Plant Circular RNA Database

Detail information of Zm00001d040202_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d040202_circ_g.3
					
						ID in PlantcircBase
						zma_circ_000193
					
						Alias
						NA
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 31837654-31837806  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						SMALT, Segemehl
					
						Parent gene
						
							Zm00001d040202						
					
						Parent gene annotation
						
							SNF7 family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d040202_circ_g.2 						
					
						Support reads
						16
					
						Tissues
						shoot
					
						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
						Zm00001d040202_T007:1
Zm00001d040202_T003:1
Zm00001d040202_T006:1
Zm00001d040202_T004:1
Zm00001d040202_T005:1
Zm00001d040202_T009:1

General Information
CircRNA Name	Zm00001d040202_circ_g.3
ID in PlantcircBase	zma_circ_000193
Alias	NA
Organism	Zea mays
Position	chr3: 31837654-31837806 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	SMALT, Segemehl
Parent gene	Zm00001d040202
Parent gene annotation	SNF7 family protein
Parent gene strand	+
Alternative splicing	Zm00001d040202_circ_g.2
Support reads	16
Tissues	shoot
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	Zm00001d040202_T007:1 Zm00001d040202_T003:1 Zm00001d040202_T006:1 Zm00001d040202_T004:1 Zm00001d040202_T005:1 Zm00001d040202_T009:1

			
						 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  
						
							CCTCGGCGGCGGCGGCGGCGAGCAGGAGTGTGGTCGGGGTGGACAGGGACTACCTGTCCTACGA
CGAGCCAAAGACggtgttcccgatggaggcctgcgacctgcttggtggcgacgcgtgcaacggg
cccatgttcccggaggccaagcccg

						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: 153
Transcript exons: 31837654-31837806
GGTGTTCCCGATGGAGGCCTGCGACCTGCTTGGTGGCGACGCGTGCAACGGGCCCATGTTCCCG
GAGGCCAAGCCCGCCTCGGCGGCGGCGGCGGCGAGCAGGAGTGTGGTCGGGGTGGACAGGGACT
ACCTGTCCTACGACGAGCCAAAGAC
						
						Genomic sequence
						
							GGTGTTCCCGATGGAGGCCTGCGACCTGCTTGGTGGCGACGCGTGCAACGGGCCCATGTTCCCG
GAGGCCAAGCCCGCCTCGGCGGCGGCGGCGGCGAGCAGGAGTGTGGTCGGGGTGGACAGGGACT
ACCTGTCCTACGACGAGCCAAAGAC

Sequences
Splice junction sequence	CCTCGGCGGCGGCGGCGGCGAGCAGGAGTGTGGTCGGGGTGGACAGGGACTACCTGTCCTACGA CGAGCCAAAGACggtgttcccgatggaggcctgcgacctgcttggtggcgacgcgtgcaacggg cccatgttcccggaggccaagcccg
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: 153 Transcript exons: 31837654-31837806 GGTGTTCCCGATGGAGGCCTGCGACCTGCTTGGTGGCGACGCGTGCAACGGGCCCATGTTCCCG GAGGCCAAGCCCGCCTCGGCGGCGGCGGCGGCGAGCAGGAGTGTGGTCGGGGTGGACAGGGACT ACCTGTCCTACGACGAGCCAAAGAC
Genomic sequence	GGTGTTCCCGATGGAGGCCTGCGACCTGCTTGGTGGCGACGCGTGCAACGGGCCCATGTTCCCG GAGGCCAAGCCCGCCTCGGCGGCGGCGGCGGCGAGCAGGAGTGTGGTCGGGGTGGACAGGGACT ACCTGTCCTACGACGAGCCAAAGAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.541642958

Conservation Information
Conserved circRNAs	NA
PMCS	0.541642958

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							31837665-31837803(+)
31837712-31837791(-)
						
						Potential amino acid sequence
						
							MEACDLLGGDACNGPMFPEAKPASAAAAASRSVVGVDRDYLSYDEPKTVFPMEACDLLGGDACN
GPMFPEAKPASAAAAASRSVVGVDRDYLSYDEPKTVFPMEACDLLGGDACNGPMFPEAKPASAA
AAASRSVVGVDRDYLSYDEPKTVFPMEACDLLGGDACNGPMFPEAKPASAAAAASRSVVGVDRD
YLSYDEPK(+)
MGPLHASPPSRSQASIGNTVFGSS*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	31837665-31837803(+) 31837712-31837791(-)
Potential amino acid sequence	MEACDLLGGDACNGPMFPEAKPASAAAAASRSVVGVDRDYLSYDEPKTVFPMEACDLLGGDACN GPMFPEAKPASAAAAASRSVVGVDRDYLSYDEPKTVFPMEACDLLGGDACNGPMFPEAKPASAA AAASRSVVGVDRDYLSYDEPKTVFPMEACDLLGGDACNGPMFPEAKPASAAAAASRSVVGVDRD YLSYDEPK(+) MGPLHASPPSRSQASIGNTVFGSS*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Lu et al., 2015

circRNA

Detail information of Zm00001d040202_circ_g.3

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