Plant Circular RNA Database

Detail information of Zm00001d006780_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d006780_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007384
					
						Alias
						zma_circ_0000927, GRMZM2G457889_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 216493387-216494054  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d006780						
					
						Parent gene annotation
						
							 histone deacetylase
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d006780_circ_g.1 Zm00001d006780_circ_g.2 Zm00001d006780_circ_g.4 Zm00001d006780_circ_g.5 						
					
						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
						Zm00001d006780_T004:3
Zm00001d006780_T015:3
Zm00001d006780_T002:3
Zm00001d006780_T006:3
Zm00001d006780_T001:3
Zm00001d006780_T007:3
Zm00001d006780_T013:3
Zm00001d006780_T017:3
Zm00001d006780_T016:3
Zm00001d006780_T018:3
Zm00001d006780_T010:3
Zm00001d006780_T011:3
Zm00001d006780_T014:3
Zm00001d006780_T003:3

General Information
CircRNA Name	Zm00001d006780_circ_g.3
ID in PlantcircBase	zma_circ_007384
Alias	zma_circ_0000927, GRMZM2G457889_C1
Organism	Zea mays
Position	chr2: 216493387-216494054 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d006780
Parent gene annotation	histone deacetylase
Parent gene strand	+
Alternative splicing	Zm00001d006780_circ_g.1 Zm00001d006780_circ_g.2 Zm00001d006780_circ_g.4 Zm00001d006780_circ_g.5
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	Zm00001d006780_T004:3 Zm00001d006780_T015:3 Zm00001d006780_T002:3 Zm00001d006780_T006:3 Zm00001d006780_T001:3 Zm00001d006780_T007:3 Zm00001d006780_T013:3 Zm00001d006780_T017:3 Zm00001d006780_T016:3 Zm00001d006780_T018:3 Zm00001d006780_T010:3 Zm00001d006780_T011:3 Zm00001d006780_T014:3 Zm00001d006780_T003:3

			
						 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  
						
							TCAAGAAGATATTGATTGTCGATTGGGATGTTCACCATGGAAATGGCACACAGAAAATGTTTTA
CGATGATCCTCGTGTATTGTTCTTCTCAGTTCACAGgtgtgtggcccttaaggcaaaggaagct
gaggacaagtatatagcttctgttcacagcaagaggcatataaagctgatgaaggaaattagct
caacaata

						Assembled circRNA sequence  
						
							Yes
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
						
							Transcript length: 462
Transcript exons: 216493387-216493588,216493692-216493838,216493942-216494
054
GTGTGTGGCCCTTAAGGCAAAGGAAGCTGAGGACAAGTATATAGCTTCTGTTCACAGCAAGAGG
CATATAAAGCTGATGAAGGAAATTAGCTCAACAATATATGATGCCAGCAGGAACAAGATTGCTA
GGAAATTCAATTCCATTTACTTGAATAAGGGTTCCTCGGAATCTGCTGTTCTTGCAGCTGGTTC
TGTCATAGAGGTAGCTGAGAAAGTTGCTGCAGGTGAGTTAAGTTCTGCTATTGCTCTAGTCAGA
CCTCCAGGCCACCATGCAGAACATGATGAGGCTATGGGATTTTGCCTCTTCAACAATGTGGCAG
TTGCAGCTAATTATCTCTTAAACGAGAGGCCTGATTTAGGTATCAAGAAGATATTGATTGTCGA
TTGGGATGTTCACCATGGAAATGGCACACAGAAAATGTTTTACGATGATCCTCGTGTATTGTTC
TTCTCAGTTCACAG
						
						Genomic sequence
						
							GTGTGTGGCCCTTAAGGCAAAGGAAGCTGAGGACAAGTATATAGCTTCTGTTCACAGCAAGAGG
CATATAAAGCTGATGAAGGAAATTAGCTCAACAATATATGATGCCAGCAGGAACAAGATTGCTA
GGAAATTCAATTCCATTTACTTGAATAAGGGTTCCTCGGAATCTGCTGTTCTTGCAGCTGGTTC
TGTCATAGAGGTCATTTTACATGTTACATAAGCCCATTTCCTTCTTTTCTGCTGCTATTATACC
CCACCTTATTAGTAGGAAATAACTGAAAAGTGGATTATTTGGCAATTAGGTAGCTGAGAAAGTT
GCTGCAGGTGAGTTAAGTTCTGCTATTGCTCTAGTCAGACCTCCAGGCCACCATGCAGAACATG
ATGAGGCTATGGGATTTTGCCTCTTCAACAATGTGGCAGTTGCAGCTAATTATCTCTTAAACGA
GAGGGTATATACTGAAACCTCTCTCCCTCTGTGTGTGTGCGCGCGCGCACGCCTGTTTTTTTGG
GGGACCATTTGTTCACTTTTGAACTTTGTTCTTTATATTGCAGCCTGATTTAGGTATCAAGAAG
ATATTGATTGTCGATTGGGATGTTCACCATGGAAATGGCACACAGAAAATGTTTTACGATGATC
CTCGTGTATTGTTCTTCTCAGTTCACAG

Sequences
Splice junction sequence	TCAAGAAGATATTGATTGTCGATTGGGATGTTCACCATGGAAATGGCACACAGAAAATGTTTTA CGATGATCCTCGTGTATTGTTCTTCTCAGTTCACAGgtgtgtggcccttaaggcaaaggaagct gaggacaagtatatagcttctgttcacagcaagaggcatataaagctgatgaaggaaattagct caacaata
Assembled circRNA sequence	Yes 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	Transcript length: 462 Transcript exons: 216493387-216493588,216493692-216493838,216493942-216494 054 GTGTGTGGCCCTTAAGGCAAAGGAAGCTGAGGACAAGTATATAGCTTCTGTTCACAGCAAGAGG CATATAAAGCTGATGAAGGAAATTAGCTCAACAATATATGATGCCAGCAGGAACAAGATTGCTA GGAAATTCAATTCCATTTACTTGAATAAGGGTTCCTCGGAATCTGCTGTTCTTGCAGCTGGTTC TGTCATAGAGGTAGCTGAGAAAGTTGCTGCAGGTGAGTTAAGTTCTGCTATTGCTCTAGTCAGA CCTCCAGGCCACCATGCAGAACATGATGAGGCTATGGGATTTTGCCTCTTCAACAATGTGGCAG TTGCAGCTAATTATCTCTTAAACGAGAGGCCTGATTTAGGTATCAAGAAGATATTGATTGTCGA TTGGGATGTTCACCATGGAAATGGCACACAGAAAATGTTTTACGATGATCCTCGTGTATTGTTC TTCTCAGTTCACAG
Genomic sequence	GTGTGTGGCCCTTAAGGCAAAGGAAGCTGAGGACAAGTATATAGCTTCTGTTCACAGCAAGAGG CATATAAAGCTGATGAAGGAAATTAGCTCAACAATATATGATGCCAGCAGGAACAAGATTGCTA GGAAATTCAATTCCATTTACTTGAATAAGGGTTCCTCGGAATCTGCTGTTCTTGCAGCTGGTTC TGTCATAGAGGTCATTTTACATGTTACATAAGCCCATTTCCTTCTTTTCTGCTGCTATTATACC CCACCTTATTAGTAGGAAATAACTGAAAAGTGGATTATTTGGCAATTAGGTAGCTGAGAAAGTT GCTGCAGGTGAGTTAAGTTCTGCTATTGCTCTAGTCAGACCTCCAGGCCACCATGCAGAACATG ATGAGGCTATGGGATTTTGCCTCTTCAACAATGTGGCAGTTGCAGCTAATTATCTCTTAAACGA GAGGGTATATACTGAAACCTCTCTCCCTCTGTGTGTGTGCGCGCGCGCACGCCTGTTTTTTTGG GGGACCATTTGTTCACTTTTGAACTTTGTTCTTTATATTGCAGCCTGATTTAGGTATCAAGAAG ATATTGATTGTCGATTGGGATGTTCACCATGGAAATGGCACACAGAAAATGTTTTACGATGATC CTCGTGTATTGTTCTTCTCAGTTCACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							osi_circ_017305 						
					
						PMCS
						0.208168596

Conservation Information
Conserved circRNAs	osi_circ_017305
PMCS	0.208168596

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							216493464-216494051(+)
216493983-216493427(+)
216493455-216494046(-)
						
						Potential amino acid sequence
						
							MKEISSTIYDASRNKIARKFNSIYLNKGSSESAVLAAGSVIEVAEKVAAGELSSAIALVRPPGH
HAEHDEAMGFCLFNNVAVAANYLLNERPDLGIKKILIVDWDVHHGNGTQKMFYDDPRVLFFSVH
RCVALKAKEAEDKYIASVHSKRHIKLMKEISSTIYDASRNKIARKFNSIYLNKGSSESAVLAAG
SVIEVAEKVAAGELSSAIALVRPPGHHAEHDEAMGFCLFNNVAVAANYLLNERPDLGIKKILIV
DWDVHHGNGTQKMFYDDPRVLFFSVHRCVALKAKEAEDKYIASVHSKRHIKLMKEISSTIYDAS
RNKIARKFNSIYLNKGSSESAVLAAGSVIEVAEKVAAGELSSAIALVRPPGHHAEHDEAMGFCL
FNNVAVAANYLLNERPDLGIKKILIVDWDVHHGNGTQKMFYDDPRVLFFSVHRCVALKAKEAED
KYIASVHSKRHIKLMKEISSTIYDASRNKIARKFNSIYLNKGSSESAVLAAGSVIEVAEKVAAG
ELSSAIALVRPPGHHAEHDEAMGFCLFNNVAVAANYLLNERPDLGIKKILIVDWDVHHGNGTQK
MFYDDPRVLFFSVH(+)
MFTMEMAHRKCFTMILVYCSSQFTGVWPLRQRKLRTSI*(+)
MPLAVNRSYILVLSFLCLKGHTPVN*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	216493464-216494051(+) 216493983-216493427(+) 216493455-216494046(-)
Potential amino acid sequence	MKEISSTIYDASRNKIARKFNSIYLNKGSSESAVLAAGSVIEVAEKVAAGELSSAIALVRPPGH HAEHDEAMGFCLFNNVAVAANYLLNERPDLGIKKILIVDWDVHHGNGTQKMFYDDPRVLFFSVH RCVALKAKEAEDKYIASVHSKRHIKLMKEISSTIYDASRNKIARKFNSIYLNKGSSESAVLAAG SVIEVAEKVAAGELSSAIALVRPPGHHAEHDEAMGFCLFNNVAVAANYLLNERPDLGIKKILIV DWDVHHGNGTQKMFYDDPRVLFFSVHRCVALKAKEAEDKYIASVHSKRHIKLMKEISSTIYDAS RNKIARKFNSIYLNKGSSESAVLAAGSVIEVAEKVAAGELSSAIALVRPPGHHAEHDEAMGFCL FNNVAVAANYLLNERPDLGIKKILIVDWDVHHGNGTQKMFYDDPRVLFFSVHRCVALKAKEAED KYIASVHSKRHIKLMKEISSTIYDASRNKIARKFNSIYLNKGSSESAVLAAGSVIEVAEKVAAG ELSSAIALVRPPGHHAEHDEAMGFCLFNNVAVAANYLLNERPDLGIKKILIVDWDVHHGNGTQK MFYDDPRVLFFSVH(+) MFTMEMAHRKCFTMILVYCSSQFTGVWPLRQRKLRTSI(+) MPLAVNRSYILVLSFLCLKGHTPVN(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d006780_circ_g.3

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