Plant Circular RNA Database

Detail information of Zm00001d015890_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d015890_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008652
					
						Alias
						Zm05circ00079
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 129471368-129517151  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							e-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d015890						
					
						Parent gene annotation
						
							SNARE-interacting protein KEULE
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d015890_circ_g.1 Zm00001d015890_circ_g.2 Zm00001d015890_circ_g.4 Zm00001d015890_circ_g.5 Zm00001d015890_circ_g.6 Zm00001d015890_circ_g.7 Zm00001d015890_circ_g.8 Zm00001d015890_circ_g.9 						
					
						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  
						
							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
						Zm00001d015890_T001:11
Zm00001d015890_T002:11

General Information
CircRNA Name	Zm00001d015890_circ_g.3
ID in PlantcircBase	zma_circ_008652
Alias	Zm05circ00079
Organism	Zea mays
Position	chr5: 129471368-129517151 JBrowse»
Reference genome	AGPv4.38
Type	e-circRNA
Identification method	CIRI2
Parent gene	Zm00001d015890
Parent gene annotation	SNARE-interacting protein KEULE
Parent gene strand	-
Alternative splicing	Zm00001d015890_circ_g.1 Zm00001d015890_circ_g.2 Zm00001d015890_circ_g.4 Zm00001d015890_circ_g.5 Zm00001d015890_circ_g.6 Zm00001d015890_circ_g.7 Zm00001d015890_circ_g.8 Zm00001d015890_circ_g.9
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	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	Zm00001d015890_T001:11 Zm00001d015890_T002:11

			
						 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  
						
							GAGTAGCCATTGTGTTCAGACAAGCATTATACTTGTGAGATCCTTCTGCATTTTCACTAAAAAG
TTCTTCCAATGCCCTCTCATGGTCAGTTATGAAACCcttgaatatccatcatcagagccacgag
gtcttgcccatgtgccacctgttcgtctggatcgcattgagtgagcggggcttgttcgggcaga
gctactgg

						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	GAGTAGCCATTGTGTTCAGACAAGCATTATACTTGTGAGATCCTTCTGCATTTTCACTAAAAAG TTCTTCCAATGCCCTCTCATGGTCAGTTATGAAACCcttgaatatccatcatcagagccacgag gtcttgcccatgtgccacctgttcgtctggatcgcattgagtgagcggggcttgttcgggcaga gctactgg
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
						0.129509074

Conservation Information
Conserved circRNAs	NA
PMCS	0.129509074

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							129517145-129471485(+)
129517135-129471436(+)
129517063-129517144(-)
129471502-129517140(-)
						
						Potential amino acid sequence
						
							MKPLNIHHQSHEVLPMCHLFVWIALSERGLFGQSYWLAVHEQ*(+)
MVSYETLEYPSSEPRGLAHVPPVRLDRIE*(+)
MATRISTVFASMREFPRVHYRIAKTIDASTMTTLRDLVPTKLAASVWNCLAKYKTTIPEFPQTE
TCELLIVDRSIDQIAPIIHEWTYDAMCHDLLCMDGNKYVHEVPTKNGSATEKKEVLLEDHDPVW
LELRHAHIADASERLHDKMTNFISKNKAAQLHQARTDGELSTRDLQKMVQALPQYSDQIDKLSL
HVEIAGKLNNIIREQCLRDVGQLEQDLVFGDAGTKELINFLRTQLVVSRENKLRLLMIYAALNP
EKFESDKATLNLRNAVLQLAGLSADDMIAVNNMRCLCGPDTKKSSVGGFTLKFDVHKKKHTNRK
ERTGEESTWALSRFYPILEQLIENLSKGELPKDEYNCMNDPSPTVHGLPTSSSARTSPAHSMRS
RRTGGTWARPRGSDDGYSRVS*(-)
MTLVLLFMDCQPVALPEQAPLTQCDPDEQVAHGQDLVALMMDIQGFHN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	129517145-129471485(+) 129517135-129471436(+) 129517063-129517144(-) 129471502-129517140(-)
Potential amino acid sequence	MKPLNIHHQSHEVLPMCHLFVWIALSERGLFGQSYWLAVHEQ(+) MVSYETLEYPSSEPRGLAHVPPVRLDRIE(+) MATRISTVFASMREFPRVHYRIAKTIDASTMTTLRDLVPTKLAASVWNCLAKYKTTIPEFPQTE TCELLIVDRSIDQIAPIIHEWTYDAMCHDLLCMDGNKYVHEVPTKNGSATEKKEVLLEDHDPVW LELRHAHIADASERLHDKMTNFISKNKAAQLHQARTDGELSTRDLQKMVQALPQYSDQIDKLSL HVEIAGKLNNIIREQCLRDVGQLEQDLVFGDAGTKELINFLRTQLVVSRENKLRLLMIYAALNP EKFESDKATLNLRNAVLQLAGLSADDMIAVNNMRCLCGPDTKKSSVGGFTLKFDVHKKKHTNRK ERTGEESTWALSRFYPILEQLIENLSKGELPKDEYNCMNDPSPTVHGLPTSSSARTSPAHSMRS RRTGGTWARPRGSDDGYSRVS(-) MTLVLLFMDCQPVALPEQAPLTQCDPDEQVAHGQDLVALMMDIQGFHN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d015890_circ_g.3

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