Plant Circular RNA Database

Detail information of Zm00001d043160_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d043160_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007761
					
						Alias
						Zm03circ00077, zma_circ_0001228
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 190377135-190383904  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d043160						
					
						Parent gene annotation
						
							Stomatal closure-related actin-binding protein 1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d043160_circ_g.1 Zm00001d043160_circ_g.2 						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm, 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
						Zm00001d043160_T004:6
Zm00001d043160_T006:6
Zm00001d043160_T005:6
Zm00001d043160_T003:6
Zm00001d043160_T001:5
Zm00001d043160_T002:5

General Information
CircRNA Name	Zm00001d043160_circ_g.3
ID in PlantcircBase	zma_circ_007761
Alias	Zm03circ00077, zma_circ_0001228
Organism	Zea mays
Position	chr3: 190377135-190383904 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d043160
Parent gene annotation	Stomatal closure-related actin-binding protein 1
Parent gene strand	+
Alternative splicing	Zm00001d043160_circ_g.1 Zm00001d043160_circ_g.2
Support reads	NA
Tissues	leaf, endosperm, 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	Zm00001d043160_T004:6 Zm00001d043160_T006:6 Zm00001d043160_T005:6 Zm00001d043160_T003:6 Zm00001d043160_T001:5 Zm00001d043160_T002:5

			
						 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  
						
							GCTGAAGTTTCACTTAAATAGCTGACTTATGCTTTGAACAGCTGCAGGACTTGAACATTATGTG
GACTCACTCATGAAACGGACGGATATTGAGTTCAACgctactgtagatgcacgcaaagtagctg
aagaggaaagggctcttgcacttgctgaaattgaaaaggctagagctgcaatcgaaaaagtcga
gaaagcat

						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: 645
Transcript exons: 190377135-190377272,190377392-190377460,190377607-190377
690,190377794-190377971,190378169-190378285,190383846-19
0383904
GCTACTGTAGATGCACGCAAAGTAGCTGAAGAGGAAAGGGCTCTTGCACTTGCTGAAATTGAAA
AGGCTAGAGCTGCAATCGAAAAAGTCGAGAAAGCATTTCATGTGCATGATTCTACGAAAAGCAG
CAGAGAGGAGGAAATAGAAGAACTTAGGAAAGAGGTCCGAGAGGCTAGGAGGATAAAAATGCTA
CACCAGCCAATCAAGGTCATGGACATGGAGTTTGAGCTTCAGGCACTGCGGACTCTCATCTCAC
AGAAGACTCAGCTATGCAATCAGCTAAATAAAGAGCTTGCCACGATCAAGAGGTTAGAAGTAGA
TAGTTCTGACCTCTTTGAGCTTGAAGGTTCTAATACCCTTGGATCGCAGTTTTGTATTATTCCT
CGAGTTGATGGTGCTCCAAACATTGCGAACTGTCCAATTCAGTGGTATCGTGTAATTTCTGGTG
GCAGTAGAGGACTCATATCGGGAGCAACAAAATTTACGTATGCCCCAGAACCGTTTGATGTTGG
TCGATTATTACAAGCAGAGATTATTTTGAATGCAGATAAAATCATAGTTCAGACGGATGGCCCT
ATAGATAATGCTGCAGGACTTGAACATTATGTGGACTCACTCATGAAACGGACGGATATTGAGT
TCAAC
						
						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	GCTGAAGTTTCACTTAAATAGCTGACTTATGCTTTGAACAGCTGCAGGACTTGAACATTATGTG GACTCACTCATGAAACGGACGGATATTGAGTTCAACgctactgtagatgcacgcaaagtagctg aagaggaaagggctcttgcacttgctgaaattgaaaaggctagagctgcaatcgaaaaagtcga gaaagcat
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: 645 Transcript exons: 190377135-190377272,190377392-190377460,190377607-190377 690,190377794-190377971,190378169-190378285,190383846-19 0383904 GCTACTGTAGATGCACGCAAAGTAGCTGAAGAGGAAAGGGCTCTTGCACTTGCTGAAATTGAAA AGGCTAGAGCTGCAATCGAAAAAGTCGAGAAAGCATTTCATGTGCATGATTCTACGAAAAGCAG CAGAGAGGAGGAAATAGAAGAACTTAGGAAAGAGGTCCGAGAGGCTAGGAGGATAAAAATGCTA CACCAGCCAATCAAGGTCATGGACATGGAGTTTGAGCTTCAGGCACTGCGGACTCTCATCTCAC AGAAGACTCAGCTATGCAATCAGCTAAATAAAGAGCTTGCCACGATCAAGAGGTTAGAAGTAGA TAGTTCTGACCTCTTTGAGCTTGAAGGTTCTAATACCCTTGGATCGCAGTTTTGTATTATTCCT CGAGTTGATGGTGCTCCAAACATTGCGAACTGTCCAATTCAGTGGTATCGTGTAATTTCTGGTG GCAGTAGAGGACTCATATCGGGAGCAACAAAATTTACGTATGCCCCAGAACCGTTTGATGTTGG TCGATTATTACAAGCAGAGATTATTTTGAATGCAGATAAAATCATAGTTCAGACGGATGGCCCT ATAGATAATGCTGCAGGACTTGAACATTATGTGGACTCACTCATGAAACGGACGGATATTGAGT TCAAC
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
						0.136385961

Conservation Information
Conserved circRNAs	NA
PMCS	0.136385961

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							190377441-190383901(+)
190377247-190383874(-)
						
						Potential amino acid sequence
						
							MLHQPIKVMDMEFELQALRTLISQKTQLCNQLNKELATIKRLEVDSSDLFELEGSNTLGSQFCI
IPRVDGAPNIANCPIQWYRVISGGSRGLISGATKFTYAPEPFDVGRLLQAEIILNADKIIVQTD
GPIDNAAGLEHYVDSLMKRTDIEFNATVDARKVAEEERALALAEIEKARAAIEKVEKAFHVHDS
TKSSREEEIEELRKEVREARRIKMLHQPIKVMDMEFELQALRTLISQKTQLCNQLNKELATIKR
LEVDSSDLFELEGSNTLGSQFCIIPRVDGAPNIANCPIQWYRVISGGSRGLISGATKFTYAPEP
FDVGRLLQAEIILNADKIIVQTDGPIDNAAGLEHYVDSLMKRTDIEFNATVDARKVAEEERALA
LAEIEKARAAIEKVEKAFHVHDSTKSSREEEIEELRKEVREARRIKMLHQPIKVMDMEFELQAL
RTLISQKTQLCNQLNKELATIKRLEVDSSDLFELEGSNTLGSQFCIIPRVDGAPNIANCPIQWY
RVISGGSRGLISGATKFTYAPEPFDVGRLLQAEIILNADKIIVQTDGPIDNAAGLEHYVDSLMK
RTDIEFNATVDARKVAEEERALALAEIEKARAAIEKVEKAFHVHDSTKSSREEEIEELRKEVRE
ARRIKMLHQPIKVMDMEFELQALRTLISQKTQLCNQLNKELATIKRLEVDSSDLFELEGSNTLG
SQFCIIPRVDGAPNIANCPIQWYRVISGGSRGLISGATKFTYAPEPFDVGRLLQAEIILNADKI
IVQTDGPIDNAAGLEHYVDSLMKRTDIEFN(+)
MHMKCFLDFFDCSSSLFNFSKCKSPFLFSYFACIYSSVELNIRPFHE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	190377441-190383901(+) 190377247-190383874(-)
Potential amino acid sequence	MLHQPIKVMDMEFELQALRTLISQKTQLCNQLNKELATIKRLEVDSSDLFELEGSNTLGSQFCI IPRVDGAPNIANCPIQWYRVISGGSRGLISGATKFTYAPEPFDVGRLLQAEIILNADKIIVQTD GPIDNAAGLEHYVDSLMKRTDIEFNATVDARKVAEEERALALAEIEKARAAIEKVEKAFHVHDS TKSSREEEIEELRKEVREARRIKMLHQPIKVMDMEFELQALRTLISQKTQLCNQLNKELATIKR LEVDSSDLFELEGSNTLGSQFCIIPRVDGAPNIANCPIQWYRVISGGSRGLISGATKFTYAPEP FDVGRLLQAEIILNADKIIVQTDGPIDNAAGLEHYVDSLMKRTDIEFNATVDARKVAEEERALA LAEIEKARAAIEKVEKAFHVHDSTKSSREEEIEELRKEVREARRIKMLHQPIKVMDMEFELQAL RTLISQKTQLCNQLNKELATIKRLEVDSSDLFELEGSNTLGSQFCIIPRVDGAPNIANCPIQWY RVISGGSRGLISGATKFTYAPEPFDVGRLLQAEIILNADKIIVQTDGPIDNAAGLEHYVDSLMK RTDIEFNATVDARKVAEEERALALAEIEKARAAIEKVEKAFHVHDSTKSSREEEIEELRKEVRE ARRIKMLHQPIKVMDMEFELQALRTLISQKTQLCNQLNKELATIKRLEVDSSDLFELEGSNTLG SQFCIIPRVDGAPNIANCPIQWYRVISGGSRGLISGATKFTYAPEPFDVGRLLQAEIILNADKI IVQTDGPIDNAAGLEHYVDSLMKRTDIEFN(+) MHMKCFLDFFDCSSSLFNFSKCKSPFLFSYFACIYSSVELNIRPFHE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b

circRNA

Detail information of Zm00001d043160_circ_g.3

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