Plant Circular RNA Database

Detail information of Zm00001d039518_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d039518_circ_g.4
					
						ID in PlantcircBase
						zma_circ_001307
					
						Alias
						circ31
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 6558103-6559608  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						KNIFE
					
						Parent gene
						
							Zm00001d039518						
					
						Parent gene annotation
						
							 eukaryotic initiation factor3
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d039518_circ_g.2 Zm00001d039518_circ_g.3 Zm00001d039518_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						seedling leaves
					
						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-TA							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
						Zm00001d039518_T008:4
Zm00001d039518_T012:4
Zm00001d039518_T006:1
Zm00001d039518_T007:4
Zm00001d039518_T001:4
Zm00001d039518_T002:4
Zm00001d039518_T011:1
Zm00001d039518_T005:4
Zm00001d039518_T009:4
Zm00001d039518_T013:3

General Information
CircRNA Name	Zm00001d039518_circ_g.4
ID in PlantcircBase	zma_circ_001307
Alias	circ31
Organism	Zea mays
Position	chr3: 6558103-6559608 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	KNIFE
Parent gene	Zm00001d039518
Parent gene annotation	eukaryotic initiation factor3
Parent gene strand	+
Alternative splicing	Zm00001d039518_circ_g.2 Zm00001d039518_circ_g.3 Zm00001d039518_circ_g.5
Support reads	NA
Tissues	seedling leaves
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-TA 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	Zm00001d039518_T008:4 Zm00001d039518_T012:4 Zm00001d039518_T006:1 Zm00001d039518_T007:4 Zm00001d039518_T001:4 Zm00001d039518_T002:4 Zm00001d039518_T011:1 Zm00001d039518_T005:4 Zm00001d039518_T009:4 Zm00001d039518_T013:3

			
						 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  
						
							AATTTATTTATGCTTGCAGCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAA
GAGAAAAATAGACTTTCACGGATGTTGGAGCACAAGggacatagaatctgatggcttaagtgat
caccttagtgttcttgctgattcattaaataaagcaaggattcatatctgtccaccagtgaaaa
agccatct

									
								

					

						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
						
							GGACATAGAATCTGATGGCTTAAGTGATCACCTTAGTGTTCTTGCTGATTCATTAAATAAAGCA
AGGATTCATATCTGTCCACCAGTGAAAAAGCCATCTAAACTCGGTGAAAGTCTCATTAGTTTGG
CTGCAATAGTGGAGAATGAACATAAGAGGCTGCTTGCAAGGAAGTCCATCATTGAAAAACGTAA
AGAAGAGCTTGAGCGTCAAATATTGGAGAAGGTGCACATTTTTTTATTACTCAATACTTGTTCA
TTTGTTCTTTTGAACTTTTTAATTAATTACTTCTTTTATGGTTGCTATCTTTTCCAGGAAAAAG
AAGAAGAAAAAAAGAGAATGAGCAGTCAAAAGAAAACTGTGGATGAGGAAAGGGTGAGGCTTCT
CAATGAACAGAGGCAGAGGGAGCAGGACCGGATTCGTAGAGAGATAGAGGAAAAAAATAAAGCA
GAAGCAAAAAAGATGCTAGAAGATTTGAATAAGGCAGGGAAAAAACATGTCGTTGTTGAAGGGG
TAAGCAGTTATCGCCTTATGGTATTGTTTGGTTTGTGGAGTCACCCTATGCTATATGGATTTTC
TCACACATTTTTTTATTTGCTTTGTGGAATAAAATGAGTTGACCCATCACACATCATTCTTCAT
AAGCTAATAATTAGTATATACATGAGGAATGAGTTGATTCCACCAAAATTTATGGGATGAACTC
ATGATGCATCACCTCATGAAGCATAGGATACCTCCACAAACCAAACACACCGTAAATATTTGAT
ATGGTTCGTGGATAATTGAATGTTATTTTGGCTATGGACTAAAATTTGATGGTACAAGGGTACA
ATATTACTAAATTTTCATTTTGAATCATATAGTACACCTTCCGCTAAAAAATAACTGTACATCT
TACATTTCGAGCAGTCAACCAGTCTCAAGTTCGACCAAATTTATGTAAAAAATTCTTTATTTAT
GATCCAAATAAATTTGGAATTATTTGTCTCATTGAAGGGAATATATCAGGTGCAATTGTACTTT
AATTATTCTAGTGTTGGCTAAAGTCCTCATTCTAGTGTTGGCTAGAACTTTAATTATTATATTT
TTTATTTTTAAACCTCTTCAATATATTCTTATAGACCTGAATGTTTGGTTGCAGGAGCTTACTA
AGGAGGCCATCATGGAATTGGCACGGAATGAACAGTTAAAGGAGCGCCACGAAATGGAGAAAAA
ACTGCAGAAGTTTGCAAAAACAATGGATTATCTGGAAAGGGCAAAAAGGCAGGAAGAGGCACCA
CTGATTGAGCAAGCTTTTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGC
TTGTCAGTTTTCTACTATTCTTTTGTTGTTTCTGCAGTTCAGATAACTGTCAGTGCTTTATTAA
TTTATTTATGCTTGCAGCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGA
GAAAAATAGACTTTCACGGATGTTGGAGCACAAG
						
					

			
		

Sequences
Splice junction sequence	AATTTATTTATGCTTGCAGCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAA GAGAAAAATAGACTTTCACGGATGTTGGAGCACAAGggacatagaatctgatggcttaagtgat caccttagtgttcttgctgattcattaaataaagcaaggattcatatctgtccaccagtgaaaa agccatct
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	GGACATAGAATCTGATGGCTTAAGTGATCACCTTAGTGTTCTTGCTGATTCATTAAATAAAGCA AGGATTCATATCTGTCCACCAGTGAAAAAGCCATCTAAACTCGGTGAAAGTCTCATTAGTTTGG CTGCAATAGTGGAGAATGAACATAAGAGGCTGCTTGCAAGGAAGTCCATCATTGAAAAACGTAA AGAAGAGCTTGAGCGTCAAATATTGGAGAAGGTGCACATTTTTTTATTACTCAATACTTGTTCA TTTGTTCTTTTGAACTTTTTAATTAATTACTTCTTTTATGGTTGCTATCTTTTCCAGGAAAAAG AAGAAGAAAAAAAGAGAATGAGCAGTCAAAAGAAAACTGTGGATGAGGAAAGGGTGAGGCTTCT CAATGAACAGAGGCAGAGGGAGCAGGACCGGATTCGTAGAGAGATAGAGGAAAAAAATAAAGCA GAAGCAAAAAAGATGCTAGAAGATTTGAATAAGGCAGGGAAAAAACATGTCGTTGTTGAAGGGG TAAGCAGTTATCGCCTTATGGTATTGTTTGGTTTGTGGAGTCACCCTATGCTATATGGATTTTC TCACACATTTTTTTATTTGCTTTGTGGAATAAAATGAGTTGACCCATCACACATCATTCTTCAT AAGCTAATAATTAGTATATACATGAGGAATGAGTTGATTCCACCAAAATTTATGGGATGAACTC ATGATGCATCACCTCATGAAGCATAGGATACCTCCACAAACCAAACACACCGTAAATATTTGAT ATGGTTCGTGGATAATTGAATGTTATTTTGGCTATGGACTAAAATTTGATGGTACAAGGGTACA ATATTACTAAATTTTCATTTTGAATCATATAGTACACCTTCCGCTAAAAAATAACTGTACATCT TACATTTCGAGCAGTCAACCAGTCTCAAGTTCGACCAAATTTATGTAAAAAATTCTTTATTTAT GATCCAAATAAATTTGGAATTATTTGTCTCATTGAAGGGAATATATCAGGTGCAATTGTACTTT AATTATTCTAGTGTTGGCTAAAGTCCTCATTCTAGTGTTGGCTAGAACTTTAATTATTATATTT TTTATTTTTAAACCTCTTCAATATATTCTTATAGACCTGAATGTTTGGTTGCAGGAGCTTACTA AGGAGGCCATCATGGAATTGGCACGGAATGAACAGTTAAAGGAGCGCCACGAAATGGAGAAAAA ACTGCAGAAGTTTGCAAAAACAATGGATTATCTGGAAAGGGCAAAAAGGCAGGAAGAGGCACCA CTGATTGAGCAAGCTTTTCAAAAACGTCTTGAGGAAGAGAAGATCCTTCACGAGCAAGAGCAGC TTGTCAGTTTTCTACTATTCTTTTGTTGTTTCTGCAGTTCAGATAACTGTCAGTGCTTTATTAA TTTATTTATGCTTGCAGCGGGAGATTGAACTCAGCAAGCAACACCATGCCAGCGACTTGCAAGA GAAAAATAGACTTTCACGGATGTTGGAGCACAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.093694527

Conservation Information
Conserved circRNAs	NA
PMCS	0.093694527

			
						 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
						Chen et al., 2017b

circRNA

Detail information of Zm00001d039518_circ_g.4

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