Plant Circular RNA Database

Detail information of Zm00001d001978_circ_g.1

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d001978_circ_g.1
					

						ID in PlantcircBase
						zma_circ_007019
					

						Alias
						zma_circ_0001039
					

						Organism
						
							Zea mays						
					

						Position
						
							chr2: 3806218-3807524  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						find_circ
					

						Parent gene
						
							Zm00001d001978						
					

						Parent gene annotation
						
							MAP3K epsilon protein kinase 1
							
					

						Parent gene strand
						+
					

						Alternative splicing
						
							Zm00001d001977_circ_ag.1 Zm00001d001977_circ_ag.2 						
					

						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
						Zm00001d001978_T077:4
Zm00001d001978_T055:4
Zm00001d001978_T030:4
Zm00001d001978_T071:4
Zm00001d001978_T081:4
Zm00001d001978_T114:4
Zm00001d001978_T084:4
Zm00001d001978_T074:4
Zm00001d001978_T049:4
Zm00001d001978_T037:4
Zm00001d001978_T120:1
Zm00001d001978_T075:4
Zm00001d001978_T014:4
Zm00001d001978_T008:4
Zm00001d001978_T011:4
Zm00001d001978_T042:4
Zm00001d001978_T003:4
Zm00001d001978_T013:4
Zm00001d001978_T017:4
Zm00001d001978_T018:4
Zm00001d001978_T073:4
Zm00001d001978_T004:1
Zm00001d001978_T096:4
Zm00001d001978_T039:4
Zm00001d001978_T089:4
Zm00001d001978_T022:4
Zm00001d001978_T090:4
Zm00001d001978_T060:4
Zm00001d001978_T103:4
Zm00001d001978_T109:4
Zm00001d001978_T104:4
Zm00001d001978_T031:4
Zm00001d001978_T101:4
Zm00001d001978_T076:4
Zm00001d001978_T016:4
Zm00001d001978_T079:4
Zm00001d001978_T020:4
Zm00001d001978_T026:4
Zm00001d001978_T009:4
Zm00001d001978_T015:4
Zm00001d001978_T088:4
Zm00001d001978_T028:4
Zm00001d001978_T107:3
Zm00001d001978_T058:4
Zm00001d001978_T006:4
Zm00001d001978_T007:4
Zm00001d001978_T005:4
Zm00001d001978_T080:4
Zm00001d001978_T115:4
Zm00001d001978_T118:1
Zm00001d001978_T019:4
Zm00001d001978_T091:4
Zm00001d001978_T121:1
Zm00001d001978_T033:4
Zm00001d001978_T111:4
Zm00001d001978_T117:4
Zm00001d001978_T012:4
Zm00001d001978_T002:4
Zm00001d001978_T010:4
Zm00001d001978_T087:4

					

			
		

General Information
CircRNA Name	Zm00001d001978_circ_g.1
ID in PlantcircBase	zma_circ_007019
Alias	zma_circ_0001039
Organism	Zea mays
Position	chr2: 3806218-3807524 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ
Parent gene	Zm00001d001978
Parent gene annotation	MAP3K epsilon protein kinase 1
Parent gene strand	+
Alternative splicing	Zm00001d001977_circ_ag.1 Zm00001d001977_circ_ag.2
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	Zm00001d001978_T077:4 Zm00001d001978_T055:4 Zm00001d001978_T030:4 Zm00001d001978_T071:4 Zm00001d001978_T081:4 Zm00001d001978_T114:4 Zm00001d001978_T084:4 Zm00001d001978_T074:4 Zm00001d001978_T049:4 Zm00001d001978_T037:4 Zm00001d001978_T120:1 Zm00001d001978_T075:4 Zm00001d001978_T014:4 Zm00001d001978_T008:4 Zm00001d001978_T011:4 Zm00001d001978_T042:4 Zm00001d001978_T003:4 Zm00001d001978_T013:4 Zm00001d001978_T017:4 Zm00001d001978_T018:4 Zm00001d001978_T073:4 Zm00001d001978_T004:1 Zm00001d001978_T096:4 Zm00001d001978_T039:4 Zm00001d001978_T089:4 Zm00001d001978_T022:4 Zm00001d001978_T090:4 Zm00001d001978_T060:4 Zm00001d001978_T103:4 Zm00001d001978_T109:4 Zm00001d001978_T104:4 Zm00001d001978_T031:4 Zm00001d001978_T101:4 Zm00001d001978_T076:4 Zm00001d001978_T016:4 Zm00001d001978_T079:4 Zm00001d001978_T020:4 Zm00001d001978_T026:4 Zm00001d001978_T009:4 Zm00001d001978_T015:4 Zm00001d001978_T088:4 Zm00001d001978_T028:4 Zm00001d001978_T107:3 Zm00001d001978_T058:4 Zm00001d001978_T006:4 Zm00001d001978_T007:4 Zm00001d001978_T005:4 Zm00001d001978_T080:4 Zm00001d001978_T115:4 Zm00001d001978_T118:1 Zm00001d001978_T019:4 Zm00001d001978_T091:4 Zm00001d001978_T121:1 Zm00001d001978_T033:4 Zm00001d001978_T111:4 Zm00001d001978_T117:4 Zm00001d001978_T012:4 Zm00001d001978_T002:4 Zm00001d001978_T010:4 Zm00001d001978_T087:4

			
						 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  
						
							CCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCAT
TCTGTGGTCGGCACTCCATACTGGATGGCGCCTGAGaatcttaatcataaaaatattgtcaagt
atttgggatcattgaagacaaagagccacctccatattattttggagtaagcaattatcgttga
aaatgtct

						Assembled circRNA sequence  
						
							NA
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
						
							NA						
					
						Genomic sequence
						
							AATCTTAATCATAAAAATATTGTCAAGTATTTGGGATCATTGAAGACAAAGAGCCACCTCCATA
TTATTTTGGAGTAAGCAATTATCGTTGAAAATGTCTTCATAGTTGATACGAGATAGATGTATAC
AGTATACATCTAGTGAATTTCGACATGTAAGTTCTAATACCATAGGGATAATTGCAGGTATGTG
GAGAATGGCTCACTTGCTAATATTATCAAGCCAAACAAATTCGGACCTTTTCCTGAATCTTTGG
TGGCTGTATACATTGCTCAGGTTCTTGTGGTGGTTCAATACTACTACTTTTCTCTTTTTTCCTT
ATTTTTATCTGATTTTAGTTTTTATGTGTCCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAAC
AAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAGGTTAATGGCTG
TATATTATCTGCCCCCTTTTTTCTTTGTTTCAATCGTTGAATTTGGTAAATTTTTTTTGGAACA
CCTAGAAATCTGAATGCTGCTAAAAAATTATGGTGCAAGGATACTTATCTTCTAACTTGGAAGC
AATATTCTAATACCACAATTGGTAGCATAAAACCATGAAAACATGTAGTGACATGAAGGGCTGT
GTACCCTCGGGTAGCTGGACCGTGGCTACGTAGTTCGTAGCCGCCGTCCGTCTTCTCCGGCGAG
GTATTCCTCAGCCGCAGACTTAGTGAAGACAGGGAGATCGGAGATTAGGGCTTTCAAAGTGTGG
CTTATATATATATGCCCCATGGCCCCAACCGATCAGCCCTATACTTTAGGATCTAAGCTAGCAC
TAATCCTTATCTTTCCTAACTTCTCTCCTGGCGGTTACCTGACCTATCCAACCAGGCCGGCTGC
TTCCAGCGTGTTGCTGCGCTCGGCCTCTGCCTGTGCCGCATGCTCAGCCGCCCGTCGTACATCC
CTAGCCCTACGGCGCGTGGCATACTTGAGTCCCCACATGACAACATGACTGATGCAGCGGTGAA
GAAAGAAATAAAGGGGCACCCTAGAGATAAACTCATGGACAAATAGTGGGCTAGCATAGATTTT
GGGAACATGAATTGCTAATATGAAATATGTATCCCCCTTTATTCTAAACTTCCAATAGAAACAT
AACAATAACACTTTTTCTCTACATATCTTCATTTGTGTACCCTGCTTGTTTAGGGCCTTGTCAA
ACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTC
GGCACTCCATACTGGATGGCGCCTGAG

Sequences
Splice junction sequence	CCTTGTCAAACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCAT TCTGTGGTCGGCACTCCATACTGGATGGCGCCTGAGaatcttaatcataaaaatattgtcaagt atttgggatcattgaagacaaagagccacctccatattattttggagtaagcaattatcgttga aaatgtct
Assembled circRNA sequence	NA 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	NA
Genomic sequence	AATCTTAATCATAAAAATATTGTCAAGTATTTGGGATCATTGAAGACAAAGAGCCACCTCCATA TTATTTTGGAGTAAGCAATTATCGTTGAAAATGTCTTCATAGTTGATACGAGATAGATGTATAC AGTATACATCTAGTGAATTTCGACATGTAAGTTCTAATACCATAGGGATAATTGCAGGTATGTG GAGAATGGCTCACTTGCTAATATTATCAAGCCAAACAAATTCGGACCTTTTCCTGAATCTTTGG TGGCTGTATACATTGCTCAGGTTCTTGTGGTGGTTCAATACTACTACTTTTCTCTTTTTTCCTT ATTTTTATCTGATTTTAGTTTTTATGTGTCCAGGTGTTGGAAGGTCTTGTTTATCTGCATGAAC AAGGTGTCATTCATAGAGATATCAAGGGCGCAAATATACTGACTACCAAAGAGGTTAATGGCTG TATATTATCTGCCCCCTTTTTTCTTTGTTTCAATCGTTGAATTTGGTAAATTTTTTTTGGAACA CCTAGAAATCTGAATGCTGCTAAAAAATTATGGTGCAAGGATACTTATCTTCTAACTTGGAAGC AATATTCTAATACCACAATTGGTAGCATAAAACCATGAAAACATGTAGTGACATGAAGGGCTGT GTACCCTCGGGTAGCTGGACCGTGGCTACGTAGTTCGTAGCCGCCGTCCGTCTTCTCCGGCGAG GTATTCCTCAGCCGCAGACTTAGTGAAGACAGGGAGATCGGAGATTAGGGCTTTCAAAGTGTGG CTTATATATATATGCCCCATGGCCCCAACCGATCAGCCCTATACTTTAGGATCTAAGCTAGCAC TAATCCTTATCTTTCCTAACTTCTCTCCTGGCGGTTACCTGACCTATCCAACCAGGCCGGCTGC TTCCAGCGTGTTGCTGCGCTCGGCCTCTGCCTGTGCCGCATGCTCAGCCGCCCGTCGTACATCC CTAGCCCTACGGCGCGTGGCATACTTGAGTCCCCACATGACAACATGACTGATGCAGCGGTGAA GAAAGAAATAAAGGGGCACCCTAGAGATAAACTCATGGACAAATAGTGGGCTAGCATAGATTTT GGGAACATGAATTGCTAATATGAAATATGTATCCCCCTTTATTCTAAACTTCCAATAGAAACAT AACAATAACACTTTTTCTCTACATATCTTCATTTGTGTACCCTGCTTGTTTAGGGCCTTGTCAA ACTTGCTGACTTTGGAGTTGCCACTAAATTGACTGAAGCTGACATCAACACTCATTCTGTGGTC GGCACTCCATACTGGATGGCGCCTGAG

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.101594721

Conservation Information
Conserved circRNAs	NA
PMCS	0.101594721

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							3807514-3807521(+)
3806231-3806421(-)
						
						Potential amino acid sequence
						
							MAPENLNHKNIVKYLGSLKTKSHLHIILEYVENGSLANIIKPNKFGPFPESLVAVYIAQVLEGL
VYLHEQGVIHRDIKGANILTTKEGLVKLADFGVATKLTEADINTHSVVGTPYWMAPENLNHKNI
VKYLGSLKTKSHLHIILEYVENGSLANIIKPNKFGPFPESLVAVYIAQVLEGLVYLHEQGVIHR
DIKGANILTTKEGLVKLADFGVATKLTEADINTHSVVGTPYWMAPENLNHKNIVKYLGSLKTKS
HLHIILEYVENGSLANIIKPNKFGPFPESLVAVYIAQVLEGLVYLHEQGVIHRDIKGANILTTK
EGLVKLADFGVATKLTEADINTHSVVGTPYWMAPE(+)
MIKILRRHPVWSADHRMSVDVSFSQFSGNSKVSKFDKALFGSQYICALDISMNDTLFMQINKTF
QHLSNVYSHQRFRKRSEFVWLDNISK*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	3807514-3807521(+) 3806231-3806421(-)
Potential amino acid sequence	MAPENLNHKNIVKYLGSLKTKSHLHIILEYVENGSLANIIKPNKFGPFPESLVAVYIAQVLEGL VYLHEQGVIHRDIKGANILTTKEGLVKLADFGVATKLTEADINTHSVVGTPYWMAPENLNHKNI VKYLGSLKTKSHLHIILEYVENGSLANIIKPNKFGPFPESLVAVYIAQVLEGLVYLHEQGVIHR DIKGANILTTKEGLVKLADFGVATKLTEADINTHSVVGTPYWMAPENLNHKNIVKYLGSLKTKS HLHIILEYVENGSLANIIKPNKFGPFPESLVAVYIAQVLEGLVYLHEQGVIHRDIKGANILTTK EGLVKLADFGVATKLTEADINTHSVVGTPYWMAPE(+) MIKILRRHPVWSADHRMSVDVSFSQFSGNSKVSKFDKALFGSQYICALDISMNDTLFMQINKTF QHLSNVYSHQRFRKRSEFVWLDNISK*(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Ma et al., 2021b

circRNA

Detail information of Zm00001d001978_circ_g.1

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