Plant Circular RNA Database

Detail information of Zm00001d046581_circ_g.1

			
						 General Information
					
						CircRNA Name
						Zm00001d046581_circ_g.1
					
						ID in PlantcircBase
						zma_circ_009994
					
						Alias
						Zm09circ00052
					
						Organism
						
							Zea mays						
					
						Position
						
							chr9: 96884838-96886250  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d046581						
					
						Parent gene annotation
						
							Isoleucine--tRNA ligase cytoplasmic
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, endosperm
					
						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  
						
							CT-AC							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
						Zm00001d046581_T003:5
Zm00001d046581_T015:5
Zm00001d046581_T019:5
Zm00001d046581_T010:5
Zm00001d046581_T021:5
Zm00001d046581_T014:5
Zm00001d046581_T005:5
Zm00001d046581_T009:5
Zm00001d046581_T017:5
Zm00001d046581_T011:5
Zm00001d046581_T024:5
Zm00001d046581_T018:5
Zm00001d046581_T004:5
Zm00001d046581_T020:5
Zm00001d046581_T012:5
Zm00001d046581_T002:5
Zm00001d046581_T001:5
Zm00001d046581_T016:5
Zm00001d046581_T008:5
Zm00001d046581_T006:5
Zm00001d046581_T022:5

General Information
CircRNA Name	Zm00001d046581_circ_g.1
ID in PlantcircBase	zma_circ_009994
Alias	Zm09circ00052
Organism	Zea mays
Position	chr9: 96884838-96886250 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d046581
Parent gene annotation	Isoleucine--tRNA ligase cytoplasmic
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	leaf, endosperm
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	CT-AC 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	Zm00001d046581_T003:5 Zm00001d046581_T015:5 Zm00001d046581_T019:5 Zm00001d046581_T010:5 Zm00001d046581_T021:5 Zm00001d046581_T014:5 Zm00001d046581_T005:5 Zm00001d046581_T009:5 Zm00001d046581_T017:5 Zm00001d046581_T011:5 Zm00001d046581_T024:5 Zm00001d046581_T018:5 Zm00001d046581_T004:5 Zm00001d046581_T020:5 Zm00001d046581_T012:5 Zm00001d046581_T002:5 Zm00001d046581_T001:5 Zm00001d046581_T016:5 Zm00001d046581_T008:5 Zm00001d046581_T006:5 Zm00001d046581_T022:5

			
						 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  
						
							TTTCTTACCATCCTCAGCCAAGACAAGCCCATTGCATATAAGATTCTTAAATGCAGGCTTCCCA
AACAGTGCTGTTGAGAGAACCATCAGAGTATAGAACctcgccagttgtggaagggaacttgcaa
aagtggatgctctcctcagaattacttgacaccttccgcaaattttgataaagaacttcagtaa
agaatggt

									
								

					

						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: 721
Transcript exons: 96884838-96884975,96885297-96885422,96885511-96885723,96
885894-96885977,96886091-96886250
CTCGCCAGTTGTGGAAGGGAACTTGCAAAAGTGGATGCTCTCCTCAGAATTACTTGACACCTTC
CGCAAATTTTGATAAAGAACTTCAGTAAAGAATGGTGTAAATGGAGCCATCACCACGCAAGTTG
TTACAAGAACATGGTAGAGTGTTGAAAGAGAAATTCTGCAGTCTTCTTCTCCAGTACGCCCTTT
GAACCGTTTGCGGTTCAAACGCACATATATGTTAGTAAGATAGTCAATGTATTTTACCAAATAC
GGCACAACCGTGTAAAGCCGATATGCATCCATCTCCTGGTGAACAAAGCTAACTAGACTTTCAG
TTGCAGAGTTTATCCAGTGATCCAACACATTGGATGACTTCAGAAGTACCACTTGTTCCATCGG
AGAAAATGAGGCAAGACCCTCAACTTCCAGTCTCTTTGCATTTTGGACAAAAAATCTATATGCG
TTATACCATGGGAGGAAGACATCTTTCACAACAGCAAAGACACCAGTACGTTTGAATCGTAGAG
ACTCTGCACGTACAACTGGGGAGTTTACCAAATATAGTCGCAGAGCATCCGCTCCAAACTCATC
AATGAGATCCTTGGGTGGAGGATAGTTCTTTTTACTCTTGCTCATTTTCTTACCATCCTCAGCC
AAGACAAGCCCATTGCATATAAGATTCTTAAATGCAGGCTTCCCAAACAGTGCTGTTGAGAGAA
CCATCAGAGTATAGAAC
						
					

						Genomic sequence
						
							CTCGCCAGTTGTGGAAGGGAACTTGCAAAAGTGGATGCTCTCCTCAGAATTACTTGACACCTTC
CGCAAATTTTGATAAAGAACTTCAGTAAAGAATGGTGTAAATGGAGCCATCACCACGCAAGTTG
TTACAAGAACCTGCATTTTCATAATTCGGGTATCTTATAAGCAATTGCAGAAAGAACCAGCAAG
AAATAAAAAAACGAAGTATGCATGATTGGGAGCTTTAAATATTTGAAGGTACAGAAATGATGAA
ACGCATGATATTTGGTTTCCAGGATTGTTTCAGATGTTCAGATTAACATATCACAGTGAAGCAA
AACAACAGAATCACCGCAGTACCACCCTAACTATACAAATTATGTATGAGCTTGCTTTAAAATA
CCATTTTCAGTAATATATAAACACTTTGCAGCAGCACTGACCAGATGAAGTGCATGCTACATGA
TATATACTTACATGGTAGAGTGTTGAAAGAGAAATTCTGCAGTCTTCTTCTCCAGTACGCCCTT
TGAACCGTTTGCGGTTCAAACGCACATATATGTTAGTAAGATAGTCAATGTATTTTACCAAATA
CGGCACAACCTGCAGGAGTAATTATATCAAATGATCATAACACAGAAAGATCTTACAAGGGAAC
TAATATCCAGAAAAAACTGTGAAAGCATTCAACCGTGTAAAGCCGATATGCATCCATCTCCTGG
TGAACAAAGCTAACTAGACTTTCAGTTGCAGAGTTTATCCAGTGATCCAACACATTGGATGACT
TCAGAAGTACCACTTGTTCCATCGGAGAAAATGAGGCAAGACCCTCAACTTCCAGTCTCTTTGC
ATTTTGGACAAAAAATCTATATGCGTTATACCATGGGAGGAAGACATCTTTCACCTGATAAATT
AAAGCATGTCAAATTGTGGGTCAGATTGGGGGCCATGCCCTTTTCCTCAAGATAGCAAAAAATG
ATAGCTTTGGGTAAATAATATCATGTGATCTATGTATACCAGTAGCCTGACCAAAAGATAATAA
GGAAACACGGAACTTAAAATAAATTAACTTACAACAGCAAAGACACCAGTACGTTTGAATCGTA
GAGACTCTGCACGTACAACTGGGGAGTTTACCAAATATAGTCGCAGAGCATCCTGAAACAGAAC
AGAATTCATTCTAACTACAAATTCTAACACCGAGTCTGTTGCATGTATCTTTCAGTAATAGCCA
TTGGCTTATTCAAAGCAAGCAGCCAGGCATCACATACCGCTCCAAACTCATCAATGAGATCCTT
GGGTGGAGGATAGTTCTTTTTACTCTTGCTCATTTTCTTACCATCCTCAGCCAAGACAAGCCCA
TTGCATATAAGATTCTTAAATGCAGGCTTCCCAAACAGTGCTGTTGAGAGAACCATCAGAGTAT
AGAAC
						
					

			
		

Sequences
Splice junction sequence	TTTCTTACCATCCTCAGCCAAGACAAGCCCATTGCATATAAGATTCTTAAATGCAGGCTTCCCA AACAGTGCTGTTGAGAGAACCATCAGAGTATAGAACctcgccagttgtggaagggaacttgcaa aagtggatgctctcctcagaattacttgacaccttccgcaaattttgataaagaacttcagtaa agaatggt
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: 721 Transcript exons: 96884838-96884975,96885297-96885422,96885511-96885723,96 885894-96885977,96886091-96886250 CTCGCCAGTTGTGGAAGGGAACTTGCAAAAGTGGATGCTCTCCTCAGAATTACTTGACACCTTC CGCAAATTTTGATAAAGAACTTCAGTAAAGAATGGTGTAAATGGAGCCATCACCACGCAAGTTG TTACAAGAACATGGTAGAGTGTTGAAAGAGAAATTCTGCAGTCTTCTTCTCCAGTACGCCCTTT GAACCGTTTGCGGTTCAAACGCACATATATGTTAGTAAGATAGTCAATGTATTTTACCAAATAC GGCACAACCGTGTAAAGCCGATATGCATCCATCTCCTGGTGAACAAAGCTAACTAGACTTTCAG TTGCAGAGTTTATCCAGTGATCCAACACATTGGATGACTTCAGAAGTACCACTTGTTCCATCGG AGAAAATGAGGCAAGACCCTCAACTTCCAGTCTCTTTGCATTTTGGACAAAAAATCTATATGCG TTATACCATGGGAGGAAGACATCTTTCACAACAGCAAAGACACCAGTACGTTTGAATCGTAGAG ACTCTGCACGTACAACTGGGGAGTTTACCAAATATAGTCGCAGAGCATCCGCTCCAAACTCATC AATGAGATCCTTGGGTGGAGGATAGTTCTTTTTACTCTTGCTCATTTTCTTACCATCCTCAGCC AAGACAAGCCCATTGCATATAAGATTCTTAAATGCAGGCTTCCCAAACAGTGCTGTTGAGAGAA CCATCAGAGTATAGAAC
Genomic sequence	CTCGCCAGTTGTGGAAGGGAACTTGCAAAAGTGGATGCTCTCCTCAGAATTACTTGACACCTTC CGCAAATTTTGATAAAGAACTTCAGTAAAGAATGGTGTAAATGGAGCCATCACCACGCAAGTTG TTACAAGAACCTGCATTTTCATAATTCGGGTATCTTATAAGCAATTGCAGAAAGAACCAGCAAG AAATAAAAAAACGAAGTATGCATGATTGGGAGCTTTAAATATTTGAAGGTACAGAAATGATGAA ACGCATGATATTTGGTTTCCAGGATTGTTTCAGATGTTCAGATTAACATATCACAGTGAAGCAA AACAACAGAATCACCGCAGTACCACCCTAACTATACAAATTATGTATGAGCTTGCTTTAAAATA CCATTTTCAGTAATATATAAACACTTTGCAGCAGCACTGACCAGATGAAGTGCATGCTACATGA TATATACTTACATGGTAGAGTGTTGAAAGAGAAATTCTGCAGTCTTCTTCTCCAGTACGCCCTT TGAACCGTTTGCGGTTCAAACGCACATATATGTTAGTAAGATAGTCAATGTATTTTACCAAATA CGGCACAACCTGCAGGAGTAATTATATCAAATGATCATAACACAGAAAGATCTTACAAGGGAAC TAATATCCAGAAAAAACTGTGAAAGCATTCAACCGTGTAAAGCCGATATGCATCCATCTCCTGG TGAACAAAGCTAACTAGACTTTCAGTTGCAGAGTTTATCCAGTGATCCAACACATTGGATGACT TCAGAAGTACCACTTGTTCCATCGGAGAAAATGAGGCAAGACCCTCAACTTCCAGTCTCTTTGC ATTTTGGACAAAAAATCTATATGCGTTATACCATGGGAGGAAGACATCTTTCACCTGATAAATT AAAGCATGTCAAATTGTGGGTCAGATTGGGGGCCATGCCCTTTTCCTCAAGATAGCAAAAAATG ATAGCTTTGGGTAAATAATATCATGTGATCTATGTATACCAGTAGCCTGACCAAAAGATAATAA GGAAACACGGAACTTAAAATAAATTAACTTACAACAGCAAAGACACCAGTACGTTTGAATCGTA GAGACTCTGCACGTACAACTGGGGAGTTTACCAAATATAGTCGCAGAGCATCCTGAAACAGAAC AGAATTCATTCTAACTACAAATTCTAACACCGAGTCTGTTGCATGTATCTTTCAGTAATAGCCA TTGGCTTATTCAAAGCAAGCAGCCAGGCATCACATACCGCTCCAAACTCATCAATGAGATCCTT GGGTGGAGGATAGTTCTTTTTACTCTTGCTCATTTTCTTACCATCCTCAGCCAAGACAAGCCCA TTGCATATAAGATTCTTAAATGCAGGCTTCCCAAACAGTGCTGTTGAGAGAACCATCAGAGTAT AGAAC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.191563327

Conservation Information
Conserved circRNAs	NA
PMCS	0.191563327

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							96886202-96884910(+)
96886239-96886199(-)
						
						Potential amino acid sequence
						
							MQASQTVLLREPSEYRTSPVVEGNLQKWMLSSELLDTFRKF*(+)
MVLSTALFGKPAFKNLICNGLVLAEDGKKMSKSKKNYPPPKDLIDEFGADALRLYLVNSPVVRA
ESLRFKRTGVFAVVKDVFLPWYNAYRFFVQNAKRLEVEGLASFSPMEQVVLLKSSNVLDHWINS
ATESLVSFVHQEMDAYRLYTVVPYLVKYIDYLTNIYVRLNRKRFKGRTGEEDCRISLSTLYHVL
VTTCVVMAPFTPFFTEVLYQNLRKVSSNSEESIHFCKFPSTTGEVLYSDGSLNSTVWEACI*(-
)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	96886202-96884910(+) 96886239-96886199(-)
Potential amino acid sequence	MQASQTVLLREPSEYRTSPVVEGNLQKWMLSSELLDTFRKF(+) MVLSTALFGKPAFKNLICNGLVLAEDGKKMSKSKKNYPPPKDLIDEFGADALRLYLVNSPVVRA ESLRFKRTGVFAVVKDVFLPWYNAYRFFVQNAKRLEVEGLASFSPMEQVVLLKSSNVLDHWINS ATESLVSFVHQEMDAYRLYTVVPYLVKYIDYLTNIYVRLNRKRFKGRTGEEDCRISLSTLYHVL VTTCVVMAPFTPFFTEVLYQNLRKVSSNSEESIHFCKFPSTTGEVLYSDGSLNSTVWEACI(- )
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d046581_circ_g.1

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