Plant Circular RNA Database

Detail information of Zm00001d046047_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d046047_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009948
					
						Alias
						zma_circ_0003228
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 58928998-58931116  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							ue-circRNA							
									
						Identification method
						find_circ
					
						Parent gene
						
							Zm00001d046047						
					
						Parent gene annotation
						
							Transducin/WD40 repeat-like superfamily protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d046047_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
						Zm00001d046047_T004:2
Zm00001d046047_T022:2
Zm00001d046047_T018:2
Zm00001d046047_T001:2
Zm00001d046047_T009:2
Zm00001d046047_T012:2
Zm00001d046047_T017:2
Zm00001d046047_T021:2
Zm00001d046047_T011:1
Zm00001d046047_T003:2
Zm00001d046047_T002:2
Zm00001d046047_T007:2
Zm00001d046047_T005:2
Zm00001d046047_T015:2

General Information
CircRNA Name	Zm00001d046047_circ_g.1
ID in PlantcircBase	zma_circ_009948
Alias	zma_circ_0003228
Organism	Zea mays
Position	chr9: 58928998-58931116 JBrowse»
Reference genome	AGPv4.38
Type	ue-circRNA
Identification method	find_circ
Parent gene	Zm00001d046047
Parent gene annotation	Transducin/WD40 repeat-like superfamily protein
Parent gene strand	+
Alternative splicing	Zm00001d046047_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	Zm00001d046047_T004:2 Zm00001d046047_T022:2 Zm00001d046047_T018:2 Zm00001d046047_T001:2 Zm00001d046047_T009:2 Zm00001d046047_T012:2 Zm00001d046047_T017:2 Zm00001d046047_T021:2 Zm00001d046047_T011:1 Zm00001d046047_T003:2 Zm00001d046047_T002:2 Zm00001d046047_T007:2 Zm00001d046047_T005:2 Zm00001d046047_T015:2

			
						 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  
						
							TTCCGATGGTTGCTCTCAATGAGTCAATGACAAAGCTAGCTGTTGGTGATGCTATTGGAGAGAT
TTATGATGGTACAATTCGAGTCTATGACATAGAAAGcttttggtgagcttttggcaacaccctt
cggaacatgtgcgaatggctgcacgttccttgttccactgtgcagctccccgttctattccaca
accactac

									
								

					

						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: 1010
Transcript exons: 58928998-58929804,58930914-58931116
CTTTTGGTGAGCTTTTGGCAACACCCTTCGGAACATGTGCGAATGGCTGCACGTTCCTTGTTCC
ACTGTGCAGCTCCCCGTTCTATTCCACAACCACTACGAGTAAACAAAAATAAAGTGGTCAATGC
CCCCTTGTCTTCATCAGATAATATGAATGTTCTTATATGTGCTGTGCAGACTGCCTCTGTATCC
AATCATGGAGAGTTGAAGGAAGATGATGAAAATGTTGATAAAGATGATATTGACACTGCTAATA
TGATCTTATGGTTGGAATCATTTGAAAATCAGGAGTGGTTATCATGGATAGGAGGCACAAGCCA
GGATGCAGTGGCGTCAAATATCATAGTTGCAGCTGCTTTGGTCGTTTGGTATCCAAGTGTCGTG
AAAGCTAAACTTTCAAGTTTAGTTGTTAGTCAACTAATCAAGTTAGTTATGTCGATGAATGATC
GATATAGTTCAACTGCAGCTGAACTTCTAGCAGAGGGAATGGAAAACACTTGGAAGGCATGCTT
GGGTGCTGAGATCACTCATTTTATGAGTGATATCCTTTTCCAAATTGAGTGCCTAAGCACTGCA
CCTTCTAGCAATGCTATCAATAAAACTGCAGTGGCCATTACAATGCGAGAAGCATTGGTTGGCA
CCCTTTTACCAAGCTTGGCTATGGCTGATGTAACAGGATTTTTTGGTGTAATAGAGAGCCAAAT
TTGGGCTACTTCGTCTGATTCACCTGTTCATGTCGCTTCAATCAAAACCATTATCCGTGTAGTT
CGAGGTGCGCCGAAGTCCTTGGTCCCATACCTCGACAAGGCAATCAACTACATTCTACACACTA
TGGATCCAAGCAATCTAATAATGCGAAAAGCTTGTATTATCAGTTCAATGATGGCTCTAAGAGA
AATGGCACGTGTATTTCCGATGGTTGCTCTCAATGAGTCAATGACAAAGCTAGCTGTTGGTGAT
GCTATTGGAGAGATTTATGATGGTACAATTCGAGTCTATGACATAGAAAG
						
					

						Genomic sequence
						
							CTTTTGGTGAGCTTTTGGCAACACCCTTCGGAACATGTGCGAATGGCTGCACGTTCCTTGTTCC
ACTGTGCAGCTCCCCGTTCTATTCCACAACCACTACGAGTAAACAAAAATAAAGTGGTCAATGC
CCCCTTGTCTTCATCAGATAATATGAATGTTCTTATATGTGCTGTGCAGACTGCCTCTGTATCC
AATCATGGAGAGTTGAAGGAAGATGATGAAAATGTTGATAAAGATGATATTGACACTGCTAATA
TGATCTTATGGTTGGAATCATTTGAAAATCAGGAGTGGTTATCATGGATAGGAGGCACAAGCCA
GGATGCAGTGGCGTCAAATATCATAGTTGCAGCTGCTTTGGTCGTTTGGTATCCAAGTGTCGTG
AAAGCTAAACTTTCAAGTTTAGTTGTTAGTCAACTAATCAAGTTAGTTATGTCGATGAATGATC
GATATAGTTCAACTGCAGCTGAACTTCTAGCAGAGGGAATGGAAAACACTTGGAAGGCATGCTT
GGGTGCTGAGATCACTCATTTTATGAGTGATATCCTTTTCCAAATTGAGTGCCTAAGCACTGCA
CCTTCTAGCAATGCTATCAATAAAACTGCAGTGGCCATTACAATGCGAGAAGCATTGGTTGGCA
CCCTTTTACCAAGCTTGGCTATGGCTGATGTAACAGGATTTTTTGGTGTAATAGAGAGCCAAAT
TTGGGCTACTTCGTCTGATTCACCTGTTCATGTCGCTTCAATCAAAACCATTATCCGTGTAGTT
CGAGGTGCGCCGAAGTCCTTGGTCCCATACCTCGACAAGGTGAGAAATGTTTCTACCTATTTGT
GATTGTTGTAGCAGTTGGAATGAGAAACTCTAACCCTAACTGGGTTGTGAGTGCATATATATAA
GCTGAGTAATTGGGCTAAGCCCATTACACTGAGGGTATGCAAGTAATTACACAGGGACTAGCCC
CTTTTTTTTTTGGGAAAACGCAGGAGAACTGCGCCTTAATATATTAACTAGCCCTGAAACCCTA
GCATTAGTCTAACAGTATCTTTTGATAGAATTTTGCTGTGTCATCGAAGCTCGGAGGGCTCTCC
AATTTGTATTGCAAACCTTTTGTCTCACAAGTCCTAAACCCTGAACAATTACACTTGAAAGCTT
CTCTGCACAATGCAAAAACTGGTTTCTCACTACCAGAAATTATGCTGTATAGAACGTTTTAGGG
AAATGTTGATCTTTCATCTCTATCTTTCATTTTCTTACTCAAAATGTGTAAATCATTTCTTTAT
TGGTAAGTACTATAATTCATTGTGTTATTTTTCTTTCGTCTTATTGTTAAATATAACAAACAAC
AACAATAAAGCCTTTTATTCCAAGCAAGTTGGGGTAGGCTAGAGTTAAAAACCCAATAGAACTC
ACAAGTCATGGTTCGGGCATATGTACAACTGTTTTCCATGCACGTCTTATTGTTTAATATGTTA
TTTCAAAAAGATTATAACTACCGTTATAACCTGTGTATGTCAGGAACTTATAAACTTTTGAATC
CTAATCTTAGAAATGGGGTGCTCTTGACCTTATTTTTTATGTGTTTGGACAAATAAGGTTATGT
TTCATCCAATTTCGAGTAGCTATGGGACAAGTAAAGGAAAAGTTAAGAAGGTTTAAGTACATTT
GTTTAGCAGGCTTACTTTACAACTGTTATAGTGGATGCACTAACCAGTTCAACCCAAAAATTTA
AGCTGTTTGGAGAAGGTAGCCAATCCACTTATACACTTTAACAACAATAAAGCCTTTTGGAGGC
TTACTTTAGTTTTCACAAAGTATCCTCTAGCATTGTAACCATTTTTCGTAATGATTTCTTTAGA
GTATTGATTTAGTCAAAACATGTACTTTTATGTAGTTCTTATAGTTGAATAATTGTGCAGGCAA
TCAACTACATTCTACACACTATGGATCCAAGCAATCTAATAATGCGAAAAGCTTGTATTATCAG
TTCAATGATGGCTCTAAGAGAAATGGCACGTGTATTTCCGATGGTTGCTCTCAATGAGTCAATG
ACAAAGCTAGCTGTTGGTGATGCTATTGGAGAGATTTATGATGGTACAATTCGAGTCTATGACA
TAGAAAG
						
					

			
		

Sequences
Splice junction sequence	TTCCGATGGTTGCTCTCAATGAGTCAATGACAAAGCTAGCTGTTGGTGATGCTATTGGAGAGAT TTATGATGGTACAATTCGAGTCTATGACATAGAAAGcttttggtgagcttttggcaacaccctt cggaacatgtgcgaatggctgcacgttccttgttccactgtgcagctccccgttctattccaca accactac
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: 1010 Transcript exons: 58928998-58929804,58930914-58931116 CTTTTGGTGAGCTTTTGGCAACACCCTTCGGAACATGTGCGAATGGCTGCACGTTCCTTGTTCC ACTGTGCAGCTCCCCGTTCTATTCCACAACCACTACGAGTAAACAAAAATAAAGTGGTCAATGC CCCCTTGTCTTCATCAGATAATATGAATGTTCTTATATGTGCTGTGCAGACTGCCTCTGTATCC AATCATGGAGAGTTGAAGGAAGATGATGAAAATGTTGATAAAGATGATATTGACACTGCTAATA TGATCTTATGGTTGGAATCATTTGAAAATCAGGAGTGGTTATCATGGATAGGAGGCACAAGCCA GGATGCAGTGGCGTCAAATATCATAGTTGCAGCTGCTTTGGTCGTTTGGTATCCAAGTGTCGTG AAAGCTAAACTTTCAAGTTTAGTTGTTAGTCAACTAATCAAGTTAGTTATGTCGATGAATGATC GATATAGTTCAACTGCAGCTGAACTTCTAGCAGAGGGAATGGAAAACACTTGGAAGGCATGCTT GGGTGCTGAGATCACTCATTTTATGAGTGATATCCTTTTCCAAATTGAGTGCCTAAGCACTGCA CCTTCTAGCAATGCTATCAATAAAACTGCAGTGGCCATTACAATGCGAGAAGCATTGGTTGGCA CCCTTTTACCAAGCTTGGCTATGGCTGATGTAACAGGATTTTTTGGTGTAATAGAGAGCCAAAT TTGGGCTACTTCGTCTGATTCACCTGTTCATGTCGCTTCAATCAAAACCATTATCCGTGTAGTT CGAGGTGCGCCGAAGTCCTTGGTCCCATACCTCGACAAGGCAATCAACTACATTCTACACACTA TGGATCCAAGCAATCTAATAATGCGAAAAGCTTGTATTATCAGTTCAATGATGGCTCTAAGAGA AATGGCACGTGTATTTCCGATGGTTGCTCTCAATGAGTCAATGACAAAGCTAGCTGTTGGTGAT GCTATTGGAGAGATTTATGATGGTACAATTCGAGTCTATGACATAGAAAG
Genomic sequence	CTTTTGGTGAGCTTTTGGCAACACCCTTCGGAACATGTGCGAATGGCTGCACGTTCCTTGTTCC ACTGTGCAGCTCCCCGTTCTATTCCACAACCACTACGAGTAAACAAAAATAAAGTGGTCAATGC CCCCTTGTCTTCATCAGATAATATGAATGTTCTTATATGTGCTGTGCAGACTGCCTCTGTATCC AATCATGGAGAGTTGAAGGAAGATGATGAAAATGTTGATAAAGATGATATTGACACTGCTAATA TGATCTTATGGTTGGAATCATTTGAAAATCAGGAGTGGTTATCATGGATAGGAGGCACAAGCCA GGATGCAGTGGCGTCAAATATCATAGTTGCAGCTGCTTTGGTCGTTTGGTATCCAAGTGTCGTG AAAGCTAAACTTTCAAGTTTAGTTGTTAGTCAACTAATCAAGTTAGTTATGTCGATGAATGATC GATATAGTTCAACTGCAGCTGAACTTCTAGCAGAGGGAATGGAAAACACTTGGAAGGCATGCTT GGGTGCTGAGATCACTCATTTTATGAGTGATATCCTTTTCCAAATTGAGTGCCTAAGCACTGCA CCTTCTAGCAATGCTATCAATAAAACTGCAGTGGCCATTACAATGCGAGAAGCATTGGTTGGCA CCCTTTTACCAAGCTTGGCTATGGCTGATGTAACAGGATTTTTTGGTGTAATAGAGAGCCAAAT TTGGGCTACTTCGTCTGATTCACCTGTTCATGTCGCTTCAATCAAAACCATTATCCGTGTAGTT CGAGGTGCGCCGAAGTCCTTGGTCCCATACCTCGACAAGGTGAGAAATGTTTCTACCTATTTGT GATTGTTGTAGCAGTTGGAATGAGAAACTCTAACCCTAACTGGGTTGTGAGTGCATATATATAA GCTGAGTAATTGGGCTAAGCCCATTACACTGAGGGTATGCAAGTAATTACACAGGGACTAGCCC CTTTTTTTTTTGGGAAAACGCAGGAGAACTGCGCCTTAATATATTAACTAGCCCTGAAACCCTA GCATTAGTCTAACAGTATCTTTTGATAGAATTTTGCTGTGTCATCGAAGCTCGGAGGGCTCTCC AATTTGTATTGCAAACCTTTTGTCTCACAAGTCCTAAACCCTGAACAATTACACTTGAAAGCTT CTCTGCACAATGCAAAAACTGGTTTCTCACTACCAGAAATTATGCTGTATAGAACGTTTTAGGG AAATGTTGATCTTTCATCTCTATCTTTCATTTTCTTACTCAAAATGTGTAAATCATTTCTTTAT TGGTAAGTACTATAATTCATTGTGTTATTTTTCTTTCGTCTTATTGTTAAATATAACAAACAAC AACAATAAAGCCTTTTATTCCAAGCAAGTTGGGGTAGGCTAGAGTTAAAAACCCAATAGAACTC ACAAGTCATGGTTCGGGCATATGTACAACTGTTTTCCATGCACGTCTTATTGTTTAATATGTTA TTTCAAAAAGATTATAACTACCGTTATAACCTGTGTATGTCAGGAACTTATAAACTTTTGAATC CTAATCTTAGAAATGGGGTGCTCTTGACCTTATTTTTTATGTGTTTGGACAAATAAGGTTATGT TTCATCCAATTTCGAGTAGCTATGGGACAAGTAAAGGAAAAGTTAAGAAGGTTTAAGTACATTT GTTTAGCAGGCTTACTTTACAACTGTTATAGTGGATGCACTAACCAGTTCAACCCAAAAATTTA AGCTGTTTGGAGAAGGTAGCCAATCCACTTATACACTTTAACAACAATAAAGCCTTTTGGAGGC TTACTTTAGTTTTCACAAAGTATCCTCTAGCATTGTAACCATTTTTCGTAATGATTTCTTTAGA GTATTGATTTAGTCAAAACATGTACTTTTATGTAGTTCTTATAGTTGAATAATTGTGCAGGCAA TCAACTACATTCTACACACTATGGATCCAAGCAATCTAATAATGCGAAAAGCTTGTATTATCAG TTCAATGATGGCTCTAAGAGAAATGGCACGTGTATTTCCGATGGTTGCTCTCAATGAGTCAATG ACAAAGCTAGCTGTTGGTGATGCTATTGGAGAGATTTATGATGGTACAATTCGAGTCTATGACA TAGAAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.198414697

Conservation Information
Conserved circRNAs	NA
PMCS	0.198414697

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							58929041-58929004(+)
						
						Potential amino acid sequence
						
							MAARSLFHCAAPRSIPQPLRVNKNKVVNAPLSSSDNMNVLICAVQTASVSNHGELKEDDENVDK
DDIDTANMILWLESFENQEWLSWIGGTSQDAVASNIIVAAALVVWYPSVVKAKLSSLVVSQLIK
LVMSMNDRYSSTAAELLAEGMENTWKACLGAEITHFMSDILFQIECLSTAPSSNAINKTAVAIT
MREALVGTLLPSLAMADVTGFFGVIESQIWATSSDSPVHVASIKTIIRVVRGAPKSLVPYLDKA
INYILHTMDPSNLIMRKACIISSMMALREMARVFPMVALNESMTKLAVGDAIGEIYDGTIRVYD
IESFW*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	58929041-58929004(+)
Potential amino acid sequence	MAARSLFHCAAPRSIPQPLRVNKNKVVNAPLSSSDNMNVLICAVQTASVSNHGELKEDDENVDK DDIDTANMILWLESFENQEWLSWIGGTSQDAVASNIIVAAALVVWYPSVVKAKLSSLVVSQLIK LVMSMNDRYSSTAAELLAEGMENTWKACLGAEITHFMSDILFQIECLSTAPSSNAINKTAVAIT MREALVGTLLPSLAMADVTGFFGVIESQIWATSSDSPVHVASIKTIIRVVRGAPKSLVPYLDKA INYILHTMDPSNLIMRKACIISSMMALREMARVFPMVALNESMTKLAVGDAIGEIYDGTIRVYD IESFW*(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d046047_circ_g.1

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