Plant Circular RNA Database

Detail information of Zm00001d015505_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d015505_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008626
					
						Alias
						Zm05circ00070
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 94168258-94177187  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d015505						
					
						Parent gene annotation
						
							Nucleoid-associated protein  chloroplastic
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d015505_circ_g.1 Zm00001d015505_circ_g.2 Zm00001d015505_circ_g.3 Zm00001d015505_circ_g.5 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						Exon boundary  
						
							Yes-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-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
						Zm00001d015505_T001:4

General Information
CircRNA Name	Zm00001d015505_circ_g.4
ID in PlantcircBase	zma_circ_008626
Alias	Zm05circ00070
Organism	Zea mays
Position	chr5: 94168258-94177187 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d015505
Parent gene annotation	Nucleoid-associated protein chloroplastic
Parent gene strand	+
Alternative splicing	Zm00001d015505_circ_g.1 Zm00001d015505_circ_g.2 Zm00001d015505_circ_g.3 Zm00001d015505_circ_g.5
Support reads	NA
Tissues	leaf, endosperm
Exon boundary	Yes-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-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	Zm00001d015505_T001:4

			
						 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  
						
							CCATAACTGTTTCTGATCCTCTCAACAGGTTACACTTTCTGGAAACCAGCAACCTATTAGAGTT
GAAATCACAGAAGCTGCGATGGAGTTGGGTGCTGAAgtaatagaatgaacatagagggcgcttt
ctgtttgccgtgttccacaaggaagagagcaagttatagacctttccgagtgtacagtttattt
ggagggaa

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 353
Transcript exons: 94168258-94168397,94169582-94169682,94169771-94169810,94
177116-94177187
GTAATAGAATGAACATAGAGGGCGCTTTCTGTTTGCCGTGTTCCACAAGGAAGAGAGCAAGTTA
TAGACCTTTCCGAGTGTACAGTTTATTTGGAGGGAAGAAGGATAAAGATGAGAATGGTGATGAG
GCGCCATCGAAAGCAGGAATTTTTGGAAATATGCAAAATCTCTATGAAACTGTTAAGAAGGCCC
AAATGGTTGTCCAAGTTGAGGCTGTCCGGGTGCAAAAGGAGCTTGCAGCGACTGAGATTGATGG
TTATTGTGAAGGCGAACTAATCAAGGTTACACTTTCTGGAAACCAGCAACCTATTAGAGTTGAA
ATCACAGAAGCTGCGATGGAGTTGGGTGCTGAA
						
						Genomic sequence
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	CCATAACTGTTTCTGATCCTCTCAACAGGTTACACTTTCTGGAAACCAGCAACCTATTAGAGTT GAAATCACAGAAGCTGCGATGGAGTTGGGTGCTGAAgtaatagaatgaacatagagggcgcttt ctgtttgccgtgttccacaaggaagagagcaagttatagacctttccgagtgtacagtttattt ggagggaa
Assembled circRNA sequence	Yes 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	Transcript length: 353 Transcript exons: 94168258-94168397,94169582-94169682,94169771-94169810,94 177116-94177187 GTAATAGAATGAACATAGAGGGCGCTTTCTGTTTGCCGTGTTCCACAAGGAAGAGAGCAAGTTA TAGACCTTTCCGAGTGTACAGTTTATTTGGAGGGAAGAAGGATAAAGATGAGAATGGTGATGAG GCGCCATCGAAAGCAGGAATTTTTGGAAATATGCAAAATCTCTATGAAACTGTTAAGAAGGCCC AAATGGTTGTCCAAGTTGAGGCTGTCCGGGTGCAAAAGGAGCTTGCAGCGACTGAGATTGATGG TTATTGTGAAGGCGAACTAATCAAGGTTACACTTTCTGGAAACCAGCAACCTATTAGAGTTGAA ATCACAGAAGCTGCGATGGAGTTGGGTGCTGAA
Genomic sequence	TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.085509653

Conservation Information
Conserved circRNAs	NA
PMCS	0.085509653

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							94168267-94168266(+)
94168394-94169804(-)
						
						Potential amino acid sequence
						
							MNIEGAFCLPCSTRKRASYRPFRVYSLFGGKKDKDENGDEAPSKAGIFGNMQNLYETVKKAQMV
VQVEAVRVQKELAATEIDGYCEGELIKVTLSGNQQPIRVEITEAAMELGAEVIE*(+)
MAPHHHSHLYPSSLQINCTLGKVYNLLSSLWNTANRKRPLCSFYYFSTQLHRSFCDFNSNRLLV
SRKCNLD*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	94168267-94168266(+) 94168394-94169804(-)
Potential amino acid sequence	MNIEGAFCLPCSTRKRASYRPFRVYSLFGGKKDKDENGDEAPSKAGIFGNMQNLYETVKKAQMV VQVEAVRVQKELAATEIDGYCEGELIKVTLSGNQQPIRVEITEAAMELGAEVIE(+) MAPHHHSHLYPSSLQINCTLGKVYNLLSSLWNTANRKRPLCSFYYFSTQLHRSFCDFNSNRLLV SRKCNLD(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d015505_circ_g.4

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