Plant Circular RNA Database

Detail information of Zm00001d015446_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d015446_circ_g.3
					
						ID in PlantcircBase
						zma_circ_008618
					
						Alias
						zma_circ_0002250
					
						Organism
						
							Zea mays						
					
						Position
						
							chr5: 90512218-90512813  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d015446						
					
						Parent gene annotation
						
							Calcium-transporting ATPase 9 plasma membrane-type
							
						Parent gene strand
						-
					
						Alternative splicing
						
							Zm00001d015446_circ_g.1 Zm00001d015446_circ_g.2 						
					
						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
						Zm00001d015446_T005:3
Zm00001d015446_T006:3
Zm00001d015446_T009:3
Zm00001d015446_T020:3
Zm00001d015446_T028:3
Zm00001d015446_T027:3
Zm00001d015446_T016:3
Zm00001d015446_T002:3
Zm00001d015446_T013:3
Zm00001d015446_T008:3
Zm00001d015446_T018:3
Zm00001d015446_T001:3
Zm00001d015446_T010:3
Zm00001d015446_T030:3
Zm00001d015446_T026:3
Zm00001d015446_T015:3
Zm00001d015446_T022:3
Zm00001d015446_T017:3
Zm00001d015446_T024:3
Zm00001d015446_T004:3

General Information
CircRNA Name	Zm00001d015446_circ_g.3
ID in PlantcircBase	zma_circ_008618
Alias	zma_circ_0002250
Organism	Zea mays
Position	chr5: 90512218-90512813 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d015446
Parent gene annotation	Calcium-transporting ATPase 9 plasma membrane-type
Parent gene strand	-
Alternative splicing	Zm00001d015446_circ_g.1 Zm00001d015446_circ_g.2
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	Zm00001d015446_T005:3 Zm00001d015446_T006:3 Zm00001d015446_T009:3 Zm00001d015446_T020:3 Zm00001d015446_T028:3 Zm00001d015446_T027:3 Zm00001d015446_T016:3 Zm00001d015446_T002:3 Zm00001d015446_T013:3 Zm00001d015446_T008:3 Zm00001d015446_T018:3 Zm00001d015446_T001:3 Zm00001d015446_T010:3 Zm00001d015446_T030:3 Zm00001d015446_T026:3 Zm00001d015446_T015:3 Zm00001d015446_T022:3 Zm00001d015446_T017:3 Zm00001d015446_T024:3 Zm00001d015446_T004:3

			
						 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  
						
							CATCATTCGTTCCATCACCAGTAACAGCTACAACATGGCCTATTTTCTTAAGAGCTTTTACTAG
GAGAAGTTTGTCATTAGGAGAGGATCGTGCCATCACctgaacagcatttagaggaacatttcct
gaggaaacagcagcaacaacattgatgacaagagctgcaacatttacggtaagctggaactgaa
taaacttt

						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
						
							CTGAACAGCATTTAGAGGAACATTTCCTGAGGAAACAGCAGCAACAACATTGATGACAAGAGCT
GCAACATTTACGGTAAGCTGGAACTGAATAAACTTTTGGATATTTGCATAAACAGAGCGACCCC
AGCGAACCACCTAGAATATAAAAGATAAAGAACATGTAAGACAACGTTGTATTAGGCATGTGCG
CGTATTATCAAGATCCTTAGATTCTAAAAATAGGCCAAACCTTCACAACAGAAGAAAAATTGTC
ATCCAGAATTATTATGTCTGAGCTCTCTTTGGCTACTTCTGTTCCTTGGATGCCCATAGAAAGA
CCAATATCTGCCTGATAAGTGGGAATAATGATAAGATTGAGAAGGGGAAGAAACCTCAACATGT
TAGAAGTGCTGTATTACCAAATAGTGCTTCATATAATCACATGCATGTTGAATTCTTGTATTCA
TTTAAAATATGAACTCCCAAATTGAATGTACCTCATGCAATGCAGGAGCATCATTCGTTCCATC
ACCAGTAACAGCTACAACATGGCCTATTTTCTTAAGAGCTTTTACTAGGAGAAGTTTGTCATTA
GGAGAGGATCGTGCCATCAC

Sequences
Splice junction sequence	CATCATTCGTTCCATCACCAGTAACAGCTACAACATGGCCTATTTTCTTAAGAGCTTTTACTAG GAGAAGTTTGTCATTAGGAGAGGATCGTGCCATCACctgaacagcatttagaggaacatttcct gaggaaacagcagcaacaacattgatgacaagagctgcaacatttacggtaagctggaactgaa taaacttt
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	CTGAACAGCATTTAGAGGAACATTTCCTGAGGAAACAGCAGCAACAACATTGATGACAAGAGCT GCAACATTTACGGTAAGCTGGAACTGAATAAACTTTTGGATATTTGCATAAACAGAGCGACCCC AGCGAACCACCTAGAATATAAAAGATAAAGAACATGTAAGACAACGTTGTATTAGGCATGTGCG CGTATTATCAAGATCCTTAGATTCTAAAAATAGGCCAAACCTTCACAACAGAAGAAAAATTGTC ATCCAGAATTATTATGTCTGAGCTCTCTTTGGCTACTTCTGTTCCTTGGATGCCCATAGAAAGA CCAATATCTGCCTGATAAGTGGGAATAATGATAAGATTGAGAAGGGGAAGAAACCTCAACATGT TAGAAGTGCTGTATTACCAAATAGTGCTTCATATAATCACATGCATGTTGAATTCTTGTATTCA TTTAAAATATGAACTCCCAAATTGAATGTACCTCATGCAATGCAGGAGCATCATTCGTTCCATC ACCAGTAACAGCTACAACATGGCCTATTTTCTTAAGAGCTTTTACTAGGAGAAGTTTGTCATTA GGAGAGGATCGTGCCATCAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.234835109

Conservation Information
Conserved circRNAs	NA
PMCS	0.234835109

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							90512488-90512218(+)
90512812-90512220(-)
						
						Potential amino acid sequence
						
							MSELSLATSVPWMPIERPISASCNAGASFVPSPVTATTWPIFLRAFTRRSLSLGEDRAIT*(+)
MARSSPNDKLLLVKALKKIGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDD
NFSSVVKVVRWGRSVYANIQKFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQVMARSSPNDKL
LLVKALKKIGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDDNFSSVVKVVR
WGRSVYANIQKFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQVMARSSPNDKLLLVKALKKIG
HVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDDNFSSVVKVVRWGRSVYANIQ
KFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQVMARSSPNDKLLLVKALKKIGHVVAVTGDGT
NDAPALHEADIGLSMGIQGTEVAKESSDIIILDDNFSSVVKVVRWGRSVYANIQKFIQFQLTVN
VAALVINVVAAVSSGNVPLNAVQ(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	90512488-90512218(+) 90512812-90512220(-)
Potential amino acid sequence	MSELSLATSVPWMPIERPISASCNAGASFVPSPVTATTWPIFLRAFTRRSLSLGEDRAIT*(+) MARSSPNDKLLLVKALKKIGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDD NFSSVVKVVRWGRSVYANIQKFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQVMARSSPNDKL LLVKALKKIGHVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDDNFSSVVKVVR WGRSVYANIQKFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQVMARSSPNDKLLLVKALKKIG HVVAVTGDGTNDAPALHEADIGLSMGIQGTEVAKESSDIIILDDNFSSVVKVVRWGRSVYANIQ KFIQFQLTVNVAALVINVVAAVSSGNVPLNAVQVMARSSPNDKLLLVKALKKIGHVVAVTGDGT NDAPALHEADIGLSMGIQGTEVAKESSDIIILDDNFSSVVKVVRWGRSVYANIQKFIQFQLTVN VAALVINVVAAVSSGNVPLNAVQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d015446_circ_g.3

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