Plant Circular RNA Database

Detail information of Zm00001d042262_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d042262_circ_g.3
					
						ID in PlantcircBase
						zma_circ_001416
					
						Alias
						circ623
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 157887491-157893496  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ui-circRNA							
									
						Identification method
						CIRI
					
						Parent gene
						
							Zm00001d042262						
					
						Parent gene annotation
						
							Retrovirus-related Pol polyprotein LINE-1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d042262_circ_g.1 Zm00001d042262_circ_g.2 Zm00001d042262_circ_g.4 						
					
						Support reads
						3
					
						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-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
						Zm00001d042262_T004:6
Zm00001d042262_T005:5
Zm00001d042262_T002:5
Zm00001d042262_T003:7

General Information
CircRNA Name	Zm00001d042262_circ_g.3
ID in PlantcircBase	zma_circ_001416
Alias	circ623
Organism	Zea mays
Position	chr3: 157887491-157893496 JBrowse»
Reference genome	AGPv4.38
Type	ui-circRNA
Identification method	CIRI
Parent gene	Zm00001d042262
Parent gene annotation	Retrovirus-related Pol polyprotein LINE-1
Parent gene strand	+
Alternative splicing	Zm00001d042262_circ_g.1 Zm00001d042262_circ_g.2 Zm00001d042262_circ_g.4
Support reads	3
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-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	Zm00001d042262_T004:6 Zm00001d042262_T005:5 Zm00001d042262_T002:5 Zm00001d042262_T003:7

			
						 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  
						
							AAAACCCAAATTCCTGTTATTATCATGTAGGTGGAAGATGCTGTTGTAGTTGCAGTTGGCCAAC
ATCGCAGACCTAGCATAGTTCGTCAGTTCACATCAGggctgcgctaaaagctgcaagagaatca
aaggatggcagagatggggaagtaacaacactaaggcaagaacttgaggtaattattattttga
caaattta

						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
						
							TOO LONG (>5KB) TO SHOW GENOMIC SEQUENCE OF THIS CIRCULAR RNA. PLEASE FIND THE CORRESPONDING GENOMIC SEQUENCE AT DOWNLOAD SECTION.

Sequences
Splice junction sequence	AAAACCCAAATTCCTGTTATTATCATGTAGGTGGAAGATGCTGTTGTAGTTGCAGTTGGCCAAC ATCGCAGACCTAGCATAGTTCGTCAGTTCACATCAGggctgcgctaaaagctgcaagagaatca aaggatggcagagatggggaagtaacaacactaaggcaagaacttgaggtaattattattttga caaattta
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	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
						0.108577912

Conservation Information
Conserved circRNAs	NA
PMCS	0.108577912

			
						 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 Zm00001d042262_circ_g.3

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