Plant Circular RNA Database

Detail information of Zm00001d049543_circ_g.8

			
						 General Information
					
						CircRNA Name
						Zm00001d049543_circ_g.8
					
						ID in PlantcircBase
						zma_circ_008015
					
						Alias
						Zm04circ00024, GRMZM2G014902_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 34084649-34085777  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d049543						
					
						Parent gene annotation
						
							 circadian clock associated1
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d049543_circ_g.3 Zm00001d049543_circ_g.4 Zm00001d049543_circ_g.5 Zm00001d049543_circ_g.6 Zm00001d049543_circ_g.7 Zm00001d049543_circ_g.9 						
					
						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  
						
							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
						Zm00001d049543_T012:4
Zm00001d049543_T003:3
Zm00001d049543_T016:4
Zm00001d049543_T007:3
Zm00001d049543_T002:4
Zm00001d049543_T009:4
Zm00001d049543_T015:4
Zm00001d049543_T013:4
Zm00001d049543_T005:4
Zm00001d049543_T011:4
Zm00001d049543_T001:3
Zm00001d049543_T010:4
Zm00001d049543_T014:4

General Information
CircRNA Name	Zm00001d049543_circ_g.8
ID in PlantcircBase	zma_circ_008015
Alias	Zm04circ00024, GRMZM2G014902_C2
Organism	Zea mays
Position	chr4: 34084649-34085777 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d049543
Parent gene annotation	circadian clock associated1
Parent gene strand	+
Alternative splicing	Zm00001d049543_circ_g.3 Zm00001d049543_circ_g.4 Zm00001d049543_circ_g.5 Zm00001d049543_circ_g.6 Zm00001d049543_circ_g.7 Zm00001d049543_circ_g.9
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	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	Zm00001d049543_T012:4 Zm00001d049543_T003:3 Zm00001d049543_T016:4 Zm00001d049543_T007:3 Zm00001d049543_T002:4 Zm00001d049543_T009:4 Zm00001d049543_T015:4 Zm00001d049543_T013:4 Zm00001d049543_T005:4 Zm00001d049543_T011:4 Zm00001d049543_T001:3 Zm00001d049543_T010:4 Zm00001d049543_T014:4

			
						 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  
						
							CTTTGTTTTGTTTGTTTGGCTTCTGAGTTGCTCCATAGAGCATGTTGGGACAAAGACAGCCGTG
CAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAGagtaacagaaattggatcaattcaagta
ggtgagtgtaattgatccttttgaagattctgatcccagattaattcacgactagagttgtgaa
ctctatag

									
								

					

						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: 569
Transcript exons: 34084649-34085043,34085112-34085223,34085716-34085777
AGTAACAGAAATTGGATCAATTCAAGTAGGTGAGTGTAATTGATCCTTTTGAAGATTCTGATCC
CAGATTAATTCACGACTAGAGTTGTGAACTCTATAGGTTTTCTTGTGTAAATTTAACACTAATT
TGGCTGCTCTTTGGGTCTGGGGGCACAAATTTGAAATATTGGGAGTGCTGGTGTGATATAGAGG
TCTAGGAGGAGATATGAGGTACTACTTGCGTCAGGTCCAGCGTTTGGTTGGAGATATGGAAGGA
GGAGCTCTCTTGTTTATAGACGACCTCAACTCCAAGTGACAAAGCGAACAGCTGTTGAACGTTT
CCCTTCTATTTCTGTTTCTTTTTGCCGGATTTGGAGATGGAGGTGAATTCCTCTGGCGAGGAAA
CTGTGGTAAAGGTAAGAAAGCCGTACACAATAACGAAGCAGCGGGAGCGGTGGACAGAGGCTGA
ACACAAACGGTTCCTTGAAGCCTTGAAACTTTATGGCAGAGCATGGCAGCGCATAGAAGAGCAT
GTTGGGACAAAGACAGCCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAG
						
					

						Genomic sequence
						
							AGTAACAGAAATTGGATCAATTCAAGTAGGTGAGTGTAATTGATCCTTTTGAAGATTCTGATCC
CAGATTAATTCACGACTAGAGTTGTGAACTCTATAGGTTTTCTTGTGTAAATTTAACACTAATT
TGGCTGCTCTTTGGGTCTGGGGGCACAAATTTGAAATATTGGGAGTGCTGGTGTGATATAGAGG
TCTAGGAGGAGATATGAGGTACTACTTGCGTCAGGTCCAGCGTTTGGTTGGAGATATGGAAGGA
GGAGCTCTCTTGTTTATAGACGACCTCAACTCCAAGTGACAAAGCGAACAGCTGTTGAACGTTT
CCCTTCTATTTCTGTTTCTTTTTGCCGGATTTGGAGATGGAGGTGAATTCCTCTGGCGAGGAAA
CTGTGGTAAAGGTGAGTTGTTATATAATGTGCTTGTTGATTCTGGTAAAGAAGGAACATTTTAT
CATTGTTCTTTGTAGGTAAGAAAGCCGTACACAATAACGAAGCAGCGGGAGCGGTGGACAGAGG
CTGAACACAAACGGTTCCTTGAAGCCTTGAAACTTTATGGCAGAGCATGGCAGCGCATAGAAGG
TAAAATCTCTACCGTTTGTTTCGTTGGAATTGAATTCCATTCTTATAATCATAATTTAGACACA
AACTAATTAAGTTAATATATTTGTATATTATCCTAAATCATATGAGAGAGATAGTTATACACTA
CACTTATGCTATAGAGAAGCAAGTAGAAGAGTATGTTATAAGTTATACATTAGAAAAATATCAT
GTAAAACTATAGAATCAATTTCCATCTCTTACCCTATGAATTTGATATGGACTTATATATAAAC
TTGGGAAACTTGTGGAATGTTACATTCTAAAAAATAGCCTACTCCATTAGTTAGATTCCAATTC
TTAAAATGAAGGGAAACAAACGGAGCCTAAGCGATTATATCCAAGTAGTTTTATGCTATTGTTT
TCTGACTTCATCAATCTGTAACCACTGAGGTTTATTCATGTCGATTTAGTTTGCTTTATACTGA
TTGCACTTTGTTTTGTTTGTTTGGCTTCTGAGTTGCTCCATAGAGCATGTTGGGACAAAGACAG
CCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAG
						
					

			
		

Sequences
Splice junction sequence	CTTTGTTTTGTTTGTTTGGCTTCTGAGTTGCTCCATAGAGCATGTTGGGACAAAGACAGCCGTG CAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAGagtaacagaaattggatcaattcaagta ggtgagtgtaattgatccttttgaagattctgatcccagattaattcacgactagagttgtgaa ctctatag
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: 569 Transcript exons: 34084649-34085043,34085112-34085223,34085716-34085777 AGTAACAGAAATTGGATCAATTCAAGTAGGTGAGTGTAATTGATCCTTTTGAAGATTCTGATCC CAGATTAATTCACGACTAGAGTTGTGAACTCTATAGGTTTTCTTGTGTAAATTTAACACTAATT TGGCTGCTCTTTGGGTCTGGGGGCACAAATTTGAAATATTGGGAGTGCTGGTGTGATATAGAGG TCTAGGAGGAGATATGAGGTACTACTTGCGTCAGGTCCAGCGTTTGGTTGGAGATATGGAAGGA GGAGCTCTCTTGTTTATAGACGACCTCAACTCCAAGTGACAAAGCGAACAGCTGTTGAACGTTT CCCTTCTATTTCTGTTTCTTTTTGCCGGATTTGGAGATGGAGGTGAATTCCTCTGGCGAGGAAA CTGTGGTAAAGGTAAGAAAGCCGTACACAATAACGAAGCAGCGGGAGCGGTGGACAGAGGCTGA ACACAAACGGTTCCTTGAAGCCTTGAAACTTTATGGCAGAGCATGGCAGCGCATAGAAGAGCAT GTTGGGACAAAGACAGCCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAG
Genomic sequence	AGTAACAGAAATTGGATCAATTCAAGTAGGTGAGTGTAATTGATCCTTTTGAAGATTCTGATCC CAGATTAATTCACGACTAGAGTTGTGAACTCTATAGGTTTTCTTGTGTAAATTTAACACTAATT TGGCTGCTCTTTGGGTCTGGGGGCACAAATTTGAAATATTGGGAGTGCTGGTGTGATATAGAGG TCTAGGAGGAGATATGAGGTACTACTTGCGTCAGGTCCAGCGTTTGGTTGGAGATATGGAAGGA GGAGCTCTCTTGTTTATAGACGACCTCAACTCCAAGTGACAAAGCGAACAGCTGTTGAACGTTT CCCTTCTATTTCTGTTTCTTTTTGCCGGATTTGGAGATGGAGGTGAATTCCTCTGGCGAGGAAA CTGTGGTAAAGGTGAGTTGTTATATAATGTGCTTGTTGATTCTGGTAAAGAAGGAACATTTTAT CATTGTTCTTTGTAGGTAAGAAAGCCGTACACAATAACGAAGCAGCGGGAGCGGTGGACAGAGG CTGAACACAAACGGTTCCTTGAAGCCTTGAAACTTTATGGCAGAGCATGGCAGCGCATAGAAGG TAAAATCTCTACCGTTTGTTTCGTTGGAATTGAATTCCATTCTTATAATCATAATTTAGACACA AACTAATTAAGTTAATATATTTGTATATTATCCTAAATCATATGAGAGAGATAGTTATACACTA CACTTATGCTATAGAGAAGCAAGTAGAAGAGTATGTTATAAGTTATACATTAGAAAAATATCAT GTAAAACTATAGAATCAATTTCCATCTCTTACCCTATGAATTTGATATGGACTTATATATAAAC TTGGGAAACTTGTGGAATGTTACATTCTAAAAAATAGCCTACTCCATTAGTTAGATTCCAATTC TTAAAATGAAGGGAAACAAACGGAGCCTAAGCGATTATATCCAAGTAGTTTTATGCTATTGTTT TCTGACTTCATCAATCTGTAACCACTGAGGTTTATTCATGTCGATTTAGTTTGCTTTATACTGA TTGCACTTTGTTTTGTTTGTTTGGCTTCTGAGTTGCTCCATAGAGCATGTTGGGACAAAGACAG CCGTGCAGATCAGAAGTCACGCTCAAAAGTTCTTCACTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.274751246

Conservation Information
Conserved circRNAs	NA
PMCS	0.274751246

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							34085720-34084688(+)
34085006-34084678(+)
						
						Potential amino acid sequence
						
							MLGQRQPCRSEVTLKSSSLRVTEIGSIQVGECN*(+)
MEVNSSGEETVVKVRKPYTITKQRERWTEAEHKRFLEALKLYGRAWQRIEEHVGTKTAVQIRSH
AQKFFTKSNRNWINSSR*(+)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	34085720-34084688(+) 34085006-34084678(+)
Potential amino acid sequence	MLGQRQPCRSEVTLKSSSLRVTEIGSIQVGECN(+) MEVNSSGEETVVKVRKPYTITKQRERWTEAEHKRFLEALKLYGRAWQRIEEHVGTKTAVQIRSH AQKFFTKSNRNWINSSR(+)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020;Zhang et al., 2019

circRNA

Detail information of Zm00001d049543_circ_g.8

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