Plant Circular RNA Database

Detail information of Zm00001d004559_circ_g.2

			
						 General Information
					
						CircRNA Name
						Zm00001d004559_circ_g.2
					
						ID in PlantcircBase
						zma_circ_007254
					
						Alias
						zma_circ_0000778, GRMZM2G165597_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr2: 118073879-118076104  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d004559						
					
						Parent gene annotation
						
							Leucine-rich repeat protein kinase family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d004559_circ_g.1 						
					
						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
						Zm00001d004559_T003:2
Zm00001d004559_T011:3
Zm00001d004559_T025:3
Zm00001d004559_T022:3
Zm00001d004559_T009:3
Zm00001d004559_T027:3
Zm00001d004559_T023:4
Zm00001d004559_T021:3
Zm00001d004559_T005:3
Zm00001d004559_T006:3
Zm00001d004559_T016:3
Zm00001d004559_T024:3
Zm00001d004559_T010:3
Zm00001d004559_T017:3
Zm00001d004559_T001:3
Zm00001d004559_T008:3
Zm00001d004559_T004:3
Zm00001d004559_T002:3
Zm00001d004559_T018:3
Zm00001d004559_T020:4
Zm00001d004559_T026:2
Zm00001d004559_T007:3
Zm00001d004559_T028:3

General Information
CircRNA Name	Zm00001d004559_circ_g.2
ID in PlantcircBase	zma_circ_007254
Alias	zma_circ_0000778, GRMZM2G165597_C1
Organism	Zea mays
Position	chr2: 118073879-118076104 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d004559
Parent gene annotation	Leucine-rich repeat protein kinase family protein
Parent gene strand	+
Alternative splicing	Zm00001d004559_circ_g.1
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	Zm00001d004559_T003:2 Zm00001d004559_T011:3 Zm00001d004559_T025:3 Zm00001d004559_T022:3 Zm00001d004559_T009:3 Zm00001d004559_T027:3 Zm00001d004559_T023:4 Zm00001d004559_T021:3 Zm00001d004559_T005:3 Zm00001d004559_T006:3 Zm00001d004559_T016:3 Zm00001d004559_T024:3 Zm00001d004559_T010:3 Zm00001d004559_T017:3 Zm00001d004559_T001:3 Zm00001d004559_T008:3 Zm00001d004559_T004:3 Zm00001d004559_T002:3 Zm00001d004559_T018:3 Zm00001d004559_T020:4 Zm00001d004559_T026:2 Zm00001d004559_T007:3 Zm00001d004559_T028:3

			
						 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  
						
							AGGTTCTAAGGAATTCTTCACAGAGATAGAGTTGCTATCGAGGCTGCATCACCGTAATCTAGTC
TCTTTGCTCGGTTATTGTGATGAAGATGATGAACAGattacatggaaacccagtatgcattggg
caaaaccaactgaatatttctcagtattgtcagtcaggaacatatgttgcacgtggaggttcag
cagataac

									
								

					

						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: 928
Transcript exons: 118073879-118074369,118075459-118075611,118075821-118076
104
ATTACATGGAAACCCAGTATGCATTGGGCAAAACCAACTGAATATTTCTCAGTATTGTCAGTCA
GGAACATATGTTGCACGTGGAGGTTCAGCAGATAACAGTACAGTTTGTCCACCATGCTCTAGCG
ACTTTCCTTTTGAAAGAATACCGATGTCACCAATACCATGCTCATGTGTCGTTCCAGTTTATGT
GGGTTACCGGCTTAAGAGTCCTGGGTTCTCAAATTTCATTCCATACGAATCCCAGTTCCAGCAG
TACTTAACATCTGGGCTTTCACTGTCATCGTACCAATTAGAAGTTTCTACTTTTATGTGGGAAG
AAGGCCCAAGGCTGAAGATGGACCTGAAAATATTTCCAAATAACACTCCCTTTTTCACTGTAAG
TGAGGTGTTCAGGCTTAATGGTATGTTCACAGCTTGGCAGATTGCAGACTCTGATATATTTGGC
CCATATGAACTTATCAGCTTCAACCAAGGGTGGTACAACACAATAATACCACAGGGTACAAAGT
CTGGTCTGAGTACAGGTGCCATTGTTGGGGTGGTCATGGCGGCATTTGTTGCAGCTGCCATTCT
TTCATCCCTCGTTACTATCATCATATTGCGGAGACGCTCAAGACAGTCTTCTTCAAATAAACGC
ACCGCGAAAAGAATTTCAATGAAAATTGCTGGTGTAAAAGACTTCACTTTTGATGAATTGTCAC
ATTGTACACATGACTTTAATGATTCAACACTAATTGGCCAAGGAGGGTATGGCAAGGTATACAG
AGGTGTGTTGGCTGATGGAATAGTAGTAGCAATAAAGCGAGCACAGCAAGGGTCTCTTCAAGGT
TCTAAGGAATTCTTCACAGAGATAGAGTTGCTATCGAGGCTGCATCACCGTAATCTAGTCTCTT
TGCTCGGTTATTGTGATGAAGATGATGAACAG
						
					

						Genomic sequence
						
							ATTACATGGAAACCCAGTATGCATTGGGCAAAACCAACTGAATATTTCTCAGTATTGTCAGTCA
GGAACATATGTTGCACGTGGAGGTTCAGCAGATAACAGTACAGTTTGTCCACCATGCTCTAGCG
ACTTTCCTTTTGAAAGAATACCGATGTCACCAATACCATGCTCATGTGTCGTTCCAGTTTATGT
GGGTTACCGGCTTAAGAGTCCTGGGTTCTCAAATTTCATTCCATACGAATCCCAGTTCCAGCAG
TACTTAACATCTGGGCTTTCACTGTCATCGTACCAATTAGAAGTTTCTACTTTTATGTGGGAAG
AAGGCCCAAGGCTGAAGATGGACCTGAAAATATTTCCAAATAACACTCCCTTTTTCACTGTAAG
TGAGGTGTTCAGGCTTAATGGTATGTTCACAGCTTGGCAGATTGCAGACTCTGATATATTTGGC
CCATATGAACTTATCAGCTTCAACCAAGGGTGGTACAACACAAGTATGATATATCTTCTCTTAT
TTTTATTTCTGTATTGTCCATTTATTGGAGGACTCTATTAGAGCATTTATGAGTTTTTTTCTGA
ACGCAATTAAGAAAAAAATAGAATGAACTCGGTTTGTAAGGAAAGCCAGGCCTATAAACCTCGC
AGCTCACAATTTATTGAAGGAAAATTAACGAAAAACTAAACACGACAACCCTGACGATTAACTC
TAAGAAACCCACCACACGTCATTGTTGCCAAGCTTATCACACAAAAGCGATAAGCAGGTCTGAC
TTCCACGGCCGAAGCCCTAACATGTCACCACCTACTCACAACAAGCCTATTAGCCTCCAAAAGT
GGACACACCATGTCACCACTCAACGCTAGATGTGGCATGCGCTGTCCACCCGCAGCAGACCACA
GCCTGGATGAAGCCATGGCCTGCACCGGCGACCAGCGACGTCGGGCCAGATCTGCAACCATCCA
GCCACCAAACAACCGCAGCTCGCCGGACTTCCGGCCAGCAGCAGCGGCAGCACGATCTGGAGTG
AATGACAACATTTATGAGTTTTAACCATCATAAGGATGCCTGATGCAGTTAAACTTGAATCTAA
CCAGTAACTGTGATAACGTATGTGTGAGCAAGTTATGAAAAGATGTTTATAATAATAGGCCTAT
CTACTCTTGTGCTTAGCTTCTTAGCTGCTACTCCACATTGGTAAGAAAATTGCCTCTGTAGAAT
GTCCATTGGTGAACGTGTTAAGTTTGGTCATTTGGGGCGGTGGTGATTGGTGGATACCGAACTC
AACTGCAGGGTTAATTCTTTTAAAATATTTGGAGGTTTACAGTTTTCTCATAAATATTTTATAT
TATAGAAACATTTTTACAAAAACCTTCAGGTATGAGCCTAAAAGTTACAATATTTGAGGTTTGA
ATGTGTTATGGCACTGATATGACGCTGTTGGTCAAACATGCCTACAAAAGTTAGTGTTATGGAA
AAGTTTACCGACCATTTTTTGCATATTCTAGAAAATCCATTTGAATTTCCACAATCTTAGCAAG
TCTAGAAGATAAAGGTCTCACCTGTTCTTATGCTATCTTTCCAGTAATACCACAGGGTACAAAG
TCTGGTCTGAGTACAGGTGCCATTGTTGGGGTGGTCATGGCGGCATTTGTTGCAGCTGCCATTC
TTTCATCCCTCGTTACTATCATCATATTGCGGAGACGCTCAAGACAGTCTTCTTCAAATAAACG
CACCGGTAAACACTCCACCTCTACTTTCTATGTTTTTAATAAACAATTAAAAAAGTTAGAATTA
TCATTTTTTTCTGAAAATTGTAAGTGTTCCAATTTCCCTCCTCTGCATTAATTTATTTACTATT
TTAGTAGGACTTACTGTCCATAAAACAATGCCCTTTCCATACAAGTTATGTACTGTTCAAATGA
CAAGCTTTTATTGTCATTGTAGCGAAAAGAATTTCAATGAAAATTGCTGGTGTAAAAGACTTCA
CTTTTGATGAATTGTCACATTGTACACATGACTTTAATGATTCAACACTAATTGGCCAAGGAGG
GTATGGCAAGGTATACAGAGGTGTGTTGGCTGATGGAATAGTAGTAGCAATAAAGCGAGCACAG
CAAGGGTCTCTTCAAGGTTCTAAGGAATTCTTCACAGAGATAGAGTTGCTATCGAGGCTGCATC
ACCGTAATCTAGTCTCTTTGCTCGGTTATTGTGATGAAGATGATGAACAG
						
					

			
		

Sequences
Splice junction sequence	AGGTTCTAAGGAATTCTTCACAGAGATAGAGTTGCTATCGAGGCTGCATCACCGTAATCTAGTC TCTTTGCTCGGTTATTGTGATGAAGATGATGAACAGattacatggaaacccagtatgcattggg caaaaccaactgaatatttctcagtattgtcagtcaggaacatatgttgcacgtggaggttcag cagataac
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: 928 Transcript exons: 118073879-118074369,118075459-118075611,118075821-118076 104 ATTACATGGAAACCCAGTATGCATTGGGCAAAACCAACTGAATATTTCTCAGTATTGTCAGTCA GGAACATATGTTGCACGTGGAGGTTCAGCAGATAACAGTACAGTTTGTCCACCATGCTCTAGCG ACTTTCCTTTTGAAAGAATACCGATGTCACCAATACCATGCTCATGTGTCGTTCCAGTTTATGT GGGTTACCGGCTTAAGAGTCCTGGGTTCTCAAATTTCATTCCATACGAATCCCAGTTCCAGCAG TACTTAACATCTGGGCTTTCACTGTCATCGTACCAATTAGAAGTTTCTACTTTTATGTGGGAAG AAGGCCCAAGGCTGAAGATGGACCTGAAAATATTTCCAAATAACACTCCCTTTTTCACTGTAAG TGAGGTGTTCAGGCTTAATGGTATGTTCACAGCTTGGCAGATTGCAGACTCTGATATATTTGGC CCATATGAACTTATCAGCTTCAACCAAGGGTGGTACAACACAATAATACCACAGGGTACAAAGT CTGGTCTGAGTACAGGTGCCATTGTTGGGGTGGTCATGGCGGCATTTGTTGCAGCTGCCATTCT TTCATCCCTCGTTACTATCATCATATTGCGGAGACGCTCAAGACAGTCTTCTTCAAATAAACGC ACCGCGAAAAGAATTTCAATGAAAATTGCTGGTGTAAAAGACTTCACTTTTGATGAATTGTCAC ATTGTACACATGACTTTAATGATTCAACACTAATTGGCCAAGGAGGGTATGGCAAGGTATACAG AGGTGTGTTGGCTGATGGAATAGTAGTAGCAATAAAGCGAGCACAGCAAGGGTCTCTTCAAGGT TCTAAGGAATTCTTCACAGAGATAGAGTTGCTATCGAGGCTGCATCACCGTAATCTAGTCTCTT TGCTCGGTTATTGTGATGAAGATGATGAACAG
Genomic sequence	ATTACATGGAAACCCAGTATGCATTGGGCAAAACCAACTGAATATTTCTCAGTATTGTCAGTCA GGAACATATGTTGCACGTGGAGGTTCAGCAGATAACAGTACAGTTTGTCCACCATGCTCTAGCG ACTTTCCTTTTGAAAGAATACCGATGTCACCAATACCATGCTCATGTGTCGTTCCAGTTTATGT GGGTTACCGGCTTAAGAGTCCTGGGTTCTCAAATTTCATTCCATACGAATCCCAGTTCCAGCAG TACTTAACATCTGGGCTTTCACTGTCATCGTACCAATTAGAAGTTTCTACTTTTATGTGGGAAG AAGGCCCAAGGCTGAAGATGGACCTGAAAATATTTCCAAATAACACTCCCTTTTTCACTGTAAG TGAGGTGTTCAGGCTTAATGGTATGTTCACAGCTTGGCAGATTGCAGACTCTGATATATTTGGC CCATATGAACTTATCAGCTTCAACCAAGGGTGGTACAACACAAGTATGATATATCTTCTCTTAT TTTTATTTCTGTATTGTCCATTTATTGGAGGACTCTATTAGAGCATTTATGAGTTTTTTTCTGA ACGCAATTAAGAAAAAAATAGAATGAACTCGGTTTGTAAGGAAAGCCAGGCCTATAAACCTCGC AGCTCACAATTTATTGAAGGAAAATTAACGAAAAACTAAACACGACAACCCTGACGATTAACTC TAAGAAACCCACCACACGTCATTGTTGCCAAGCTTATCACACAAAAGCGATAAGCAGGTCTGAC TTCCACGGCCGAAGCCCTAACATGTCACCACCTACTCACAACAAGCCTATTAGCCTCCAAAAGT GGACACACCATGTCACCACTCAACGCTAGATGTGGCATGCGCTGTCCACCCGCAGCAGACCACA GCCTGGATGAAGCCATGGCCTGCACCGGCGACCAGCGACGTCGGGCCAGATCTGCAACCATCCA GCCACCAAACAACCGCAGCTCGCCGGACTTCCGGCCAGCAGCAGCGGCAGCACGATCTGGAGTG AATGACAACATTTATGAGTTTTAACCATCATAAGGATGCCTGATGCAGTTAAACTTGAATCTAA CCAGTAACTGTGATAACGTATGTGTGAGCAAGTTATGAAAAGATGTTTATAATAATAGGCCTAT CTACTCTTGTGCTTAGCTTCTTAGCTGCTACTCCACATTGGTAAGAAAATTGCCTCTGTAGAAT GTCCATTGGTGAACGTGTTAAGTTTGGTCATTTGGGGCGGTGGTGATTGGTGGATACCGAACTC AACTGCAGGGTTAATTCTTTTAAAATATTTGGAGGTTTACAGTTTTCTCATAAATATTTTATAT TATAGAAACATTTTTACAAAAACCTTCAGGTATGAGCCTAAAAGTTACAATATTTGAGGTTTGA ATGTGTTATGGCACTGATATGACGCTGTTGGTCAAACATGCCTACAAAAGTTAGTGTTATGGAA AAGTTTACCGACCATTTTTTGCATATTCTAGAAAATCCATTTGAATTTCCACAATCTTAGCAAG TCTAGAAGATAAAGGTCTCACCTGTTCTTATGCTATCTTTCCAGTAATACCACAGGGTACAAAG TCTGGTCTGAGTACAGGTGCCATTGTTGGGGTGGTCATGGCGGCATTTGTTGCAGCTGCCATTC TTTCATCCCTCGTTACTATCATCATATTGCGGAGACGCTCAAGACAGTCTTCTTCAAATAAACG CACCGGTAAACACTCCACCTCTACTTTCTATGTTTTTAATAAACAATTAAAAAAGTTAGAATTA TCATTTTTTTCTGAAAATTGTAAGTGTTCCAATTTCCCTCCTCTGCATTAATTTATTTACTATT TTAGTAGGACTTACTGTCCATAAAACAATGCCCTTTCCATACAAGTTATGTACTGTTCAAATGA CAAGCTTTTATTGTCATTGTAGCGAAAAGAATTTCAATGAAAATTGCTGGTGTAAAAGACTTCA CTTTTGATGAATTGTCACATTGTACACATGACTTTAATGATTCAACACTAATTGGCCAAGGAGG GTATGGCAAGGTATACAGAGGTGTGTTGGCTGATGGAATAGTAGTAGCAATAAAGCGAGCACAG CAAGGGTCTCTTCAAGGTTCTAAGGAATTCTTCACAGAGATAGAGTTGCTATCGAGGCTGCATC ACCGTAATCTAGTCTCTTTGCTCGGTTATTGTGATGAAGATGATGAACAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.12173679

Conservation Information
Conserved circRNAs	NA
PMCS	0.12173679

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							118074031-118073974(+)
118076089-118073974(+)
118073904-118076065(-)
118073999-118076082(-)
						
						Potential amino acid sequence
						
							MSPIPCSCVVPVYVGYRLKSPGFSNFIPYESQFQQYLTSGLSLSSYQLEVSTFMWEEGPRLKMD
LKIFPNNTPFFTVSEVFRLNGMFTAWQIADSDIFGPYELISFNQGWYNTIIPQGTKSGLSTGAI
VGVVMAAFVAAAILSSLVTIIILRRRSRQSSSNKRTAKRISMKIAGVKDFTFDELSHCTHDFND
STLIGQGGYGKVYRGVLADGIVVAIKRAQQGSLQGSKEFFTEIELLSRLHHRNLVSLLGYCDED
DEQITWKPSMHWAKPTEYFSVLSVRNICCTWRFSR*(+)
MKMMNRLHGNPVCIGQNQLNISQYCQSGTYVARGGSADNSTVCPPCSSDFPFERIPMSPIPCSC
VVPVYVGYRLKSPGFSNFIPYESQFQQYLTSGLSLSSYQLEVSTFMWEEGPRLKMDLKIFPNNT
PFFTVSEVFRLNGMFTAWQIADSDIFGPYELISFNQGWYNTIIPQGTKSGLSTGAIVGVVMAAF
VAAAILSSLVTIIILRRRSRQSSSNKRTAKRISMKIAGVKDFTFDELSHCTHDFNDSTLIGQGG
YGKVYRGVLADGIVVAIKRAQQGSLQGSKEFFTEIELLSRLHHRNLVSLLGYCDEDDEQITWKP
SMHWAKPTEYFSVLSVRNICCTWRFSR*(+)
MHTGFPCNLFIIFITITEQRD*(-)
MVDKLYCYLLNLHVQHMFLTDNTEKYSVGFAQCILGFHVICSSSSSQ*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	118074031-118073974(+) 118076089-118073974(+) 118073904-118076065(-) 118073999-118076082(-)
Potential amino acid sequence	MSPIPCSCVVPVYVGYRLKSPGFSNFIPYESQFQQYLTSGLSLSSYQLEVSTFMWEEGPRLKMD LKIFPNNTPFFTVSEVFRLNGMFTAWQIADSDIFGPYELISFNQGWYNTIIPQGTKSGLSTGAI VGVVMAAFVAAAILSSLVTIIILRRRSRQSSSNKRTAKRISMKIAGVKDFTFDELSHCTHDFND STLIGQGGYGKVYRGVLADGIVVAIKRAQQGSLQGSKEFFTEIELLSRLHHRNLVSLLGYCDED DEQITWKPSMHWAKPTEYFSVLSVRNICCTWRFSR(+) MKMMNRLHGNPVCIGQNQLNISQYCQSGTYVARGGSADNSTVCPPCSSDFPFERIPMSPIPCSC VVPVYVGYRLKSPGFSNFIPYESQFQQYLTSGLSLSSYQLEVSTFMWEEGPRLKMDLKIFPNNT PFFTVSEVFRLNGMFTAWQIADSDIFGPYELISFNQGWYNTIIPQGTKSGLSTGAIVGVVMAAF VAAAILSSLVTIIILRRRSRQSSSNKRTAKRISMKIAGVKDFTFDELSHCTHDFNDSTLIGQGG YGKVYRGVLADGIVVAIKRAQQGSLQGSKEFFTEIELLSRLHHRNLVSLLGYCDEDDEQITWKP SMHWAKPTEYFSVLSVRNICCTWRFSR(+) MHTGFPCNLFIIFITITEQRD(-) MVDKLYCYLLNLHVQHMFLTDNTEKYSVGFAQCILGFHVICSSSSSQ(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

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

circRNA

Detail information of Zm00001d004559_circ_g.2

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