Plant Circular RNA Database

Detail information of Zm00001d033551_circ_g.3

			
						 General Information
					
						CircRNA Name
						Zm00001d033551_circ_g.3
					
						ID in PlantcircBase
						zma_circ_006891
					
						Alias
						Zm01circ00168, ZmciR43
					
						Organism
						
							Zea mays						
					
						Position
						
							chr1: 266952073-266953168  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						CIRI2
					
						Parent gene
						
							Zm00001d033551						
					
						Parent gene annotation
						
							Phosphoglycerate mutase-like family protein
							
						Parent gene strand
						+
					
						Alternative splicing
						
							Zm00001d033551_circ_g.4 						
					
						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
						Zm00001d033551_T004:3
Zm00001d033551_T014:3
Zm00001d033551_T045:3
Zm00001d033551_T044:3
Zm00001d033551_T015:3
Zm00001d033551_T018:3
Zm00001d033551_T019:3
Zm00001d033551_T023:3
Zm00001d033551_T031:3
Zm00001d033551_T034:3
Zm00001d033551_T028:3
Zm00001d033551_T042:3
Zm00001d033551_T040:3
Zm00001d033551_T022:3
Zm00001d033551_T024:3
Zm00001d033551_T037:3
Zm00001d033551_T046:3
Zm00001d033551_T006:3
Zm00001d033551_T002:3
Zm00001d033551_T025:3
Zm00001d033551_T008:3
Zm00001d033551_T030:3
Zm00001d033551_T001:3
Zm00001d033551_T013:3
Zm00001d033551_T036:3
Zm00001d033551_T010:3
Zm00001d033551_T033:3

General Information
CircRNA Name	Zm00001d033551_circ_g.3
ID in PlantcircBase	zma_circ_006891
Alias	Zm01circ00168, ZmciR43
Organism	Zea mays
Position	chr1: 266952073-266953168 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d033551
Parent gene annotation	Phosphoglycerate mutase-like family protein
Parent gene strand	+
Alternative splicing	Zm00001d033551_circ_g.4
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	Zm00001d033551_T004:3 Zm00001d033551_T014:3 Zm00001d033551_T045:3 Zm00001d033551_T044:3 Zm00001d033551_T015:3 Zm00001d033551_T018:3 Zm00001d033551_T019:3 Zm00001d033551_T023:3 Zm00001d033551_T031:3 Zm00001d033551_T034:3 Zm00001d033551_T028:3 Zm00001d033551_T042:3 Zm00001d033551_T040:3 Zm00001d033551_T022:3 Zm00001d033551_T024:3 Zm00001d033551_T037:3 Zm00001d033551_T046:3 Zm00001d033551_T006:3 Zm00001d033551_T002:3 Zm00001d033551_T025:3 Zm00001d033551_T008:3 Zm00001d033551_T030:3 Zm00001d033551_T001:3 Zm00001d033551_T013:3 Zm00001d033551_T036:3 Zm00001d033551_T010:3 Zm00001d033551_T033:3

			
						 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  
						
							ACACACTCACTTTATACTTCTTCAGGTATCTTTAGTAAGTAAAGACTCATCTATGCTAGATGGA
CTAGAAGATGCAAGCACCGAGATGGATGAAGCTAAGgtgaaggaactggtttgcttcgtctgca
tagcacttatagacatgatttaaaaatatacagctcggacgaaggtcgtgtacaggtacattta
gtcacatg

						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: 221
Transcript exons: 266952073-266952155,266952929-266952991,266953094-266953
168
GTGAAGGAACTGGTTTGCTTCGTCTGCATAGCACTTATAGACATGATTTAAAAATATACAGCTC
GGACGAAGGTCGTGTACAGATGTCTGCAGCAGCATTTGCAAAAGGCCTTCTTGATTTGGAAGGG
CAGTTGACTCCGATACTGGTATCTTTAGTAAGTAAAGACTCATCTATGCTAGATGGACTAGAAG
ATGCAAGCACCGAGATGGATGAAGCTAAG
						
						Genomic sequence
						
							GTGAAGGAACTGGTTTGCTTCGTCTGCATAGCACTTATAGACATGATTTAAAAATATACAGCTC
GGACGAAGGTCGTGTACAGGTACATTTAGTCACATGTATGCTTTTTCCCCAATCTATAGCACCC
TATGGATATGTTTTCCTTGGAACCTTGGTTGCTTGGCTATCACACTACACTTCTAGTTAGTTTT
CACCTTTGATATTTTCCCACATGAATGGCCAAAGTACCACTATGAAATTACACTTACCTACTTT
GTCGCTCTTTCATGAAATTACACTTAACCTACTTTGGCAAATTTGGAACACTAGGTTTAATTAG
AAATTGCATGTGGTCTTAGGAATGACTACTTTTTGTCACAGAAAGCACAGCATTGATTCTTTCT
TGGAAAGTCATCTCGTATAGGCTATACCGGTCAAAACACACATTATTCTTTTTTGTGCTTATAT
CACTGGAGTTGTGACTAATGGAAAAAATACAATCTTTCAAGTTGTCCCACATGAAAATTAATGA
AGGCAATGATCTTACTTGCCTGCAAGATTTTATGTTGCATTTATGGACTAGGCATGGATGTTGG
TTACAAACTTGAAATTACCATGATATCCCTGGTATTGTCTTGTAATGCATGAGAAAGTTTTGTT
AAGATTTGCTCAATGTGGAAGGAAGAGGGAAAATAAGGGCAACTATCAGTTAAAACAACATCCC
TTATTTGAAGAAGACCCGAGAAACCCTTCCCCTCCTCCAACCCACCCACTGCTCAGTCTATGAT
TCTGCAGTTCATGCATATGTCTAACTGCAATATTTTCTTGGCAATCAACTGATATTCGTAATTT
ACATGTTCATGGTGTACTTTTCAGATGTCTGCAGCAGCATTTGCAAAAGGCCTTCTTGATTTGG
AAGGGCAGTTGACTCCGATACTGGTAGGTTGCTTATGATCTAGAAGAGCAAATATTTGGAAGGG
CAGTTCACACATCTTTTTTTTTAAAAAAACACACACACACACTCACTTTATACTTCTTCAGGTA
TCTTTAGTAAGTAAAGACTCATCTATGCTAGATGGACTAGAAGATGCAAGCACCGAGATGGATG
AAGCTAAG

Sequences
Splice junction sequence	ACACACTCACTTTATACTTCTTCAGGTATCTTTAGTAAGTAAAGACTCATCTATGCTAGATGGA CTAGAAGATGCAAGCACCGAGATGGATGAAGCTAAGgtgaaggaactggtttgcttcgtctgca tagcacttatagacatgatttaaaaatatacagctcggacgaaggtcgtgtacaggtacattta gtcacatg
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: 221 Transcript exons: 266952073-266952155,266952929-266952991,266953094-266953 168 GTGAAGGAACTGGTTTGCTTCGTCTGCATAGCACTTATAGACATGATTTAAAAATATACAGCTC GGACGAAGGTCGTGTACAGATGTCTGCAGCAGCATTTGCAAAAGGCCTTCTTGATTTGGAAGGG CAGTTGACTCCGATACTGGTATCTTTAGTAAGTAAAGACTCATCTATGCTAGATGGACTAGAAG ATGCAAGCACCGAGATGGATGAAGCTAAG
Genomic sequence	GTGAAGGAACTGGTTTGCTTCGTCTGCATAGCACTTATAGACATGATTTAAAAATATACAGCTC GGACGAAGGTCGTGTACAGGTACATTTAGTCACATGTATGCTTTTTCCCCAATCTATAGCACCC TATGGATATGTTTTCCTTGGAACCTTGGTTGCTTGGCTATCACACTACACTTCTAGTTAGTTTT CACCTTTGATATTTTCCCACATGAATGGCCAAAGTACCACTATGAAATTACACTTACCTACTTT GTCGCTCTTTCATGAAATTACACTTAACCTACTTTGGCAAATTTGGAACACTAGGTTTAATTAG AAATTGCATGTGGTCTTAGGAATGACTACTTTTTGTCACAGAAAGCACAGCATTGATTCTTTCT TGGAAAGTCATCTCGTATAGGCTATACCGGTCAAAACACACATTATTCTTTTTTGTGCTTATAT CACTGGAGTTGTGACTAATGGAAAAAATACAATCTTTCAAGTTGTCCCACATGAAAATTAATGA AGGCAATGATCTTACTTGCCTGCAAGATTTTATGTTGCATTTATGGACTAGGCATGGATGTTGG TTACAAACTTGAAATTACCATGATATCCCTGGTATTGTCTTGTAATGCATGAGAAAGTTTTGTT AAGATTTGCTCAATGTGGAAGGAAGAGGGAAAATAAGGGCAACTATCAGTTAAAACAACATCCC TTATTTGAAGAAGACCCGAGAAACCCTTCCCCTCCTCCAACCCACCCACTGCTCAGTCTATGAT TCTGCAGTTCATGCATATGTCTAACTGCAATATTTTCTTGGCAATCAACTGATATTCGTAATTT ACATGTTCATGGTGTACTTTTCAGATGTCTGCAGCAGCATTTGCAAAAGGCCTTCTTGATTTGG AAGGGCAGTTGACTCCGATACTGGTAGGTTGCTTATGATCTAGAAGAGCAAATATTTGGAAGGG CAGTTCACACATCTTTTTTTTTAAAAAAACACACACACACACTCACTTTATACTTCTTCAGGTA TCTTTAGTAAGTAAAGACTCATCTATGCTAGATGGACTAGAAGATGCAAGCACCGAGATGGATG AAGCTAAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.07891178

Conservation Information
Conserved circRNAs	NA
PMCS	0.07891178

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							266952930-266952120(+)
266952118-266952109(-)
266953120-266953135(-)
						
						Potential amino acid sequence
						
							MSAAAFAKGLLDLEGQLTPILVSLVSKDSSMLDGLEDASTEMDEAKVKELVCFVCIALIDMI*(
+)
MSISAMQTKQTSSFTLASSISVLASSSPSSIDESLLTKDTSIGVNCPSKSRRPFANAAADICTR
PSSELYIFKSCL*(-)
MSLYLLKIPVSESTALPNQEGLLQMLLQTSVHDLRPSCIFLNHVYKCYADEANQFLHLSFIHLG
ACIF*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	266952930-266952120(+) 266952118-266952109(-) 266953120-266953135(-)
Potential amino acid sequence	MSAAAFAKGLLDLEGQLTPILVSLVSKDSSMLDGLEDASTEMDEAKVKELVCFVCIALIDMI( +) MSISAMQTKQTSSFTLASSISVLASSSPSSIDESLLTKDTSIGVNCPSKSRRPFANAAADICTR PSSELYIFKSCL(-) MSLYLLKIPVSESTALPNQEGLLQMLLQTSVHDLRPSCIFLNHVYKCYADEANQFLHLSFIHLG ACIF*(-)
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 Zm00001d033551_circ_g.3

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