Plant Circular RNA Database

Detail information of Zm00001d047074_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d047074_circ_g.2
					
						ID in PlantcircBase
						zma_circ_010017
					
						Alias
						zma_circ_0003049
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 117416112-117422549  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d047074						
					
						Parent gene annotation
						
							pleckstrin homology (PH) domain-containing protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d047074_circ_g.3 						
					
						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  
						
							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
						Zm00001d047074_T017:10
Zm00001d047074_T018:10
Zm00001d047074_T008:6
Zm00001d047074_T020:9
Zm00001d047074_T002:9
Zm00001d047074_T023:1
Zm00001d047074_T022:9
Zm00001d047074_T010:10
Zm00001d047074_T012:10
Zm00001d047074_T014:10
Zm00001d047074_T016:10

General Information
CircRNA Name	Zm00001d047074_circ_g.2
ID in PlantcircBase	zma_circ_010017
Alias	zma_circ_0003049
Organism	Zea mays
Position	chr9: 117416112-117422549 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d047074
Parent gene annotation	pleckstrin homology (PH) domain-containing protein
Parent gene strand	+
Alternative splicing	Zm00001d047074_circ_g.3
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	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	Zm00001d047074_T017:10 Zm00001d047074_T018:10 Zm00001d047074_T008:6 Zm00001d047074_T020:9 Zm00001d047074_T002:9 Zm00001d047074_T023:1 Zm00001d047074_T022:9 Zm00001d047074_T010:10 Zm00001d047074_T012:10 Zm00001d047074_T014:10 Zm00001d047074_T016:10

			
						 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  
						
							GTACTTAAAACTTAGTATTGAGGATGAGCCAAAGGTCTTACATGCATATGACTGGAGGGTTTCC
TTTATGTACTCCAAGGGGACTACTGACAAACTGCAGgtaccaattcgacatgaatacaccaggt
tctcctagacaactccgtattacctcaactcaagaccttaatttgaacatatctgtttccaata
caaacatg

						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	GTACTTAAAACTTAGTATTGAGGATGAGCCAAAGGTCTTACATGCATATGACTGGAGGGTTTCC TTTATGTACTCCAAGGGGACTACTGACAAACTGCAGgtaccaattcgacatgaatacaccaggt tctcctagacaactccgtattacctcaactcaagaccttaatttgaacatatctgtttccaata caaacatg
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
						0.115429903

Conservation Information
Conserved circRNAs	NA
PMCS	0.115429903

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							117416126-117416144(+)
117422474-117416144(+)
117416128-117422489(-)
						
					

						Potential amino acid sequence
						
							MNTPGSPRQLRITSTQDLNLNISVSNTNMLSQAYASWNNISCGDELYKKETFSSTERPVLDVHQ
RRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPSGDDRSIKVPALRDLSDSHLNGRSVKPYRLMI
TAILADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQSARTCAAIGEHLSQNTRKVNWNEMFF
FKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLPPTSNPDSVKFDLALGDLMSTKTVEQ
ETVKPSGKIRFAVLVSGRASVQQGNRASPESKTGYIQISPSKEGPWTSMKLNYAVPAACWRFGN
CVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGRISQSARADEQGDSFGKEDQILIGTL
EPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSDVQERRSQTEFRKEEILDLCISDLYE
SENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEPIYDWCIIIKSPLCLTYYLPIAAHYT
VSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSLVPHGGWELMHEPVVISHPTQAPSKF
INLRSSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWISFSRLPTLTLRLIDISGRKEKRRLLS
RSHLERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSSVGHGGRFGSVKELSPLGDMDGAVDL
SAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTNRAGQDLYLKLSIEDEPKVLHAYDWR
VSFMYSKGTTDKLQVPIRHEYTRFS*(+)
MSQRSYMHMTGGFPLCTPRGLLTNCRYQFDMNTPGSPRQLRITSTQDLNLNISVSNTNMLSQAY
ASWNNISCGDELYKKETFSSTERPVLDVHQRRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPSG
DDRSIKVPALRDLSDSHLNGRSVKPYRLMITAILADAEVKDDEGLETGEYMTAVRLFSENHSIS
VQQQSARTCAAIGEHLSQNTRKVNWNEMFFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQV
VQKLPPTSNPDSVKFDLALGDLMSTKTVEQETVKPSGKIRFAVLVSGRASVQQGNRASPESKTG
YIQISPSKEGPWTSMKLNYAVPAACWRFGNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDL
RLKGRISQSARADEQGDSFGKEDQILIGTLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHEN
YSWSDVQERRSQTEFRKEEILDLCISDLYESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKD
VQMEPIYDWCIIIKSPLCLTYYLPIAAHYTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNP
LYLSLVPHGGWELMHEPVVISHPTQAPSKFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIYV
PYWISFSRLPTLTLRLIDISGRKEKRRLLSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKGL
GLLSSVGHGGRFGSVKELSPLGDMDGAVDLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPY
ITFTNRAGQDLYLKLSIEDEPKVLHAYDWRVSFMYSKGTTDKLQVPIRHEYTRFS*(+)
MSNWYLQFVSSPLGVHKGNPPVICM*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	117416126-117416144(+) 117422474-117416144(+) 117416128-117422489(-)
Potential amino acid sequence	MNTPGSPRQLRITSTQDLNLNISVSNTNMLSQAYASWNNISCGDELYKKETFSSTERPVLDVHQ RRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPSGDDRSIKVPALRDLSDSHLNGRSVKPYRLMI TAILADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQSARTCAAIGEHLSQNTRKVNWNEMFF FKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLPPTSNPDSVKFDLALGDLMSTKTVEQ ETVKPSGKIRFAVLVSGRASVQQGNRASPESKTGYIQISPSKEGPWTSMKLNYAVPAACWRFGN CVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGRISQSARADEQGDSFGKEDQILIGTL EPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSDVQERRSQTEFRKEEILDLCISDLYE SENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEPIYDWCIIIKSPLCLTYYLPIAAHYT VSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSLVPHGGWELMHEPVVISHPTQAPSKF INLRSSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWISFSRLPTLTLRLIDISGRKEKRRLLS RSHLERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSSVGHGGRFGSVKELSPLGDMDGAVDL SAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTNRAGQDLYLKLSIEDEPKVLHAYDWR VSFMYSKGTTDKLQVPIRHEYTRFS(+) MSQRSYMHMTGGFPLCTPRGLLTNCRYQFDMNTPGSPRQLRITSTQDLNLNISVSNTNMLSQAY ASWNNISCGDELYKKETFSSTERPVLDVHQRRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPSG DDRSIKVPALRDLSDSHLNGRSVKPYRLMITAILADAEVKDDEGLETGEYMTAVRLFSENHSIS VQQQSARTCAAIGEHLSQNTRKVNWNEMFFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQV VQKLPPTSNPDSVKFDLALGDLMSTKTVEQETVKPSGKIRFAVLVSGRASVQQGNRASPESKTG YIQISPSKEGPWTSMKLNYAVPAACWRFGNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDL RLKGRISQSARADEQGDSFGKEDQILIGTLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHEN YSWSDVQERRSQTEFRKEEILDLCISDLYESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKD VQMEPIYDWCIIIKSPLCLTYYLPIAAHYTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNP LYLSLVPHGGWELMHEPVVISHPTQAPSKFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIYV PYWISFSRLPTLTLRLIDISGRKEKRRLLSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKGL GLLSSVGHGGRFGSVKELSPLGDMDGAVDLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPY ITFTNRAGQDLYLKLSIEDEPKVLHAYDWRVSFMYSKGTTDKLQVPIRHEYTRFS(+) MSNWYLQFVSSPLGVHKGNPPVICM*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d047074_circ_g.2

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