Plant Circular RNA Database

Detail information of Zm00001d039537_circ_g.1

			
				
						 General Information
					

				
						CircRNA Name
						Zm00001d039537_circ_g.1
					

						ID in PlantcircBase
						zma_circ_007479
					

						Alias
						Zm03circ00007
					

						Organism
						
							Zea mays						
					

						Position
						
							chr3: 7492872-7494635  JBrowse»						
					

						Reference genome
						
							AGPv4.38						
					

						Type  
						
							u-circRNA							
									
								

					

						Identification method
						CIRI2
					

						Parent gene
						
							Zm00001d039537						
					

						Parent gene annotation
						
							Protein ALWAYS EARLY 3
							
					

						Parent gene strand
						-
					

						Alternative splicing
						
							NA						
					

						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  
						
							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
						Zm00001d039537_T030:5
Zm00001d039537_T026:5
Zm00001d039537_T041:5
Zm00001d039537_T023:5
Zm00001d039537_T056:5
Zm00001d039537_T042:5
Zm00001d039537_T035:5
Zm00001d039537_T036:5
Zm00001d039537_T047:5
Zm00001d039537_T033:5
Zm00001d039537_T012:5
Zm00001d039537_T057:5
Zm00001d039537_T019:5
Zm00001d039537_T045:5
Zm00001d039537_T014:5
Zm00001d039537_T053:5
Zm00001d039537_T009:5
Zm00001d039537_T029:5
Zm00001d039537_T017:5
Zm00001d039537_T039:5
Zm00001d039537_T027:5
Zm00001d039537_T038:5
Zm00001d039537_T016:5
Zm00001d039537_T005:5
Zm00001d039537_T008:5
Zm00001d039537_T037:5
Zm00001d039537_T002:5
Zm00001d039537_T021:5
Zm00001d039537_T040:5
Zm00001d039537_T024:5
Zm00001d039537_T001:5
Zm00001d039537_T010:5
Zm00001d039537_T032:5
Zm00001d039537_T003:5
Zm00001d039537_T049:5
Zm00001d039537_T034:5
Zm00001d039537_T015:5
Zm00001d039537_T011:5
Zm00001d039537_T004:5
Zm00001d039537_T043:5
Zm00001d039537_T050:3
Zm00001d039537_T054:5
Zm00001d039537_T007:5
Zm00001d039537_T022:5
Zm00001d039537_T018:5
Zm00001d039537_T013:5
Zm00001d039537_T051:5
Zm00001d039537_T052:5
Zm00001d039537_T006:5
Zm00001d039537_T031:5
Zm00001d039537_T048:5

					

			
		

General Information
CircRNA Name	Zm00001d039537_circ_g.1
ID in PlantcircBase	zma_circ_007479
Alias	Zm03circ00007
Organism	Zea mays
Position	chr3: 7492872-7494635 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	CIRI2
Parent gene	Zm00001d039537
Parent gene annotation	Protein ALWAYS EARLY 3
Parent gene strand	-
Alternative splicing	NA
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	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	Zm00001d039537_T030:5 Zm00001d039537_T026:5 Zm00001d039537_T041:5 Zm00001d039537_T023:5 Zm00001d039537_T056:5 Zm00001d039537_T042:5 Zm00001d039537_T035:5 Zm00001d039537_T036:5 Zm00001d039537_T047:5 Zm00001d039537_T033:5 Zm00001d039537_T012:5 Zm00001d039537_T057:5 Zm00001d039537_T019:5 Zm00001d039537_T045:5 Zm00001d039537_T014:5 Zm00001d039537_T053:5 Zm00001d039537_T009:5 Zm00001d039537_T029:5 Zm00001d039537_T017:5 Zm00001d039537_T039:5 Zm00001d039537_T027:5 Zm00001d039537_T038:5 Zm00001d039537_T016:5 Zm00001d039537_T005:5 Zm00001d039537_T008:5 Zm00001d039537_T037:5 Zm00001d039537_T002:5 Zm00001d039537_T021:5 Zm00001d039537_T040:5 Zm00001d039537_T024:5 Zm00001d039537_T001:5 Zm00001d039537_T010:5 Zm00001d039537_T032:5 Zm00001d039537_T003:5 Zm00001d039537_T049:5 Zm00001d039537_T034:5 Zm00001d039537_T015:5 Zm00001d039537_T011:5 Zm00001d039537_T004:5 Zm00001d039537_T043:5 Zm00001d039537_T050:3 Zm00001d039537_T054:5 Zm00001d039537_T007:5 Zm00001d039537_T022:5 Zm00001d039537_T018:5 Zm00001d039537_T013:5 Zm00001d039537_T051:5 Zm00001d039537_T052:5 Zm00001d039537_T006:5 Zm00001d039537_T031:5 Zm00001d039537_T048:5

			
						 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  
						
							GAGTTAACTTTCTGCTCATACACTGATACTGCCGCAGGCATGCCAGGCCTGTCATCAGAATCAA
CATCTTTGTTTTCATCCTTAATTTGGGCTGAAGATTcatcacaaactcaacacccagctcaggc
cgatcaaactgaacccgacaacgattattgtcaactgtcagaatattcccatcatgaagttccc
ttgttcta

									
								

					

						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: 959
Transcript exons: 7492872-7493154,7493221-7493399,7493494-7493666,7493765-
7493801,7494349-7494635
CATCACAAACTCAACACCCAGCTCAGGCCGATCAAACTGAACCCGACAACGATTATTGTCAACT
GTCAGAATATTCCCATCATGAAGTTCCCTTGTTCTAGGATGACAGGCTATAACACGCTGTCCAA
CTGCAAGAGGTCGTGCAAGATCCGTGGGTAGTCCTTCTCTAACACCAGATCGAAGTTCAGCATA
GTGTTGCCTGACTGAATCGCGATATTGAGAAAGCTTCTCTCTCTCCTCATGCAAAAATTGTTTA
GACAATCGGCGGGGCTTCCCAAGAGAACTCCTTATGACACCCCACTCAACACGAGTCAGCCTTG
GAACATGACCCAGCTTGACATGATTCAAGTACTCCACAAATTCACTTTTTGCAAACCATGGATA
ATCAATTGCACTATAGAACCATTCAAACATACACCACCTCCGAAGCAAACGTGAGGACAAGCAG
TGAGAGAGTTTGTCCTTAAGATCAATAACATTATTCACTGAGTGAGAAAATTTATCACTTCCAG
TATCATTGGCAACCTTGGTTGATTTGCATTCTTCAATTAGTGCTTGCTGAATGCCTATTTTACG
GCAGCTTTTACCCTTTGATGATAAGTCAGCTTGTGTTGTATCACCTTGTGTGGTTGTCCCGATA
TTAGACGACACCTTCCCTTCTTCAGCAGAAACCTTTGTCGTGGATGATTTCCTCTTCTTTTTCT
CTGTTTTGACACCACATGTACAAGCTTGCTGCTTTACATCAGAAGTGGTGCTCCCATCGTGATG
AGGATCTTTAGTAACTTTAGCTTTTTTCCTAGTGACCATCTCTGAATTTGAAATTTCAGGCTGC
CTTTTAACTTTCCTTGCAGTGCTTTTGGAGTTAACTTTCTGCTCATACACTGATACTGCCGCAG
GCATGCCAGGCCTGTCATCAGAATCAACATCTTTGTTTTCATCCTTAATTTGGGCTGAAGATT
						
					

						Genomic sequence
						
							CATCACAAACTCAACACCCAGCTCAGGCCGATCAAACTGAACCCGACAACGATTATTGTCAACT
GTCAGAATATTCCCATCATGAAGTTCCCTTGTTCTAGGATGACAGGCTATAACACGCTGTCCAA
CTGCAAGAGGTCGTGCAAGATCCGTGGGTAGTCCTTCTCTAACACCAGATCGAAGTTCAGCATA
GTGTTGCCTGACTGAATCGCGATATTGAGAAAGCTTCTCTCTCTCCTCATGCAAAAATTGTTTA
GACAATCGGCGGGGCTTCCCAAGAGAACTGCAAAAGCAGTAAGATTTAGGAAACGATTACAATA
AAGCTATAGAGGAACTGAAGATTACAAACCTCCTTATGACACCCCACTCAACACGAGTCAGCCT
TGGAACATGACCCAGCTTGACATGATTCAAGTACTCCACAAATTCACTTTTTGCAAACCATGGA
TAATCAATTGCACTATAGAACCATTCAAACATACACCACCTCCGAAGCAAACGTGAGGACAAGC
AGTGAGAGAGTTTGTCCTGCATCAGAATAGATTAAATATCAGTTTTCATTATTGCAGATTACAA
AAAACATCCCTATGTGAGTTTAACTAGATAAATGGAAGTAACAGACCTTAAGATCAATAACATT
ATTCACTGAGTGAGAAAATTTATCACTTCCAGTATCATTGGCAACCTTGGTTGATTTGCATTCT
TCAATTAGTGCTTGCTGAATGCCTATTTTACGGCAGCTTTTACCCTTTGATGATAAGTCAGCTT
GTGTTGTATCACCTTGTGTGGTTGTCCCTGCGATATTCATGGCTTTTTTCTAAAATCAGTATGA
GAATATTCCTGTGTGAACTTACTTAAAATAAATAAAAAATGGGCTAACATGAGTTGCCTACCGA
TATTAGACGACACCTTCCCTTCTTCAGCAGAAACCTATGGAACAAAATATGCAGGAACAAATAT
TATGTTGCATTAAGTAAGCAAAAAGAGATATGCAAAAGGTAAAACTTGATCCTTTCTTTTAATC
GGAAACCCTTGCGAAAGCTGCTTTCCATTGCACATAGCATGAAACATATATGTTTGTAGCTATG
TTATTTATGTATTAAACAGTGAAAGGCAAAGATCAATCACGTAAATATGTAACAACAGCAATAG
TTCTAAGTTTATGTGATCTTACACTTTCATTTCAGCTTGCTCATTACAACAACAACAATATTTA
TGCGATACTAGACACTTATTGTGCAGACAAATTATAGGTTGAGGTCACATATATCACAAGCTGA
AGTTGATGTTGCAGATTTAATCCAACATATAGTACATGTTATACTCGTCGATGCAAATCATTAA
TCCCACATTGGGCATAAATGCAGGTTCACAAGCCAGATCAGGCATCGACCAATTTCCCTCTATT
GACCTCCAATTGTAAAGAAAAATACTTTTCCTTACAGAAATGATCAACAAATAATAATTTGGGA
ATTACCTTTGTCGTGGATGATTTCCTCTTCTTTTTCTCTGTTTTGACACCACATGTACAAGCTT
GCTGCTTTACATCAGAAGTGGTGCTCCCATCGTGATGAGGATCTTTAGTAACTTTAGCTTTTTT
CCTAGTGACCATCTCTGAATTTGAAATTTCAGGCTGCCTTTTAACTTTCCTTGCAGTGCTTTTG
GAGTTAACTTTCTGCTCATACACTGATACTGCCGCAGGCATGCCAGGCCTGTCATCAGAATCAA
CATCTTTGTTTTCATCCTTAATTTGGGCTGAAGATT
						
					

			
		

Sequences
Splice junction sequence	GAGTTAACTTTCTGCTCATACACTGATACTGCCGCAGGCATGCCAGGCCTGTCATCAGAATCAA CATCTTTGTTTTCATCCTTAATTTGGGCTGAAGATTcatcacaaactcaacacccagctcaggc cgatcaaactgaacccgacaacgattattgtcaactgtcagaatattcccatcatgaagttccc ttgttcta
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: 959 Transcript exons: 7492872-7493154,7493221-7493399,7493494-7493666,7493765- 7493801,7494349-7494635 CATCACAAACTCAACACCCAGCTCAGGCCGATCAAACTGAACCCGACAACGATTATTGTCAACT GTCAGAATATTCCCATCATGAAGTTCCCTTGTTCTAGGATGACAGGCTATAACACGCTGTCCAA CTGCAAGAGGTCGTGCAAGATCCGTGGGTAGTCCTTCTCTAACACCAGATCGAAGTTCAGCATA GTGTTGCCTGACTGAATCGCGATATTGAGAAAGCTTCTCTCTCTCCTCATGCAAAAATTGTTTA GACAATCGGCGGGGCTTCCCAAGAGAACTCCTTATGACACCCCACTCAACACGAGTCAGCCTTG GAACATGACCCAGCTTGACATGATTCAAGTACTCCACAAATTCACTTTTTGCAAACCATGGATA ATCAATTGCACTATAGAACCATTCAAACATACACCACCTCCGAAGCAAACGTGAGGACAAGCAG TGAGAGAGTTTGTCCTTAAGATCAATAACATTATTCACTGAGTGAGAAAATTTATCACTTCCAG TATCATTGGCAACCTTGGTTGATTTGCATTCTTCAATTAGTGCTTGCTGAATGCCTATTTTACG GCAGCTTTTACCCTTTGATGATAAGTCAGCTTGTGTTGTATCACCTTGTGTGGTTGTCCCGATA TTAGACGACACCTTCCCTTCTTCAGCAGAAACCTTTGTCGTGGATGATTTCCTCTTCTTTTTCT CTGTTTTGACACCACATGTACAAGCTTGCTGCTTTACATCAGAAGTGGTGCTCCCATCGTGATG AGGATCTTTAGTAACTTTAGCTTTTTTCCTAGTGACCATCTCTGAATTTGAAATTTCAGGCTGC CTTTTAACTTTCCTTGCAGTGCTTTTGGAGTTAACTTTCTGCTCATACACTGATACTGCCGCAG GCATGCCAGGCCTGTCATCAGAATCAACATCTTTGTTTTCATCCTTAATTTGGGCTGAAGATT
Genomic sequence	CATCACAAACTCAACACCCAGCTCAGGCCGATCAAACTGAACCCGACAACGATTATTGTCAACT GTCAGAATATTCCCATCATGAAGTTCCCTTGTTCTAGGATGACAGGCTATAACACGCTGTCCAA CTGCAAGAGGTCGTGCAAGATCCGTGGGTAGTCCTTCTCTAACACCAGATCGAAGTTCAGCATA GTGTTGCCTGACTGAATCGCGATATTGAGAAAGCTTCTCTCTCTCCTCATGCAAAAATTGTTTA GACAATCGGCGGGGCTTCCCAAGAGAACTGCAAAAGCAGTAAGATTTAGGAAACGATTACAATA AAGCTATAGAGGAACTGAAGATTACAAACCTCCTTATGACACCCCACTCAACACGAGTCAGCCT TGGAACATGACCCAGCTTGACATGATTCAAGTACTCCACAAATTCACTTTTTGCAAACCATGGA TAATCAATTGCACTATAGAACCATTCAAACATACACCACCTCCGAAGCAAACGTGAGGACAAGC AGTGAGAGAGTTTGTCCTGCATCAGAATAGATTAAATATCAGTTTTCATTATTGCAGATTACAA AAAACATCCCTATGTGAGTTTAACTAGATAAATGGAAGTAACAGACCTTAAGATCAATAACATT ATTCACTGAGTGAGAAAATTTATCACTTCCAGTATCATTGGCAACCTTGGTTGATTTGCATTCT TCAATTAGTGCTTGCTGAATGCCTATTTTACGGCAGCTTTTACCCTTTGATGATAAGTCAGCTT GTGTTGTATCACCTTGTGTGGTTGTCCCTGCGATATTCATGGCTTTTTTCTAAAATCAGTATGA GAATATTCCTGTGTGAACTTACTTAAAATAAATAAAAAATGGGCTAACATGAGTTGCCTACCGA TATTAGACGACACCTTCCCTTCTTCAGCAGAAACCTATGGAACAAAATATGCAGGAACAAATAT TATGTTGCATTAAGTAAGCAAAAAGAGATATGCAAAAGGTAAAACTTGATCCTTTCTTTTAATC GGAAACCCTTGCGAAAGCTGCTTTCCATTGCACATAGCATGAAACATATATGTTTGTAGCTATG TTATTTATGTATTAAACAGTGAAAGGCAAAGATCAATCACGTAAATATGTAACAACAGCAATAG TTCTAAGTTTATGTGATCTTACACTTTCATTTCAGCTTGCTCATTACAACAACAACAATATTTA TGCGATACTAGACACTTATTGTGCAGACAAATTATAGGTTGAGGTCACATATATCACAAGCTGA AGTTGATGTTGCAGATTTAATCCAACATATAGTACATGTTATACTCGTCGATGCAAATCATTAA TCCCACATTGGGCATAAATGCAGGTTCACAAGCCAGATCAGGCATCGACCAATTTCCCTCTATT GACCTCCAATTGTAAAGAAAAATACTTTTCCTTACAGAAATGATCAACAAATAATAATTTGGGA ATTACCTTTGTCGTGGATGATTTCCTCTTCTTTTTCTCTGTTTTGACACCACATGTACAAGCTT GCTGCTTTACATCAGAAGTGGTGCTCCCATCGTGATGAGGATCTTTAGTAACTTTAGCTTTTTT CCTAGTGACCATCTCTGAATTTGAAATTTCAGGCTGCCTTTTAACTTTCCTTGCAGTGCTTTTG GAGTTAACTTTCTGCTCATACACTGATACTGCCGCAGGCATGCCAGGCCTGTCATCAGAATCAA CATCTTTGTTTTCATCCTTAATTTGGGCTGAAGATT

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.166466114

Conservation Information
Conserved circRNAs	NA
PMCS	0.166466114

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							7494576-7492969(+)
7494578-7494416(-)
						
						Potential amino acid sequence
						
							MPGLSSESTSLFSSLIWAEDSSQTQHPAQADQTEPDNDYCQLSEYSHHEVPLF*(+)
MPAAVSVYEQKVNSKSTARKVKRQPEISNSEMVTRKKAKVTKDPHHDGSTTSDVKQQACTCGVK
TEKKKRKSSTTKVSAEEGKVSSNIGTTTQGDTTQADLSSKGKSCRKIGIQQALIEECKSTKVAN
DTGSDKFSHSVNNVIDLKDKLSHCLSSRLLRRWCMFEWFYSAIDYPWFAKSEFVEYLNHVKLGH
VPRLTRVEWGVIRSSLGKPRRLSKQFLHEEREKLSQYRDSVRQHYAELRSGVREGLPTDLARPL
AVGQRVIACHPRTRELHDGNILTVDNNRCRVQFDRPELGVEFVMNLQPKLRMKTKMLILMTGLA
CLRQYQCMSRKLTPKALQGKLKGSLKFQIQRWSLGKKLKLLKILITMGAPLLM*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						NA

Functional Information
Coding potential	Y
Potential coding position	7494576-7492969(+) 7494578-7494416(-)
Potential amino acid sequence	MPGLSSESTSLFSSLIWAEDSSQTQHPAQADQTEPDNDYCQLSEYSHHEVPLF(+) MPAAVSVYEQKVNSKSTARKVKRQPEISNSEMVTRKKAKVTKDPHHDGSTTSDVKQQACTCGVK TEKKKRKSSTTKVSAEEGKVSSNIGTTTQGDTTQADLSSKGKSCRKIGIQQALIEECKSTKVAN DTGSDKFSHSVNNVIDLKDKLSHCLSSRLLRRWCMFEWFYSAIDYPWFAKSEFVEYLNHVKLGH VPRLTRVEWGVIRSSLGKPRRLSKQFLHEEREKLSQYRDSVRQHYAELRSGVREGLPTDLARPL AVGQRVIACHPRTRELHDGNILTVDNNRCRVQFDRPELGVEFVMNLQPKLRMKTKMLILMTGLA CLRQYQCMSRKLTPKALQGKLKGSLKFQIQRWSLGKKLKLLKILITMGAPLLM(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	NA

			
						 Other Information
					
						References
						Han et al., 2020

circRNA

Detail information of Zm00001d039537_circ_g.1

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