Plant Circular RNA Database

Detail information of Zm00001d043392_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d043392_circ_g.3
					
						ID in PlantcircBase
						zma_circ_007794
					
						Alias
						Zm03circ00088, zma_circ_0001273, GRMZM2G162175_C1
					
						Organism
						
							Zea mays						
					
						Position
						
							chr3: 198627180-198628662  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2, find_circ
					
						Parent gene
						
							Zm00001d043392						
					
						Parent gene annotation
						
							Plant cysteine oxidase 5
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d043392_circ_g.1 Zm00001d043392_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
						Zm00001d043392_T014:3
Zm00001d043392_T003:3
Zm00001d043392_T013:3
Zm00001d043392_T017:3
Zm00001d043392_T005:2
Zm00001d043392_T004:3
Zm00001d043392_T001:3
Zm00001d043392_T010:3
Zm00001d043392_T002:3
Zm00001d043392_T016:3
Zm00001d043392_T012:3
Zm00001d043392_T015:3
Zm00001d043392_T008:3
Zm00001d043392_T007:3
Zm00001d043392_T011:3
Zm00001d043392_T006:3
Zm00001d043392_T009:1

General Information
CircRNA Name	Zm00001d043392_circ_g.3
ID in PlantcircBase	zma_circ_007794
Alias	Zm03circ00088, zma_circ_0001273, GRMZM2G162175_C1
Organism	Zea mays
Position	chr3: 198627180-198628662 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2, find_circ
Parent gene	Zm00001d043392
Parent gene annotation	Plant cysteine oxidase 5
Parent gene strand	+
Alternative splicing	Zm00001d043392_circ_g.1 Zm00001d043392_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	Zm00001d043392_T014:3 Zm00001d043392_T003:3 Zm00001d043392_T013:3 Zm00001d043392_T017:3 Zm00001d043392_T005:2 Zm00001d043392_T004:3 Zm00001d043392_T001:3 Zm00001d043392_T010:3 Zm00001d043392_T002:3 Zm00001d043392_T016:3 Zm00001d043392_T012:3 Zm00001d043392_T015:3 Zm00001d043392_T008:3 Zm00001d043392_T007:3 Zm00001d043392_T011:3 Zm00001d043392_T006:3 Zm00001d043392_T009:1

			
						 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  
						
							CCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTGAATCTTATGACTGGG
TTGACATACCTGATCATCCAATTGATCAATTACAAAgtgcaaggataggcaacaagtgttcaaa
aacacgtctgtggatcaattgacttgtatttcagcctttcagttgaggattaaagtggaggttt
aagaagct

									
								

					

						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: 555
Transcript exons: 198627180-198627419,198628219-198628382,198628512-198628
662
GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCC
TTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCTTGAGAATTGGCATCATCTCAAGAATACA
TTGAAGTGCAAGATGCCAAAAATAAAGAGTCTATCTAATGCATGCCGAGTATCATTTTCTCCAG
AAGGTCCCATATCTGAAGAGGCGCTTGAGAGAGTCCGTGCACTGTTAGATATGATAAGACCTCT
AGATGTCGGCCTAGATAATGAAGCCCAAATTGCACGCAATTGGAGTAGTTCTACGCGTCCATCA
AATGGGAGACGAGGACGCAATGGGGCTAACCAGTTCGCGGCTCCAATCAAATATTTGCACATTC
ATGAATGTGAAAGCTTCTCTATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCA
TAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTGAATCTTAT
GACTGGGTTGACATACCTGATCATCCAATTGATCAATTACAAA
						
					

						Genomic sequence
						
							GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCC
TTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCTTGAGAATTGGCATCATCTCAAGAATACA
TTGAAGTGCAAGATGCCAAAAATAAAGAGTCTATCTAATGCATGCCGAGTATCATTTTCTCCAG
AAGGTCCCATATCTGAAGAGGCGCTTGAGAGAGTCCGTGCACTGTTAGGTGAGTCAAATTTGTT
TATATTCTGGAATGATTGGTATTGTTTACAATTGTCTAGTTGTGTTTTTCATAGTGAGCTTGAA
ATCAAATATTAAATTGTTTATATTTATTTTAATCTTTATTCTGGAATGATATCTTGTTAAATTG
AAAGTCAACCTGTTTGTGACCACCATGTTATATTTTTGCTGGTGATTTGTTTCTGGTGAACAAG
ACAATTCATGATCTTTTCTTTTATATGTTACTTCATAAACAGTGTCGTTTGCATGTTCTAGATC
AGTAACTTTCAATTGCTGGCATTGGTCAATTAGTTTAATTAATTTGTTTGTTGGTGGGTCAGAC
TGAAATTCATGGTGATGTTCCAACCCACTGTGAATAACTGATAACACAATTGAACTTGAACTGA
GTGCTGCCAGCTTTAGGTACGGGGAATTGCGTTCATAGTTTTGAATCTCTCGCCAAACAGACAA
TAGAGTTTTTTCAAAATATGTGGTTCAGGTGTTAATCTTTTGATGGGTTTATTTATGTTTTTCC
GCTGTAAGTAGTTCTGTATACTCAGTACTAAATGTTTATTTGATATATGATAGCAACAGGAGGA
TTCAATACAGCTGAATTCACTCCAAAAGGAAGCAACATCTTGGTTTATTAATTTCATTAAGGTG
TTTGTCTTGCATGAATGATATACAATTGTGTTCTGGCACTGCTGCGCTAAACTTTATTTCAGTT
CTAACATTGAGTTCTGATTGGTTCTATGAGATAAGAACATTGGCATACTTAAAAATATGACCCC
TGTTCCTTTTTGCAGATATGATAAGACCTCTAGATGTCGGCCTAGATAATGAAGCCCAAATTGC
ACGCAATTGGAGTAGTTCTACGCGTCCATCAAATGGGAGACGAGGACGCAATGGGGCTAACCAG
TTCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTGTAAGATCTCTTA
TTCATTCATTATTTTATTTCTATGTTTATTTGTGTGGTTTTCAGGAGGACAGATAAAGTGGTTT
CTCTGTGGTATTCACTGCGTTCAGGATTTACTAAATTTATGTGATTTTGCAGATGGGTATATTT
TGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGC
TTCTTTATGGACGTCTGCATGCTGAATCTTATGACTGGGTTGACATACCTGATCATCCAATTGA
TCAATTACAAA
						
					

			
		

Sequences
Splice junction sequence	CCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTGAATCTTATGACTGGG TTGACATACCTGATCATCCAATTGATCAATTACAAAgtgcaaggataggcaacaagtgttcaaa aacacgtctgtggatcaattgacttgtatttcagcctttcagttgaggattaaagtggaggttt aagaagct
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: 555 Transcript exons: 198627180-198627419,198628219-198628382,198628512-198628 662 GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCC TTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCTTGAGAATTGGCATCATCTCAAGAATACA TTGAAGTGCAAGATGCCAAAAATAAAGAGTCTATCTAATGCATGCCGAGTATCATTTTCTCCAG AAGGTCCCATATCTGAAGAGGCGCTTGAGAGAGTCCGTGCACTGTTAGATATGATAAGACCTCT AGATGTCGGCCTAGATAATGAAGCCCAAATTGCACGCAATTGGAGTAGTTCTACGCGTCCATCA AATGGGAGACGAGGACGCAATGGGGCTAACCAGTTCGCGGCTCCAATCAAATATTTGCACATTC ATGAATGTGAAAGCTTCTCTATGGGTATATTTTGTATGCCACCTTCTTCAGTTATCCCACTTCA TAATCATCCTGGAATGACTGTACTTAGCAAGCTTCTTTATGGACGTCTGCATGCTGAATCTTAT GACTGGGTTGACATACCTGATCATCCAATTGATCAATTACAAA
Genomic sequence	GTGCAAGGATAGGCAACAAGTGTTCAAAAACACGTCTGTGGATCAATTGACTTGTATTTCAGCC TTTCAGTTGAGGATTAAAGTGGAGGTTTAAGAAGCTTGAGAATTGGCATCATCTCAAGAATACA TTGAAGTGCAAGATGCCAAAAATAAAGAGTCTATCTAATGCATGCCGAGTATCATTTTCTCCAG AAGGTCCCATATCTGAAGAGGCGCTTGAGAGAGTCCGTGCACTGTTAGGTGAGTCAAATTTGTT TATATTCTGGAATGATTGGTATTGTTTACAATTGTCTAGTTGTGTTTTTCATAGTGAGCTTGAA ATCAAATATTAAATTGTTTATATTTATTTTAATCTTTATTCTGGAATGATATCTTGTTAAATTG AAAGTCAACCTGTTTGTGACCACCATGTTATATTTTTGCTGGTGATTTGTTTCTGGTGAACAAG ACAATTCATGATCTTTTCTTTTATATGTTACTTCATAAACAGTGTCGTTTGCATGTTCTAGATC AGTAACTTTCAATTGCTGGCATTGGTCAATTAGTTTAATTAATTTGTTTGTTGGTGGGTCAGAC TGAAATTCATGGTGATGTTCCAACCCACTGTGAATAACTGATAACACAATTGAACTTGAACTGA GTGCTGCCAGCTTTAGGTACGGGGAATTGCGTTCATAGTTTTGAATCTCTCGCCAAACAGACAA TAGAGTTTTTTCAAAATATGTGGTTCAGGTGTTAATCTTTTGATGGGTTTATTTATGTTTTTCC GCTGTAAGTAGTTCTGTATACTCAGTACTAAATGTTTATTTGATATATGATAGCAACAGGAGGA TTCAATACAGCTGAATTCACTCCAAAAGGAAGCAACATCTTGGTTTATTAATTTCATTAAGGTG TTTGTCTTGCATGAATGATATACAATTGTGTTCTGGCACTGCTGCGCTAAACTTTATTTCAGTT CTAACATTGAGTTCTGATTGGTTCTATGAGATAAGAACATTGGCATACTTAAAAATATGACCCC TGTTCCTTTTTGCAGATATGATAAGACCTCTAGATGTCGGCCTAGATAATGAAGCCCAAATTGC ACGCAATTGGAGTAGTTCTACGCGTCCATCAAATGGGAGACGAGGACGCAATGGGGCTAACCAG TTCGCGGCTCCAATCAAATATTTGCACATTCATGAATGTGAAAGCTTCTCTGTAAGATCTCTTA TTCATTCATTATTTTATTTCTATGTTTATTTGTGTGGTTTTCAGGAGGACAGATAAAGTGGTTT CTCTGTGGTATTCACTGCGTTCAGGATTTACTAAATTTATGTGATTTTGCAGATGGGTATATTT TGTATGCCACCTTCTTCAGTTATCCCACTTCATAATCATCCTGGAATGACTGTACTTAGCAAGC TTCTTTATGGACGTCTGCATGCTGAATCTTATGACTGGGTTGACATACCTGATCATCCAATTGA TCAATTACAAA

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.150084385

Conservation Information
Conserved circRNAs	NA
PMCS	0.150084385

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							198628595-198627188(+)
198627321-198627226(+)
						
						Potential amino acid sequence
						
							MDVCMLNLMTGLTYLIIQLINYKVQG*(+)
MPKIKSLSNACRVSFSPEGPISEEALERVRALLDMIRPLDVGLDNEAQIARNWSSSTRPSNGRR
GRNGANQFAAPIKYLHIHECESFSMGIFCMPPSSVIPLHNHPGMTVLSKLLYGRLHAESYDWVD
IPDHPIDQLQSARIGNKCSKTRLWIN*(+)
						
						Sponge-miRNAs
						
							zma-miR396g-3p 						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	198628595-198627188(+) 198627321-198627226(+)
Potential amino acid sequence	MDVCMLNLMTGLTYLIIQLINYKVQG(+) MPKIKSLSNACRVSFSPEGPISEEALERVRALLDMIRPLDVGLDNEAQIARNWSSSTRPSNGRR GRNGANQFAAPIKYLHIHECESFSMGIFCMPPSSVIPLHNHPGMTVLSKLLYGRLHAESYDWVD IPDHPIDQLQSARIGNKCSKTRLWIN(+)
Sponge-miRNAs	zma-miR396g-3p
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Han et al., 2020; Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d043392_circ_g.3

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