Plant Circular RNA Database

Detail information of Zm00001d047074_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d047074_circ_g.3
					
						ID in PlantcircBase
						zma_circ_010018
					
						Alias
						zma_circ_0003050
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 117416428-117422549  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.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  
						
							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_T008:5
Zm00001d047074_T016:9
Zm00001d047074_T022:9
Zm00001d047074_T002:8
Zm00001d047074_T010:9
Zm00001d047074_T012:9
Zm00001d047074_T020:8
Zm00001d047074_T018:9
Zm00001d047074_T014:9
Zm00001d047074_T023:1
Zm00001d047074_T017:9

General Information
CircRNA Name	Zm00001d047074_circ_g.3
ID in PlantcircBase	zma_circ_010018
Alias	zma_circ_0003050
Organism	Zea mays
Position	chr9: 117416428-117422549 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.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	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_T008:5 Zm00001d047074_T016:9 Zm00001d047074_T022:9 Zm00001d047074_T002:8 Zm00001d047074_T010:9 Zm00001d047074_T012:9 Zm00001d047074_T020:8 Zm00001d047074_T018:9 Zm00001d047074_T014:9 Zm00001d047074_T023:1 Zm00001d047074_T017:9

			
						 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
TTTATGTACTCCAAGGGGACTACTGACAAACTGCAGgaaaccttttcttctactgagcgaccag
ttcttgatgttcatcaaagaagaagttattatgttgtcccacaaaataaacttggacaagatat
ttatgtaa

						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 TTTATGTACTCCAAGGGGACTACTGACAAACTGCAGgaaaccttttcttctactgagcgaccag ttcttgatgttcatcaaagaagaagttattatgttgtcccacaaaataaacttggacaagatat ttatgtaa
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
						0.117086636

Conservation Information
Conserved circRNAs	NA
PMCS	0.117086636

			
				
						 Functional Information
					

				
						Coding potential
						Y
					

						Potential coding position
						
							117416660-117422546(+)
117422474-117416524(+)
117416471-117422489(-)
						
					

						Potential amino acid sequence
						
							MITAILADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQSARTCAAIGEHLSQNTRKVNWNEM
FFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLPPTSNPDSVKFDLALGDLMSTKTV
EQETVKPSGKIRFAVLVSGRASVQQGNRASPESKTGYIQISPSKEGPWTSMKLNYAVPAACWRF
GNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGRISQSARADEQGDSFGKEDQILIG
TLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSDVQERRSQTEFRKEEILDLCISDL
YESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEPIYDWCIIIKSPLCLTYYLPIAAH
YTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSLVPHGGWELMHEPVVISHPTQAPS
KFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWISFSRLPTLTLRLIDISGRKEKRRL
LSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSSVGHGGRFGSVKELSPLGDMDGAV
DLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTNRAGQDLYLKLSIEDEPKVLHAYD
WRVSFMYSKGTTDKLQETFSSTERPVLDVHQRRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPS
GDDRSIKVPALRDLSDSHLNGRSVKPYRLMITAILADAEVKDDEGLETGEYMTAVRLFSENHSI
SVQQQSARTCAAIGEHLSQNTRKVNWNEMFFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQ
VVQKLPPTSNPDSVKFDLALGDLMSTKTVEQETVKPSGKIRFAVLVSGRASVQQGNRASPESKT
GYIQISPSKEGPWTSMKLNYAVPAACWRFGNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVD
LRLKGRISQSARADEQGDSFGKEDQILIGTLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHE
NYSWSDVQERRSQTEFRKEEILDLCISDLYESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGK
DVQMEPIYDWCIIIKSPLCLTYYLPIAAHYTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRN
PLYLSLVPHGGWELMHEPVVISHPTQAPSKFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIY
VPYWISFSRLPTLTLRLIDISGRKEKRRLLSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKG
LGLLSSVGHGGRFGSVKELSPLGDMDGAVDLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRP
YITFTNRAGQDLYLKLSIEDEPKVLHAYDWRVSFMYSKGTTDKLQETFSSTERPVLDVHQRRSY
YVVPQNKLGQDIYVRTTENRGSLVTLLPSGDDRSIKVPALRDLSDSHLNGRSVKPYRLMITAIL
ADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQSARTCAAIGEHLSQNTRKVNWNEMFFFKVE
RVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLPPTSNPDSVKFDLALGDLMSTKTVEQETVK
PSGKIRFAVLVSGRASVQQGNRASPESKTGYIQISPSKEGPWTSMKLNYAVPAACWRFGNCVIA
SEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGRISQSARADEQGDSFGKEDQILIGTLEPNS
TIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSDVQERRSQTEFRKEEILDLCISDLYESENL
LFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEPIYDWCIIIKSPLCLTYYLPIAAHYTVSSS
HLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSLVPHGGWELMHEPVVISHPTQAPSKFINLR
SSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWISFSRLPTLTLRLIDISGRKEKRRLLSRSHL
ERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSSVGHGGRFGSVKELSPLGDMDGAVDLSAYD
DDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTNRAGQDLYLKLSIEDEPKVLHAYDWRVSFM
YSKGTTDKLQETFSSTERPVLDVHQRRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPSGDDRSI
KVPALRDLSDSHLNGRSVKPYRLMITAILADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQS
ARTCAAIGEHLSQNTRKVNWNEMFFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLP
PTSNPDSVKFDLALGDLMSTKTVEQETVKPSGKIRFAVLVSGRASVQQGNRASPESKTGYIQIS
PSKEGPWTSMKLNYAVPAACWRFGNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGR
ISQSARADEQGDSFGKEDQILIGTLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSD
VQERRSQTEFRKEEILDLCISDLYESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEP
IYDWCIIIKSPLCLTYYLPIAAHYTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSL
VPHGGWELMHEPVVISHPTQAPSKFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWIS
FSRLPTLTLRLIDISGRKEKRRLLSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSS
VGHGGRFGSVKELSPLGDMDGAVDLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTN
RAGQDLYLKLSIEDEPKVLHAYDWRVSFMYSKGTTDKLQ(+)
MSQRSYMHMTGGFPLCTPRGLLTNCRKPFLLLSDQFLMFIKEEVIMLSHKINLDKIFM*(+)
MNIKNWSLSRRKGFLQFVSSPLGVHKGNPPVICM*(-)
						
					

						Sponge-miRNAs
						
							NA						
					

						circRNA-miRNA-mRNA network
						 VISUALIZATION
					

						Potential function description
						NA
					

			
		

Functional Information
Coding potential	Y
Potential coding position	117416660-117422546(+) 117422474-117416524(+) 117416471-117422489(-)
Potential amino acid sequence	MITAILADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQSARTCAAIGEHLSQNTRKVNWNEM FFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLPPTSNPDSVKFDLALGDLMSTKTV EQETVKPSGKIRFAVLVSGRASVQQGNRASPESKTGYIQISPSKEGPWTSMKLNYAVPAACWRF GNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGRISQSARADEQGDSFGKEDQILIG TLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSDVQERRSQTEFRKEEILDLCISDL YESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEPIYDWCIIIKSPLCLTYYLPIAAH YTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSLVPHGGWELMHEPVVISHPTQAPS KFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWISFSRLPTLTLRLIDISGRKEKRRL LSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSSVGHGGRFGSVKELSPLGDMDGAV DLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTNRAGQDLYLKLSIEDEPKVLHAYD WRVSFMYSKGTTDKLQETFSSTERPVLDVHQRRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPS GDDRSIKVPALRDLSDSHLNGRSVKPYRLMITAILADAEVKDDEGLETGEYMTAVRLFSENHSI SVQQQSARTCAAIGEHLSQNTRKVNWNEMFFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQ VVQKLPPTSNPDSVKFDLALGDLMSTKTVEQETVKPSGKIRFAVLVSGRASVQQGNRASPESKT GYIQISPSKEGPWTSMKLNYAVPAACWRFGNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVD LRLKGRISQSARADEQGDSFGKEDQILIGTLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHE NYSWSDVQERRSQTEFRKEEILDLCISDLYESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGK DVQMEPIYDWCIIIKSPLCLTYYLPIAAHYTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRN PLYLSLVPHGGWELMHEPVVISHPTQAPSKFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIY VPYWISFSRLPTLTLRLIDISGRKEKRRLLSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKG LGLLSSVGHGGRFGSVKELSPLGDMDGAVDLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRP YITFTNRAGQDLYLKLSIEDEPKVLHAYDWRVSFMYSKGTTDKLQETFSSTERPVLDVHQRRSY YVVPQNKLGQDIYVRTTENRGSLVTLLPSGDDRSIKVPALRDLSDSHLNGRSVKPYRLMITAIL ADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQSARTCAAIGEHLSQNTRKVNWNEMFFFKVE RVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLPPTSNPDSVKFDLALGDLMSTKTVEQETVK PSGKIRFAVLVSGRASVQQGNRASPESKTGYIQISPSKEGPWTSMKLNYAVPAACWRFGNCVIA SEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGRISQSARADEQGDSFGKEDQILIGTLEPNS TIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSDVQERRSQTEFRKEEILDLCISDLYESENL LFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEPIYDWCIIIKSPLCLTYYLPIAAHYTVSSS HLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSLVPHGGWELMHEPVVISHPTQAPSKFINLR SSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWISFSRLPTLTLRLIDISGRKEKRRLLSRSHL ERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSSVGHGGRFGSVKELSPLGDMDGAVDLSAYD DDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTNRAGQDLYLKLSIEDEPKVLHAYDWRVSFM YSKGTTDKLQETFSSTERPVLDVHQRRSYYVVPQNKLGQDIYVRTTENRGSLVTLLPSGDDRSI KVPALRDLSDSHLNGRSVKPYRLMITAILADAEVKDDEGLETGEYMTAVRLFSENHSISVQQQS ARTCAAIGEHLSQNTRKVNWNEMFFFKVERVDSYTLELLVLDAGKGQPVGIYSAPLEQVVQKLP PTSNPDSVKFDLALGDLMSTKTVEQETVKPSGKIRFAVLVSGRASVQQGNRASPESKTGYIQIS PSKEGPWTSMKLNYAVPAACWRFGNCVIASEATVKEGNRYVSIRSLVSVTNTTNFIVDLRLKGR ISQSARADEQGDSFGKEDQILIGTLEPNSTIPVPLSGLSHPLMPYMLQLRPAKHHDHENYSWSD VQERRSQTEFRKEEILDLCISDLYESENLLFCSQVDGTSNSCHGLWFCLSIEGKEIGKDVQMEP IYDWCIIIKSPLCLTYYLPIAAHYTVSSSHLDNEDSSCSLGTLSPGEAVKVHNVDPRNPLYLSL VPHGGWELMHEPVVISHPTQAPSKFINLRSSLSGRVVQILLEQSSDSDYLMARLIRIYVPYWIS FSRLPTLTLRLIDISGRKEKRRLLSRSHLERGEKQLYDIKHDELVEGYTIASGLNFKGLGLLSS VGHGGRFGSVKELSPLGDMDGAVDLSAYDDDGKCMHILLCSKPSSYQAVPTKVIHVRPYITFTN RAGQDLYLKLSIEDEPKVLHAYDWRVSFMYSKGTTDKLQ(+) MSQRSYMHMTGGFPLCTPRGLLTNCRKPFLLLSDQFLMFIKEEVIMLSHKINLDKIFM(+) MNIKNWSLSRRKGFLQFVSSPLGVHKGNPPVICM(-)
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.3

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