:3 Zm00001d039537_T013:3 Zm00001d039537_T063:3 Zm00001d039537_T007:3 Zm00001d039537_T043:3 Zm00001d039537_T060:3 Zm00001d039537_T005:2 Zm00001d039537_T004:1 Zm00001d039537_T021:2 Zm00001d039537_T008:3 Zm00001d039537_T038:2 Zm00001d039537_T061:3 Zm00001d039537_T039:3 Zm00001d039537_T016:3 Zm00001d039537_T041:3 Zm00001d039537_T011:3 Zm00001d039537_T022:3 Zm00001d039537_T003:3 Zm00001d039537_T047:3 Zm00001d039537_T006:3 Zm00001d039537_T065:3 Zm00001d039537_T062:3 Zm00001d039537_T053:3 Zm00001d039537_T017:3 Zm00001d039537_T035:3 Zm00001d039537_T010:3 Zm00001d039537_T024:3 Zm00001d039537_T040:3 Zm00001d039537_T014:3 Zm00001d039537_T015:3

			
						 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  
						
							CGCGCCCCCCGTCTCGAACAGCGGGATCATAGCGTTCTCCGGCGCGAGCCCAATGACCACCTCG
CTCGCCCGCCTCACAGTCGCCGCCACCAAATCCGCCcttcaccaggaagtcgtctagccctgta
aggccttgttcggttacatgggatataatcccaccatggatttaattcgggtatggattgggtg
aatccata

									
								

					

						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
						
							CTTCACCAGGAAGTCGTCTAGCCCTGTAAGGCCTTGTTCGGTTACATGGGATATAATCCCACCA
TGGATTTAATTCGGGTATGGATTGGGTGAATCCATATCTCACACCCAATCCCATGGTGGGATTA
AATCCATCAACAAATCAATGCAACTTTCAAAGCTAGTTATTCTTTTGATCCATGGATTCTAATG
TAAACTTGTGCAATATCTCATGGATTTGTTCCATACCTAATGGGCTATGGATAGAATCCATGTC
TTCCATAGTTTAAAAAATTCTCAAACCTTTGGGTTATATTCCATGATGGGTTTAACCGAATAAA
AAAAATTAACTAGTCATGGATTATTTTGGGGCATGGATTGAGGCATGGATTTAATTCCAATCCA
TGCTAATCCAGAGCGGGATTGGTGTAAACGAACAAAGCCTAAAGAGGCAATTTTCCAAACAAGT
GTTAGTAATTACAATTCTACATAGATTGACAGCATGCTTAGTTAATTAACAATAGTTTAATAGA
CTTTTTTAGTCTTGACCTTGTTTCACTCTTAGACTGCACAACATTCATTTAGAATAGGGATCTT
GGTTTTGCTAATTTCTTAGCGTGCATGTTTATTAGCAGTAGCAGATAATGCTTAACATTACTTA
GGAAATGATTAATAAACAGCATTATAGCAGTAGCAGGTATGATATTGTTTAACCAGATAATAAC
ATGTATGCTTTTGTGCGAATGCCGAATGGCATGGCTTGTTTGTTTGATTGGGGATGATGCTTGG
GTAGATGGATGATAGGCAAGGGTATATTACATGTTAATTATTTAGTCAATAGCAGGTATACCCA
TTCATCAAATAATAGTGCGTTCTTAAAGGCAGGCTAATAGACATAATTAAAATGGTAGTCGAAA
CTAATATTCGACATGACAAAACATATGGTAAAAAAACTTATATCTCATTCTTGAAACAAACAAC
CGGTGAAACTGATATTGTTTTATTTTACTGATCATTAAACAATAGAGAAACCGGTGAAGTAAAT
AGAGCATAAAACTTATATCGTGGAGAGTAAGTACACTTTACCATGCTCATCTCCTTGATCCATC
TCCCATTGGCTTCCCCCTCATCCCAACCGCCCCAGCCTGAAATCAAATGAAATTACTCAAGATG
TGGTGATGTGTATAGCGAAGCATGCGATTGTAGAGCACAAACTTTATTTAGCTCTGCTGCCCGG
CCAATGATGAAGATAGGTTGACAGACCTGAAATTCTCGGATTGGAACACATGTTCCATCGCGGC
AAAGCAGAACAGCGTCCCCGACTTATCCTTGTTCTACAGATCACTGCAATAATAAGAAAACTAA
ACATAAACCGTTGATAAGAGAGAGTAAACTGAATCGTAGATAAGGGAGAGTATACGGTACCGCA
GACAGGGGAGAGTGCTAATCCACTTGATCGATCCGCCGTTGACTCTTCTGGATCTCCCGCATTG
GGAAGCTGGGATCCCCAACGTCTCTCGTGTGCATCCAACTCATGAAGCGGATCCTCTCGGCCTC
CCTTGCTCCCACCTCACGTAGGCACACGGCTCAATCTCGGCATCCCGTATGAGCTCGAGCTGCG
CGCCCCCCGTCTCGAACAGCGGGATCATAGCGTTCTCCGGCGCGAGCCCAATGACCACCTCGCT
CGCCCGCCTCACAGTCGCCGCCACCAAATCCGCC
						
					

			
		

Sequences
Splice junction sequence	CGCGCCCCCCGTCTCGAACAGCGGGATCATAGCGTTCTCCGGCGCGAGCCCAATGACCACCTCG CTCGCCCGCCTCACAGTCGCCGCCACCAAATCCGCCcttcaccaggaagtcgtctagccctgta aggccttgttcggttacatgggatataatcccaccatggatttaattcgggtatggattgggtg aatccata
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	CTTCACCAGGAAGTCGTCTAGCCCTGTAAGGCCTTGTTCGGTTACATGGGATATAATCCCACCA TGGATTTAATTCGGGTATGGATTGGGTGAATCCATATCTCACACCCAATCCCATGGTGGGATTA AATCCATCAACAAATCAATGCAACTTTCAAAGCTAGTTATTCTTTTGATCCATGGATTCTAATG TAAACTTGTGCAATATCTCATGGATTTGTTCCATACCTAATGGGCTATGGATAGAATCCATGTC TTCCATAGTTTAAAAAATTCTCAAACCTTTGGGTTATATTCCATGATGGGTTTAACCGAATAAA AAAAATTAACTAGTCATGGATTATTTTGGGGCATGGATTGAGGCATGGATTTAATTCCAATCCA TGCTAATCCAGAGCGGGATTGGTGTAAACGAACAAAGCCTAAAGAGGCAATTTTCCAAACAAGT GTTAGTAATTACAATTCTACATAGATTGACAGCATGCTTAGTTAATTAACAATAGTTTAATAGA CTTTTTTAGTCTTGACCTTGTTTCACTCTTAGACTGCACAACATTCATTTAGAATAGGGATCTT GGTTTTGCTAATTTCTTAGCGTGCATGTTTATTAGCAGTAGCAGATAATGCTTAACATTACTTA GGAAATGATTAATAAACAGCATTATAGCAGTAGCAGGTATGATATTGTTTAACCAGATAATAAC ATGTATGCTTTTGTGCGAATGCCGAATGGCATGGCTTGTTTGTTTGATTGGGGATGATGCTTGG GTAGATGGATGATAGGCAAGGGTATATTACATGTTAATTATTTAGTCAATAGCAGGTATACCCA TTCATCAAATAATAGTGCGTTCTTAAAGGCAGGCTAATAGACATAATTAAAATGGTAGTCGAAA CTAATATTCGACATGACAAAACATATGGTAAAAAAACTTATATCTCATTCTTGAAACAAACAAC CGGTGAAACTGATATTGTTTTATTTTACTGATCATTAAACAATAGAGAAACCGGTGAAGTAAAT AGAGCATAAAACTTATATCGTGGAGAGTAAGTACACTTTACCATGCTCATCTCCTTGATCCATC TCCCATTGGCTTCCCCCTCATCCCAACCGCCCCAGCCTGAAATCAAATGAAATTACTCAAGATG TGGTGATGTGTATAGCGAAGCATGCGATTGTAGAGCACAAACTTTATTTAGCTCTGCTGCCCGG CCAATGATGAAGATAGGTTGACAGACCTGAAATTCTCGGATTGGAACACATGTTCCATCGCGGC AAAGCAGAACAGCGTCCCCGACTTATCCTTGTTCTACAGATCACTGCAATAATAAGAAAACTAA ACATAAACCGTTGATAAGAGAGAGTAAACTGAATCGTAGATAAGGGAGAGTATACGGTACCGCA GACAGGGGAGAGTGCTAATCCACTTGATCGATCCGCCGTTGACTCTTCTGGATCTCCCGCATTG GGAAGCTGGGATCCCCAACGTCTCTCGTGTGCATCCAACTCATGAAGCGGATCCTCTCGGCCTC CCTTGCTCCCACCTCACGTAGGCACACGGCTCAATCTCGGCATCCCGTATGAGCTCGAGCTGCG CGCCCCCCGTCTCGAACAGCGGGATCATAGCGTTCTCCGGCGCGAGCCCAATGACCACCTCGCT CGCCCGCCTCACAGTCGCCGCCACCAAATCCGCC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.100796649

Conservation Information
Conserved circRNAs	NA
PMCS	0.100796649

			
						 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 Zm00001d039537_circ_g.12

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