Plant Circular RNA Database

Detail information of Zm00001d047253_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d047253_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010032
					
						Alias
						zma_circ_0003063
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 124179337-124179655  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d047253						
					
						Parent gene annotation
						
							 sucrose synthase1
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d047253_circ_g.2 Zm00001d047253_circ_g.4 						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						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
						Zm00001d047253_T016:1
Zm00001d047253_T004:1
Zm00001d047253_T001:1
Zm00001d047253_T018:1
Zm00001d047253_T007:1
Zm00001d047253_T005:1
Zm00001d047253_T003:1
Zm00001d047253_T015:1
Zm00001d047253_T010:1
Zm00001d047253_T002:1
Zm00001d047253_T019:1
Zm00001d047253_T008:1
Zm00001d047253_T009:1
Zm00001d047253_T014:1
Zm00001d047253_T011:1
Zm00001d047253_T012:1
Zm00001d047253_T013:1

General Information
CircRNA Name	Zm00001d047253_circ_g.3
ID in PlantcircBase	zma_circ_010032
Alias	zma_circ_0003063
Organism	Zea mays
Position	chr9: 124179337-124179655 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d047253
Parent gene annotation	sucrose synthase1
Parent gene strand	-
Alternative splicing	Zm00001d047253_circ_g.2 Zm00001d047253_circ_g.4
Support reads	NA
Tissues	leaf, root
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	Zm00001d047253_T016:1 Zm00001d047253_T004:1 Zm00001d047253_T001:1 Zm00001d047253_T018:1 Zm00001d047253_T007:1 Zm00001d047253_T005:1 Zm00001d047253_T003:1 Zm00001d047253_T015:1 Zm00001d047253_T010:1 Zm00001d047253_T002:1 Zm00001d047253_T019:1 Zm00001d047253_T008:1 Zm00001d047253_T009:1 Zm00001d047253_T014:1 Zm00001d047253_T011:1 Zm00001d047253_T012:1 Zm00001d047253_T013:1

			
						 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  
						
							GTTCCGGCCGTACAGCTCCACCAGCCCAGTCAAGTTCTTCACACGGTCGAGACGAGCCATGGAG
AAGATGATTGGCTTGTTCCTGTCGTTCAGAACGAACctgcacgaaggcgcccttggtgtcgcag
atgtagcggtacagctcgccgttgcggacgcggttcatctgggcggagatccagcggatgtgcc
cgttcagg

						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
						
							CTGCACGAAGGCGCCCTTGGTGTCGCAGATGTAGCGGTACAGCTCGCCGTTGCGGACGCGGTTC
ATCTGGGCGGAGATCCAGCGGATGTGCCCGTTCAGGTTGTACTGCTCGATGAGGTCAAACATCT
TCTTGAACTCGGCCTGCTCCTCCTTGTCCTTGGAAGGGTTGCCATGGTCGCCGCAGACGACCAC
GAGGTTCACCAGCTCCTGCAGCCGCTTGTTCCGGCCGTACAGCTCCACCAGCCCAGTCAAGTTC
TTCACACGGTCGAGACGAGCCATGGAGAAGATGATTGGCTTGTTCCTGTCGTTCAGAACGAAC

Sequences
Splice junction sequence	GTTCCGGCCGTACAGCTCCACCAGCCCAGTCAAGTTCTTCACACGGTCGAGACGAGCCATGGAG AAGATGATTGGCTTGTTCCTGTCGTTCAGAACGAACctgcacgaaggcgcccttggtgtcgcag atgtagcggtacagctcgccgttgcggacgcggttcatctgggcggagatccagcggatgtgcc cgttcagg
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	CTGCACGAAGGCGCCCTTGGTGTCGCAGATGTAGCGGTACAGCTCGCCGTTGCGGACGCGGTTC ATCTGGGCGGAGATCCAGCGGATGTGCCCGTTCAGGTTGTACTGCTCGATGAGGTCAAACATCT TCTTGAACTCGGCCTGCTCCTCCTTGTCCTTGGAAGGGTTGCCATGGTCGCCGCAGACGACCAC GAGGTTCACCAGCTCCTGCAGCCGCTTGTTCCGGCCGTACAGCTCCACCAGCCCAGTCAAGTTC TTCACACGGTCGAGACGAGCCATGGAGAAGATGATTGGCTTGTTCCTGTCGTTCAGAACGAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							osa_circ_020224* osi_circ_016749 						
					
						PMCS
						0.318234013

Conservation Information
Conserved circRNAs	osa_circ_020224* osi_circ_016749
PMCS	0.318234013

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							124179509-124179449(+)
124179423-124179449(+)
124179617-124179457(-)
						
						Potential amino acid sequence
						
							MVAADDHEVHQLLQPLVPAVQLHQPSQVLHTVETSHGEDDWLVPVVQNEPARRRPWCRRCSGTA
RRCGRGSSGRRSSGCARSGCTAR*(+)
MCPFRLYCSMRSNIFLNSACSSLSLEGLPWSPQTTTRFTSSCSRLFRPYSSTSPVKFFTRSRRA
MEKMIGLFLSFRTNLHEGALGVADVAVQLAVADAVHLGGDPADVPVQVVLLDEVKHLLELGLLL
LVLGRVAMVAADDHEVHQLLQPLVPAVQLHQPSQVLHTVETSHGEDDWLVPVVQNEPARRRPWC
RRCSGTARRCGRGSSGRRSSGCARSGCTAR*(+)
MARLDRVKNLTGLVELYGRNKRLQELVNLVVVCGDHGNPSKDKEEQAEFKKMFDLIEQYNLNGH
IRWISAQMNRVRNGELYRYICDTKGAFVQVRSERQEQANHLLHGSSRPCEELDWAGGAVRPEQA
AAGAGEPRGRLRRPWQPFQGQGGAGRVQEDV*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	124179509-124179449(+) 124179423-124179449(+) 124179617-124179457(-)
Potential amino acid sequence	MVAADDHEVHQLLQPLVPAVQLHQPSQVLHTVETSHGEDDWLVPVVQNEPARRRPWCRRCSGTA RRCGRGSSGRRSSGCARSGCTAR(+) MCPFRLYCSMRSNIFLNSACSSLSLEGLPWSPQTTTRFTSSCSRLFRPYSSTSPVKFFTRSRRA MEKMIGLFLSFRTNLHEGALGVADVAVQLAVADAVHLGGDPADVPVQVVLLDEVKHLLELGLLL LVLGRVAMVAADDHEVHQLLQPLVPAVQLHQPSQVLHTVETSHGEDDWLVPVVQNEPARRRPWC RRCSGTARRCGRGSSGRRSSGCARSGCTAR(+) MARLDRVKNLTGLVELYGRNKRLQELVNLVVVCGDHGNPSKDKEEQAEFKKMFDLIEQYNLNGH IRWISAQMNRVRNGELYRYICDTKGAFVQVRSERQEQANHLLHGSSRPCEELDWAGGAVRPEQA AAGAGEPRGRLRRPWQPFQGQGGAGRVQEDV*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d047253_circ_g.3

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