Plant Circular RNA Database

Detail information of Zm00001d007089_circ_g.2

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d007089_circ_g.2
					

						ID in PlantcircBase
						zma_circ_007402
					

						Alias
						zma_circ_0000943
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 221965100-221965945  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d007089						
					

						Parent gene annotation
						
							Protein CHROMATIN REMODELING 5
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							Zm00001d007089_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  
						
							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
						Zm00001d007089_T183:2
Zm00001d007089_T140:2
Zm00001d007089_T161:2
Zm00001d007089_T089:2
Zm00001d007089_T039:2
Zm00001d007089_T131:2
Zm00001d007089_T176:2
Zm00001d007089_T038:2
Zm00001d007089_T092:2
Zm00001d007089_T134:2
Zm00001d007089_T136:2
Zm00001d007089_T109:2
Zm00001d007089_T119:2
Zm00001d007089_T041:2
Zm00001d007089_T043:2
Zm00001d007089_T022:1
Zm00001d007089_T175:2
Zm00001d007089_T016:2
Zm00001d007089_T129:2
Zm00001d007089_T082:2
Zm00001d007089_T012:2
Zm00001d007089_T037:2
Zm00001d007089_T096:2
Zm00001d007089_T120:2
Zm00001d007089_T080:2
Zm00001d007089_T180:2
Zm00001d007089_T125:2
Zm00001d007089_T169:2
Zm00001d007089_T007:2
Zm00001d007089_T170:2
Zm00001d007089_T031:1
Zm00001d007089_T112:2
Zm00001d007089_T009:2
Zm00001d007089_T172:2
Zm00001d007089_T142:2
Zm00001d007089_T036:2
Zm00001d007089_T173:2
Zm00001d007089_T123:2
Zm00001d007089_T168:2
Zm00001d007089_T118:2
Zm00001d007089_T090:2
Zm00001d007089_T102:2
Zm00001d007089_T152:2
Zm00001d007089_T014:2
Zm00001d007089_T147:2
Zm00001d007089_T157:2
Zm00001d007089_T034:2
Zm00001d007089_T018:2
Zm00001d007089_T088:2
Zm00001d007089_T122:2
Zm00001d007089_T182:2
Zm00001d007089_T155:2
Zm00001d007089_T027:2
Zm00001d007089_T110:2
Zm00001d007089_T103:2
Zm00001d007089_T165:2
Zm00001d007089_T001:2
Zm00001d007089_T081:2
Zm00001d007089_T137:2
Zm00001d007089_T100:2
Zm00001d007089_T117:2
Zm00001d007089_T141:2
Zm00001d007089_T160:2
Zm00001d007089_T095:2
Zm00001d007089_T026:2
Zm00001d007089_T024:2
Zm00001d007089_T002:2
Zm00001d007089_T087:2
Zm00001d007089_T003:2
Zm00001d007089_T164:2
Zm00001d007089_T042:2
Zm00001d007089_T029:2
Zm00001d007089_T130:2
Zm00001d007089_T126:1
Zm00001d007089_T108:2
Zm00001d007089_T084:2
Zm00001d007089_T020:2
Zm00001d007089_T113:2
Zm00001d007089_T040:2
Zm00001d007089_T179:2
Zm00001d007089_T099:2
Zm00001d007089_T094:2
Zm00001d007089_T116:2

					

			
		

General Information
CircRNA Name	Zm00001d007089_circ_g.2
ID in PlantcircBase	zma_circ_007402
Alias	zma_circ_0000943
Organism	Zea mays
Position	chr2: 221965100-221965945 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d007089
Parent gene annotation	Protein CHROMATIN REMODELING 5
Parent gene strand	-
Alternative splicing	Zm00001d007089_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	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	Zm00001d007089_T183:2 Zm00001d007089_T140:2 Zm00001d007089_T161:2 Zm00001d007089_T089:2 Zm00001d007089_T039:2 Zm00001d007089_T131:2 Zm00001d007089_T176:2 Zm00001d007089_T038:2 Zm00001d007089_T092:2 Zm00001d007089_T134:2 Zm00001d007089_T136:2 Zm00001d007089_T109:2 Zm00001d007089_T119:2 Zm00001d007089_T041:2 Zm00001d007089_T043:2 Zm00001d007089_T022:1 Zm00001d007089_T175:2 Zm00001d007089_T016:2 Zm00001d007089_T129:2 Zm00001d007089_T082:2 Zm00001d007089_T012:2 Zm00001d007089_T037:2 Zm00001d007089_T096:2 Zm00001d007089_T120:2 Zm00001d007089_T080:2 Zm00001d007089_T180:2 Zm00001d007089_T125:2 Zm00001d007089_T169:2 Zm00001d007089_T007:2 Zm00001d007089_T170:2 Zm00001d007089_T031:1 Zm00001d007089_T112:2 Zm00001d007089_T009:2 Zm00001d007089_T172:2 Zm00001d007089_T142:2 Zm00001d007089_T036:2 Zm00001d007089_T173:2 Zm00001d007089_T123:2 Zm00001d007089_T168:2 Zm00001d007089_T118:2 Zm00001d007089_T090:2 Zm00001d007089_T102:2 Zm00001d007089_T152:2 Zm00001d007089_T014:2 Zm00001d007089_T147:2 Zm00001d007089_T157:2 Zm00001d007089_T034:2 Zm00001d007089_T018:2 Zm00001d007089_T088:2 Zm00001d007089_T122:2 Zm00001d007089_T182:2 Zm00001d007089_T155:2 Zm00001d007089_T027:2 Zm00001d007089_T110:2 Zm00001d007089_T103:2 Zm00001d007089_T165:2 Zm00001d007089_T001:2 Zm00001d007089_T081:2 Zm00001d007089_T137:2 Zm00001d007089_T100:2 Zm00001d007089_T117:2 Zm00001d007089_T141:2 Zm00001d007089_T160:2 Zm00001d007089_T095:2 Zm00001d007089_T026:2 Zm00001d007089_T024:2 Zm00001d007089_T002:2 Zm00001d007089_T087:2 Zm00001d007089_T003:2 Zm00001d007089_T164:2 Zm00001d007089_T042:2 Zm00001d007089_T029:2 Zm00001d007089_T130:2 Zm00001d007089_T126:1 Zm00001d007089_T108:2 Zm00001d007089_T084:2 Zm00001d007089_T020:2 Zm00001d007089_T113:2 Zm00001d007089_T040:2 Zm00001d007089_T179:2 Zm00001d007089_T099:2 Zm00001d007089_T094:2 Zm00001d007089_T116:2

			
						 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  
						
							TTGTACCCTTCTGAATCGGCCTTGCTCCCGGAGTTGCTGAAAAATGCCATCACAAATTATGGCA
TTACATGGAATACCTCTCACAGTCTCAGTGTCACTCcttatcagtagccttgtctgtttcgccg
tctggctcaaaatccatgtcagcaggatcatcttctacaaatataagaaaaatgccaatcaact
tgggttgt

									
								

					

						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: 731
Transcript exons: 221965100-221965161,221965277-221965945
CTTATCAGTAGCCTTGTCTGTTTCGCCGTCTGGCTCAAAATCCATGTCAGCAGGATCATCTTCA
TCTGCATCGCTGTCATCATCATTCTCATCATTATACTCATCGTTATCATAAGCATTGTACTTTG
ACATCTTCTTCATTTGTCGTGAGCCAGACTTTGCTGCTCCACCAGAAGTGGAACAGCTTGACTG
CTTCATCCCGCCACGATGCAACGATTCAATCTGATCCTCTCCGTCCTGCTCGTAATAGTCATCT
GAGAGCATTTCCTCAGCAGGCACCTCACCATTTGCTCTATTCAGTTCATCATCCTCTCTGCTAC
CATCCATGTCATCATGCGAGTTAGCAGCATCCATTCCTCTACCGCTATTTGATGCAACTTCCTT
GGCCGTCTGTTTGGACCTGGAATCCTTCAGAAAATTTGTGCCCCATGGACCACCAGACGATCTG
CCTCCTCTCTGAACATGCTGCCTTGATGCGTACAAACCTGACTGGCCAGACTCATATTGCTCTG
CTTCGCTGTGGTAAGCATCCTCTGCTTTCTCATTTAAGTTCCACTGCCTAGAGTTCAGGCCATC
ATTCCCATCCCGGATTGACTCGTGTATGCCATCATCATCGGCCTTTTCATTCAAGTTGTACCCT
TCTGAATCGGCCTTGCTCCCGGAGTTGCTGAAAAATGCCATCACAAATTATGGCATTACATGGA
ATACCTCTCACAGTCTCAGTGTCACTC
						
					

						Genomic sequence
						
							CTTATCAGTAGCCTTGTCTGTTTCGCCGTCTGGCTCAAAATCCATGTCAGCAGGATCATCTTCT
ACAAATATAAGAAAAATGCCAATCAACTTGGGTTGTAACACCATGTATAGAGACACAACTAAAG
CAATAACACATTTATTTTGTTAAGCACGAGGCTCCATGTTTCAATATACCATCTGCATCGCTGT
CATCATCATTCTCATCATTATACTCATCGTTATCATAAGCATTGTACTTTGACATCTTCTTCAT
TTGTCGTGAGCCAGACTTTGCTGCTCCACCAGAAGTGGAACAGCTTGACTGCTTCATCCCGCCA
CGATGCAACGATTCAATCTGATCCTCTCCGTCCTGCTCGTAATAGTCATCTGAGAGCATTTCCT
CAGCAGGCACCTCACCATTTGCTCTATTCAGTTCATCATCCTCTCTGCTACCATCCATGTCATC
ATGCGAGTTAGCAGCATCCATTCCTCTACCGCTATTTGATGCAACTTCCTTGGCCGTCTGTTTG
GACCTGGAATCCTTCAGAAAATTTGTGCCCCATGGACCACCAGACGATCTGCCTCCTCTCTGAA
CATGCTGCCTTGATGCGTACAAACCTGACTGGCCAGACTCATATTGCTCTGCTTCGCTGTGGTA
AGCATCCTCTGCTTTCTCATTTAAGTTCCACTGCCTAGAGTTCAGGCCATCATTCCCATCCCGG
ATTGACTCGTGTATGCCATCATCATCGGCCTTTTCATTCAAGTTGTACCCTTCTGAATCGGCCT
TGCTCCCGGAGTTGCTGAAAAATGCCATCACAAATTATGGCATTACATGGAATACCTCTCACAG
TCTCAGTGTCACTC
						
					

			
		

Sequences
Splice junction sequence	TTGTACCCTTCTGAATCGGCCTTGCTCCCGGAGTTGCTGAAAAATGCCATCACAAATTATGGCA TTACATGGAATACCTCTCACAGTCTCAGTGTCACTCcttatcagtagccttgtctgtttcgccg tctggctcaaaatccatgtcagcaggatcatcttctacaaatataagaaaaatgccaatcaact tgggttgt
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: 731 Transcript exons: 221965100-221965161,221965277-221965945 CTTATCAGTAGCCTTGTCTGTTTCGCCGTCTGGCTCAAAATCCATGTCAGCAGGATCATCTTCA TCTGCATCGCTGTCATCATCATTCTCATCATTATACTCATCGTTATCATAAGCATTGTACTTTG ACATCTTCTTCATTTGTCGTGAGCCAGACTTTGCTGCTCCACCAGAAGTGGAACAGCTTGACTG CTTCATCCCGCCACGATGCAACGATTCAATCTGATCCTCTCCGTCCTGCTCGTAATAGTCATCT GAGAGCATTTCCTCAGCAGGCACCTCACCATTTGCTCTATTCAGTTCATCATCCTCTCTGCTAC CATCCATGTCATCATGCGAGTTAGCAGCATCCATTCCTCTACCGCTATTTGATGCAACTTCCTT GGCCGTCTGTTTGGACCTGGAATCCTTCAGAAAATTTGTGCCCCATGGACCACCAGACGATCTG CCTCCTCTCTGAACATGCTGCCTTGATGCGTACAAACCTGACTGGCCAGACTCATATTGCTCTG CTTCGCTGTGGTAAGCATCCTCTGCTTTCTCATTTAAGTTCCACTGCCTAGAGTTCAGGCCATC ATTCCCATCCCGGATTGACTCGTGTATGCCATCATCATCGGCCTTTTCATTCAAGTTGTACCCT TCTGAATCGGCCTTGCTCCCGGAGTTGCTGAAAAATGCCATCACAAATTATGGCATTACATGGA ATACCTCTCACAGTCTCAGTGTCACTC
Genomic sequence	CTTATCAGTAGCCTTGTCTGTTTCGCCGTCTGGCTCAAAATCCATGTCAGCAGGATCATCTTCT ACAAATATAAGAAAAATGCCAATCAACTTGGGTTGTAACACCATGTATAGAGACACAACTAAAG CAATAACACATTTATTTTGTTAAGCACGAGGCTCCATGTTTCAATATACCATCTGCATCGCTGT CATCATCATTCTCATCATTATACTCATCGTTATCATAAGCATTGTACTTTGACATCTTCTTCAT TTGTCGTGAGCCAGACTTTGCTGCTCCACCAGAAGTGGAACAGCTTGACTGCTTCATCCCGCCA CGATGCAACGATTCAATCTGATCCTCTCCGTCCTGCTCGTAATAGTCATCTGAGAGCATTTCCT CAGCAGGCACCTCACCATTTGCTCTATTCAGTTCATCATCCTCTCTGCTACCATCCATGTCATC ATGCGAGTTAGCAGCATCCATTCCTCTACCGCTATTTGATGCAACTTCCTTGGCCGTCTGTTTG GACCTGGAATCCTTCAGAAAATTTGTGCCCCATGGACCACCAGACGATCTGCCTCCTCTCTGAA CATGCTGCCTTGATGCGTACAAACCTGACTGGCCAGACTCATATTGCTCTGCTTCGCTGTGGTA AGCATCCTCTGCTTTCTCATTTAAGTTCCACTGCCTAGAGTTCAGGCCATCATTCCCATCCCGG ATTGACTCGTGTATGCCATCATCATCGGCCTTTTCATTCAAGTTGTACCCTTCTGAATCGGCCT TGCTCCCGGAGTTGCTGAAAAATGCCATCACAAATTATGGCATTACATGGAATACCTCTCACAG TCTCAGTGTCACTC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.191541476

Conservation Information
Conserved circRNAs	NA
PMCS	0.191541476

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							221965915-221965326(+)
221965817-221965107(+)
221965890-221965340(+)
221965335-221965839(-)
221965897-221965942(-)
						
						Potential amino acid sequence
						
							MEYLSQSQCHSLSVALSVSPSGSKSMSAGSSSSASLSSSFSSLYSSLS*(+)
MPSSSAFSFKLYPSESALLPELLKNAITNYGITWNTSHSLSVTPYQ*(+)
MPSQIMALHGIPLTVSVSLLISSLVCFAVWLKIHVSRIIFICIAVIIILIIILIVIISIVL*(+
)
MLMITMSIMMRMMMTAMQMKMILLTWILSQTAKQTRLLIRSDTETVRGIPCNAIICDGIFQQLR
EQGRFRRVQLE*(-)
MAFFSNSGSKADSEGYNLNEKADDDGIHESIRDGNDGLNSRQWNLNEKAEDAYHSEAEQYESGQ
SGLYASRQHVQRGGRSSGGPWGTNFLKDSRSKQTAKEVASNSGRGMDAANSHDDMDGSREDDEL
NRANGEVPAEEMLSDDYYEQDGEDQIESLHRGGMKQSSCSTSGGAAKSGSRQMKKMSKYNAYDN
DEYNDENDDDSDADEDDPADMDFEPDGETDKATDKE*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	221965915-221965326(+) 221965817-221965107(+) 221965890-221965340(+) 221965335-221965839(-) 221965897-221965942(-)
Potential amino acid sequence	MEYLSQSQCHSLSVALSVSPSGSKSMSAGSSSSASLSSSFSSLYSSLS(+) MPSSSAFSFKLYPSESALLPELLKNAITNYGITWNTSHSLSVTPYQ(+) MPSQIMALHGIPLTVSVSLLISSLVCFAVWLKIHVSRIIFICIAVIIILIIILIVIISIVL(+ ) MLMITMSIMMRMMMTAMQMKMILLTWILSQTAKQTRLLIRSDTETVRGIPCNAIICDGIFQQLR EQGRFRRVQLE(-) MAFFSNSGSKADSEGYNLNEKADDDGIHESIRDGNDGLNSRQWNLNEKAEDAYHSEAEQYESGQ SGLYASRQHVQRGGRSSGGPWGTNFLKDSRSKQTAKEVASNSGRGMDAANSHDDMDGSREDDEL NRANGEVPAEEMLSDDYYEQDGEDQIESLHRGGMKQSSCSTSGGAAKSGSRQMKKMSKYNAYDN DEYNDENDDDSDADEDDPADMDFEPDGETDKATDKE*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d007089_circ_g.2

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